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May 2011

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commit/galaxy-central: fubar: added all_fasta.loc to buildbot - needed for picard tests
by Bitbucket 10 May '11

10 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/4524c1a80fae/ changeset: r5533:4524c1a80fae user: fubar date: 2011-05-10 16:35:19 summary: added all_fasta.loc to buildbot - needed for picard tests affected #: 1 file (36 bytes) --- a/buildbot_setup.sh Tue May 10 10:31:49 2011 -0400 +++ b/buildbot_setup.sh Tue May 10 10:35:19 2011 -0400 @@ -28,6 +28,7 @@ LINKS=" /galaxy/data/location/add_scores.loc +/galaxy/data/location/all_fasta.loc /galaxy/data/location/alignseq.loc /galaxy/data/annotation_profiler /galaxy/data/annotation_profiler/annotation_profiler.loc Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: relax number of lines_diff in insertsize test
by Bitbucket 10 May '11

10 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/aad64f351785/ changeset: r5532:aad64f351785 user: fubar date: 2011-05-10 16:31:49 summary: relax number of lines_diff in insertsize test affected #: 1 file (0 bytes) --- a/tools/picard/rgPicardInsertSize.xml Mon May 09 22:29:17 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Tue May 10 10:31:49 2011 -0400 @@ -31,7 +31,7 @@ <param name="tailLimit" value="10000" /><param name="histWidth" value="0" /><param name="minPct" value="0.01" /> - <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="30" /> + <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" lines_diff="35" /></test></tests><help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fixes for Picard: ReorderSam.
by Bitbucket 09 May '11

09 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fd3391bcd903/ changeset: r5531:fd3391bcd903 user: dan date: 2011-05-10 04:29:17 summary: Fixes for Picard: ReorderSam. affected #: 1 file (9 bytes) --- a/tools/picard/picard_ReorderSam.xml Mon May 09 16:51:14 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Mon May 09 22:29:17 2011 -0400 @@ -16,11 +16,11 @@ --allow-contig-len-discord=$allowContigLenDiscord --output-format=$outputFormat #if str( $outputFormat ) == "sam" - --output-sam=$outFileSam + --output=$outFileSam #else if str( $outputFormat ) == "bam" - --output-sam=$outFileBam + --output=$outFileBam #end if - -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/picard-1.41.jar" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar" --picard-cmd="ReorderSam" </command><inputs> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 5 new changesets
by Bitbucket 09 May '11

09 May '11

5 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ae2b97a06df1/ changeset: r5526:ae2b97a06df1 user: kellyv date: 2011-05-09 18:00:05 summary: Updated sam-to-bam to properly assign output dbkey; enhanced sam-to-bam and bam-to-sam functional tests affected #: 13 files (18.1 KB) Binary file test-data/bam_to_sam_in1.bam has changed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam_to_sam_in1.sam Mon May 09 12:00:05 2011 -0400 @@ -0,0 +1,14 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 Binary file test-data/bam_to_sam_in2.bam has changed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bam_to_sam_in2.sam Mon May 09 12:00:05 2011 -0400 @@ -0,0 +1,25 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:10001 +@SQ SN:chr2 LN:100001 +@SQ SN:chr3 LN:10001 +@SQ SN:chr4 LN:1001 +@RG ID:rg1 SM:s1 +@RG ID:rg2 SM:s3 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 --- a/test-data/bam_to_sam_out1.sam Sun May 08 22:16:18 2011 -0400 +++ b/test-data/bam_to_sam_out1.sam Mon May 09 12:00:05 2011 -0400 @@ -1,10 +1,8 @@ -HWI-EAS91_1_30788AAXX:1:1:1698:516 16 * 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1716:413 0 * 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1634:211 0 * 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1513:715 16 * 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1711:249 16 * 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1491:637 16 * 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1630:59 16 * 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 --- a/test-data/bam_to_sam_out2.sam Sun May 08 22:16:18 2011 -0400 +++ b/test-data/bam_to_sam_out2.sam Mon May 09 12:00:05 2011 -0400 @@ -1,10 +1,18 @@ -HWI-EAS91_1_30788AAXX:1:1:1095:605 0 chrM 23 25 36M * 0 0 AAGCAAGNNACTGAAAATGCCTAGATGAGTATTCTT IIIIIII""IIIIIIIIIIIIIIIEIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:606:460 0 chrM 4552 25 36M * 0 0 TTAATTTNNATTATAATAACACTCACAATATTCATA IIIIIII""IIIIIIIIIIIIIIIIII?I6IIIII6 NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1082:719 16 chrM 7191 25 36M * 0 0 TAAATTAACCCATACCAGCACCATAGANNCTCAAGA <III0EII3+3I29I>III8AIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1059:362 16 chrM 7348 25 36M * 0 0 GGCCACCAATGATACTGAAGCTACGAGNNTACCGAT II/<)2IIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:799:192 16 chrM 8421 25 36M * 0 0 CCTGTAGCCCTAGCCGTGCGGCTAACCNNTAACATT II%::I<IIIIIEIII8IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1746:1180 16 chrM 12013 25 36M * 0 0 CCTAAGCTTCAAACTAGATTACTTCTCNNTAATTTT IIIIIIIIFIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1273:600 16 chrM 13855 25 36M * 0 0 GTATTAGACACCCATACCTCAGGATACNNCTCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1650:1185 0 chrM 14956 25 36M * 0 0 ACCCCAGNNAACCCTCTCAGCACTCCCCCTCATATT IIIIIII""IIIIIIIIIIII6IIIIIIIII5I-II NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1483:1161 16 chrM 15080 25 36M * 0 0 TCCTGATCCTAGCACTCATCCCCACCCNNCACATAT HIIIIIFIIAIHIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1190:1283 16 chrM 15338 25 36M * 0 0 TATATCGCACATTACCCTGGTCTTGTANNCCAGAAA EIII?-IIIIIAIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 +bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 +bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 +bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 +bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 --- a/test-data/bam_to_sam_out3.sam Sun May 08 22:16:18 2011 -0400 +++ b/test-data/bam_to_sam_out3.sam Mon May 09 12:00:05 2011 -0400 @@ -1,178 +1,14 @@ -@SQ SN:>chrM LN:0 -@SQ SN:GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT LN:0 -@SQ SN:CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA LN:0 -@SQ SN:ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG LN:0 -@SQ SN:ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA LN:0 -@SQ SN:AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA LN:0 -@SQ SN:AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT LN:0 -@SQ SN:CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT LN:0 -@SQ SN:AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT LN:0 -@SQ SN:TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT LN:0 -@SQ SN:CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA LN:0 -@SQ SN:TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA LN:0 -@SQ SN:TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG LN:0 -@SQ SN:ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT LN:0 -@SQ SN:CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT LN:0 -@SQ SN:AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA LN:0 -@SQ SN:AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA LN:0 -@SQ SN:TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA LN:0 -@SQ SN:TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA LN:0 -@SQ SN:TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA LN:0 -@SQ SN:ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC LN:0 -@SQ SN:taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt LN:0 -@SQ SN:cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG LN:0 -@SQ SN:TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC LN:0 -@SQ SN:TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG LN:0 -@SQ SN:TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT LN:0 -@SQ SN:CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT LN:0 -@SQ SN:AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg LN:0 -@SQ SN:caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT LN:0 -@SQ SN:CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG LN:0 -@SQ SN:CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT LN:0 -@SQ SN:CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC LN:0 -@SQ SN:CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG LN:0 -@SQ SN:ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC LN:0 -@SQ SN:ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA LN:0 -@SQ SN:ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG LN:0 -@SQ SN:ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA LN:0 -@SQ SN:TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA LN:0 -@SQ SN:ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact LN:0 -@SQ SN:ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT LN:0 -@SQ SN:CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA LN:0 -@SQ SN:GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC LN:0 -@SQ SN:TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA LN:0 -@SQ SN:ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA LN:0 -@SQ SN:ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT LN:0 -@SQ SN:AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA LN:0 -@SQ SN:ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA LN:0 -@SQ SN:CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC LN:0 -@SQ SN:AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC LN:0 -@SQ SN:CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA LN:0 -@SQ SN:ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC LN:0 -@SQ SN:TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT LN:0 -@SQ SN:TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC LN:0 -@SQ SN:TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG LN:0 -@SQ SN:CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA LN:0 -@SQ SN:AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC LN:0 -@SQ SN:GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA LN:0 -@SQ SN:TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC LN:0 -@SQ SN:TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA LN:0 -@SQ SN:TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA LN:0 -@SQ SN:TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT LN:0 -@SQ SN:TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA LN:0 -@SQ SN:AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT LN:0 -@SQ SN:TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT LN:0 -@SQ SN:AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT LN:0 -@SQ SN:GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT LN:0 -@SQ SN:TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC LN:0 -@SQ SN:CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT LN:0 -@SQ SN:GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG LN:0 -@SQ SN:GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA LN:0 -@SQ SN:tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC LN:0 -@SQ SN:GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA LN:0 -@SQ SN:GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC LN:0 -@SQ SN:ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT LN:0 -@SQ SN:CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT LN:0 -@SQ SN:TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA LN:0 -@SQ SN:AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG LN:0 -@SQ SN:TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA LN:0 -@SQ SN:TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT LN:0 -@SQ SN:AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT LN:0 -@SQ SN:CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA LN:0 -@SQ SN:CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC LN:0 -@SQ SN:AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT LN:0 -@SQ SN:CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA LN:0 -@SQ SN:ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA LN:0 -@SQ SN:AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT LN:0 -@SQ SN:TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC LN:0 -@SQ SN:CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC LN:0 -@SQ SN:ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT LN:0 -@SQ SN:CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT LN:0 -@SQ SN:CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC LN:0 -@SQ SN:TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA LN:0 -@SQ SN:AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT LN:0 -@SQ SN:TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT LN:0 -@SQ SN:AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG LN:0 -@SQ SN:CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA LN:0 -@SQ SN:ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA LN:0 -@SQ SN:TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA LN:0 -@SQ SN:ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC LN:0 -@SQ SN:TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT LN:0 -@SQ SN:ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC LN:0 -@SQ SN:TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC LN:0 -@SQ SN:CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC LN:0 -@SQ SN:GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA LN:0 -@SQ SN:CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC LN:0 -@SQ SN:CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT LN:0 -@SQ SN:TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC LN:0 -@SQ SN:CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT LN:0 -@SQ SN:AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG LN:0 -@SQ SN:TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA LN:0 -@SQ SN:ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC LN:0 -@SQ SN:AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT LN:0 -@SQ SN:TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA LN:0 -@SQ SN:AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA LN:0 -@SQ SN:ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA LN:0 -@SQ SN:GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA LN:0 -@SQ SN:TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA LN:0 -@SQ SN:CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA LN:0 -@SQ SN:CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC LN:0 -@SQ SN:CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA LN:0 -@SQ SN:TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC LN:0 -@SQ SN:TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA LN:0 -@SQ SN:ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC LN:0 -@SQ SN:TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT LN:0 -@SQ SN:TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC LN:0 -@SQ SN:ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC LN:0 -@SQ SN:GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT LN:0 -@SQ SN:TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC LN:0 -@SQ SN:CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT LN:0 -@SQ SN:CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT LN:0 -@SQ SN:ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC LN:0 -@SQ SN:TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC LN:0 -@SQ SN:CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA LN:0 -@SQ SN:CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG LN:0 -@SQ SN:CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG LN:0 -@SQ SN:TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC LN:0 -@SQ SN:CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG LN:0 -@SQ SN:ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC LN:0 -@SQ SN:CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT LN:0 -@SQ SN:AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG LN:0 -@SQ SN:ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC LN:0 -@SQ SN:AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA LN:0 -@SQ SN:GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC LN:0 -@SQ SN:CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG LN:0 -@SQ SN:ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA LN:0 -@SQ SN:AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG LN:0 -@SQ SN:ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT LN:0 -@SQ SN:ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC LN:0 -@SQ SN:CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT LN:0 -@SQ SN:CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT LN:0 -@SQ SN:ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA LN:0 -@SQ SN:AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC LN:0 -@SQ SN:CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT LN:0 -@SQ SN:CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC LN:0 -@SQ SN:ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC LN:0 -@SQ SN:TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT LN:0 -@SQ SN:CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG LN:0 -@SQ SN:GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC LN:0 -@SQ SN:GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG LN:0 -@SQ SN:TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA LN:0 -@SQ SN:CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT LN:0 -@SQ SN:CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA LN:0 -@SQ SN:ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct LN:0 -@SQ SN:gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc LN:0 -@SQ SN:ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA LN:0 -@SQ SN:GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT LN:0 -@SQ SN:GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT LN:0 -@SQ SN:TTCTTCCCCC LN:0 -HWI-EAS91_1_30788AAXX:1:1:1698:516 16 * 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1716:413 0 * 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1634:211 0 * 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1513:715 16 * 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1711:249 16 * 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1491:637 16 * 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1630:59 16 * 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 -HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +@HD VN:1.0 SO:coordinate +@SQ SN:chr1 LN:101 +@SQ SN:chr7 LN:404 +@SQ SN:chr8 LN:202 +@RG ID:0 SM:Hi,Mom! +@PG ID:1 PN:Hey! VN:2.0 +both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 +both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 +both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sam_to_bam_in1.sam Mon May 09 12:00:05 2011 -0400 @@ -0,0 +1,13 @@ +@HD VN:1.0 SO:coordinate +@SQ SN:chrM LN:100001 +@RG ID:rg1 SM:s1 +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 chrM 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 chrM 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 chrM 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 chrM 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 chrM 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 chrM 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 chrM 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 chrM 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 chrM 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 chrM 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 RG:Z:rg1 Binary file test-data/sam_to_bam_out1.bam has changed Binary file test-data/sam_to_bam_out2.bam has changed --- a/tools/samtools/bam_to_sam.xml Sun May 08 22:16:18 2011 -0400 +++ b/tools/samtools/bam_to_sam.xml Mon May 09 12:00:05 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.2"> +<tool id="bam_to_sam" name="BAM-to-SAM" version="1.0.3"><requirements><requirement type="package">samtools</requirement></requirements> @@ -20,29 +20,32 @@ <test> - <param name="input1" value="1.bam" ftype="bam" /> + <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> + <param name="header" value="" /><output name="output1" file="bam_to_sam_out1.sam" sorted="True" /> - <param name="header" value="" /></test><test> - <param name="input1" value="3unsorted.bam" ftype="bam" /> + <param name="input1" value="bam_to_sam_in2.bam" ftype="bam" /> + <param name="header" value="" /><output name="output1" file="bam_to_sam_out2.sam" sorted="True" /> - <param name="header" value="" /></test><test> - <param name="input1" value="1.bam" ftype="bam" /> - <output name="output1" file="bam_to_sam_out3.sam" sorted="True" /> - <param name="header" value="True" /> + <param name="input1" value="bam_to_sam_in1.bam" ftype="bam" /> + <param name="header" value="--header" /> + <output name="output1" file="bam_to_sam_out3.sam" sorted="True" lines_diff="6" /></test></tests><help> --- a/tools/samtools/sam_to_bam.py Sun May 08 22:16:18 2011 -0400 +++ b/tools/samtools/sam_to_bam.py Mon May 09 12:00:05 2011 -0400 @@ -68,7 +68,7 @@ # and the equCab2.fa file will contain fasta sequences. seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() - if options.ref_file == 'None': + if not options.ref_file or options.ref_file == 'None': # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai --- a/tools/samtools/sam_to_bam.xml Sun May 08 22:16:18 2011 -0400 +++ b/tools/samtools/sam_to_bam.xml Mon May 09 12:00:05 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.1"> +<tool id="sam_to_bam" name="SAM-to-BAM" version="1.1.2"><description>converts SAM format to BAM format</description><requirements><requirement type="package">samtools</requirement> @@ -6,11 +6,11 @@ <command interpreter="python"> sam_to_bam.py --input1=$source.input1 - --dbkey=${input1.metadata.dbkey} #if $source.index_source == "history": + --dbkey=${ref_file.metadata.dbkey} --ref_file=$source.ref_file #else - --ref_file="None" + --dbkey=${input1.metadata.dbkey} #end if --output1=$output1 --index_dir=${GALAXY_DATA_INDEX_DIR} @@ -22,44 +22,60 @@ <option value="history">History</option></param><when value="cached"> - <param name="input1" type="data" format="sam" label="SAM File to Convert"> + <param name="input1" type="data" format="sam" metadata_name="dbkey" label="SAM File to Convert"><validator type="unspecified_build" /><validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" /></param></when><when value="history"><param name="input1" type="data" format="sam" label="Convert SAM file" /> - <param name="ref_file" type="data" format="fasta" label="Using reference file" /> + <param name="ref_file" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" /></when></conditional></inputs><outputs> - <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM" /> + <data format="bam" name="output1" label="${tool.name} on ${on_string}: converted BAM"> + <actions> + <conditional name="source.index_source"> + <when value="cached"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="source.input1" param_attribute="dbkey" /> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="source.ref_file" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions> + </data></outputs><tests><test><param name="index_source" value="history" /> - <param name="input1" value="3.sam" ftype="sam" /> + <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" /><param name="ref_file" value="chr_m.fasta" ftype="fasta" dbkey="equCab2" /> - <output name="output1" file="sam_to_bam_out1.bam" /> + <output name="output1" file="sam_to_bam_out1.bam" ftype="bam" /></test><test><param name="index_source" value="cached" /> - <param name="input1" value="3.sam" ftype="sam" dbkey="equCab2" /> + <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /><output name="output1" file="sam_to_bam_out2.bam" ftype="bam" /></test></tests> http://bitbucket.org/galaxy/galaxy-central/changeset/a8678c2d49ff/ changeset: r5527:a8678c2d49ff user: kellyv date: 2011-05-09 18:11:54 summary: Sam header suppression made optional in BFAST and default set to off for BFAST and Bowtie. Fixed dbkey setting on outputs for for BFAST, Bowtie, Mosaik. Fixed sorting of built-in builds for these tools so ordered by pretty name. affected #: 6 files (1.8 KB) --- a/tools/sr_mapping/bfast_wrapper.py Mon May 09 12:00:05 2011 -0400 +++ b/tools/sr_mapping/bfast_wrapper.py Mon May 09 12:11:54 2011 -0400 @@ -37,6 +37,7 @@ -R, --reverse=R: paired end reads are given on reverse strands -z, --random=z: output a random best scoring alignment -D, --dbkey=D: Dbkey for reference genome + -H, --suppressHeader=H: Suppress the sam header """ import optparse, os, shutil, subprocess, sys, tempfile --- a/tools/sr_mapping/bfast_wrapper.xml Mon May 09 12:00:05 2011 -0400 +++ b/tools/sr_mapping/bfast_wrapper.xml Mon May 09 12:11:54 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="bfast_wrapper" name="Map with BFAST" version="0.1.2"> +<tool id="bfast_wrapper" name="Map with BFAST" version="0.1.3"><description></description><command interpreter="python">bfast_wrapper.py --numThreads="4" ##HACK: hardcode numThreads for now, should come from a location file @@ -64,7 +64,7 @@ <options from_data_table="bfast_indexes"><filter type="multiple_splitter" column="2" separator=","/><filter type="param_value" column="2" ref="input1" ref_attribute="extension"/> - <filter type="sort_by" column="1"/> + <filter type="sort_by" column="3"/><validator type="no_options" message="No indexes are available for the selected input dataset"/></options></param> @@ -112,11 +112,11 @@ <param name="keySize" type="integer" value="-1" label="Truncate key size in 'match'" help="Set this to reduce the effective key size of all indexes in 'bfast match' (advanced users only)" /><param name="maxKeyMatches" type="integer" value="8" label="The maximum number of matches to allow before a key is ignored" help="Lower values will result in more unique regions being examined, while larger values will allow include repetitive regions" /><param name="maxNumMatches" type="integer" value="384" label="The maximum number of matches to allow before a read is discarded" help="Larger values will allow more hits to be examined" /> - <param name="whichStrand" type="select" label="The strands to consider" help="Both strands, forward strand only, or reverse strand only"> - <option value="0">Both strands</option> - <option value="1">Forward strand only</option> - <option value="2">Reverse strand only</option> - </param> + <param name="whichStrand" type="select" label="The strands to consider" help="Both strands, forward strand only, or reverse strand only"> + <option value="0">Both strands</option> + <option value="1">Forward strand only</option> + <option value="2">Reverse strand only</option> + </param><param name="scoringMatrixFileName" type="data" format="text" optional="True" label="Scoring Matrix file used to score the alignments" help="See BFAST manual for file format requirements. (advanced users only)"/><param name="ungapped" type="boolean" truevalue="--ungapped" falsevalue="" checked="no" label="Perform ungapped local alignment" help="Performing ungapped local alignment will not consider indels while providing a significant speed increase" /> @@ -124,8 +124,8 @@ <param name="offset" type="integer" value="20" label="The number of bases before and after each hit to consider in local alignment" help="Larger values will allow for larger insertions and deletions to be detected at the cost of speed" /><param name="avgMismatchQuality" type="integer" value="10" label="The average mismatch quality" help="This can be used as a scaling factor for mapping quality (advanced users only)" /> - <conditional name="localalign_params"> - <param name="algorithm" type="select" label="The post processing algorithm" help="This determines how reads with multiple candidate alignments are returned. Unique alignments will return an alignment if the read has only one candidate alignment. Uniquely best scoring alignments will return one alignment for a read if that alignment has a better alignment score than the rest of the candidate alignments. All best scoring alignments will return all alignments that have the best alignment score for a read."> + <conditional name="localalign_params"> + <param name="algorithm" type="select" label="The post processing algorithm" help="This determines how reads with multiple candidate alignments are returned. Unique alignments will return an alignment if the read has only one candidate alignment. Uniquely best scoring alignments will return one alignment for a read if that alignment has a better alignment score than the rest of the candidate alignments. All best scoring alignments will return all alignments that have the best alignment score for a read."><option value="0" selected="True">No filtering</option><option value="1">All alignments that pass filtering</option><option value="2">Unique alignments</option> @@ -154,19 +154,24 @@ </when></conditional> - <param name="suppressHeader" type="boolean" truevalue="--suppressHeader" falsevalue="" checked="True" label="Suppress the header in the output SAM file" help="BFAST produces SAM with several lines of header information" /> + <param name="suppressHeader" type="boolean" truevalue="--suppressHeader" falsevalue="" checked="False" label="Suppress the header in the output SAM file" help="BFAST produces SAM with several lines of header information" /></inputs><outputs> - <data format="sam" name="output"> + <data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"><actions><conditional name="refGenomeSource.refGenomeSource_type"><when value="indexed"><action type="metadata" name="dbkey"><option type="from_data_table" column="1" name="bfast_indexes"> - <filter type="param_value" ref="refGenomeSource.indices" column="0"/> + <filter type="param_value" ref="refGenomeSource.indices" column="0" /></option></action></when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when></conditional></actions></data> @@ -332,9 +337,9 @@ <param name="mask" value="111111111111111111" /><param name="hash_width" value="14" /><param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="False" /><param name="indexing_repeatmasker" value="False" /><param name="indexing_option_selector" value="default" /> + <param name="suppressHeader" value="" /><output name="output" ftype="sam" file="bfast_out1.sam" /></test><test> @@ -344,10 +349,10 @@ <param name="mask" value="111111111111111111" /><param name="hash_width" value="14" /><param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="True" /><param name="indexing_repeatmasker" value="False" /><param name="indexing_option_selector" value="default" /> - <output name="output" ftype="sam" file="bfast_out1.sam" lines_diff="3" /> + <param name="suppressHeader" value="--suppressHeader" /> + <output name="output" ftype="sam" file="bfast_out1.sam" lines_diff="3" /></test><test><param name="input1" ftype="fastqcssanger" value="random_phiX_1.fastqcssanger" /> @@ -356,9 +361,9 @@ <param name="mask" value="111111111111111111" /><param name="hash_width" value="14" /><param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="False" /><param name="indexing_repeatmasker" value="False" /><param name="indexing_option_selector" value="default" /> + <param name="suppressHeader" value="" /><output name="output" ftype="sam" file="bfast_out2.sam" /></test> @@ -367,7 +372,7 @@ <param name="refGenomeSource_type" value="indexed" /><param name="indices" value="phiX_nt_50" /><param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="False" /> + <param name="suppressHeader" value="" /><output name="output" ftype="sam" file="bfast_out3.sam" lines_diff="2" /></test></tests> --- a/tools/sr_mapping/bowtie_color_wrapper.xml Mon May 09 12:00:05 2011 -0400 +++ b/tools/sr_mapping/bowtie_color_wrapper.xml Mon May 09 12:11:54 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.1"> +<tool id="bowtie_color_wrapper" name="Map with Bowtie for SOLiD" version="1.1.2"><requirements><requirement type='package'>bowtie</requirement></requirements><description></description><command interpreter="python"> @@ -138,7 +138,10 @@ </param><when value="indexed"><param name="index" type="select" label="Select the reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_data_table="bowtie_indexes_color"/> + <options from_data_table="bowtie_indexes_color"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options></param></when><when value="history"> @@ -333,7 +336,7 @@ </conditional></when></conditional> - <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /> + <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /></inputs><outputs><data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> @@ -341,12 +344,17 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_file" name="bowtie_indices_color.loc" column="1" offset="0"> + <option type="from_data_table" name="bowtie_indexes_color" column="1" offset="0"><filter type="param_value" column="0" value="#" filter_by="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option></action></when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when></conditional></actions></data> --- a/tools/sr_mapping/bowtie_wrapper.py Mon May 09 12:00:05 2011 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Mon May 09 12:11:54 2011 -0400 @@ -2,7 +2,7 @@ """ Runs Bowtie on single-end or paired-end data. -For use with Bowtie v. 0.12.3 +For use with Bowtie v. 0.12.7 usage: bowtie_wrapper.py [options] -t, --threads=t: The number of threads to run --- a/tools/sr_mapping/bowtie_wrapper.xml Mon May 09 12:00:05 2011 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.xml Mon May 09 12:11:54 2011 -0400 @@ -1,4 +1,4 @@ -<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.1"> +<tool id="bowtie_wrapper" name="Map with Bowtie for Illumina" version="1.1.2"><requirements><requirement type='package'>bowtie</requirement></requirements><description></description><parallelism method="basic"></parallelism> @@ -136,7 +136,10 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> - <options from_data_table="bowtie_indexes"/> + <options from_data_table="bowtie_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options></param></when><when value="history"> @@ -325,7 +328,7 @@ </conditional></when></conditional> - <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="True" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /> + <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="Bowtie produces SAM with several lines of header information by default" /></inputs><outputs><data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> @@ -333,12 +336,17 @@ <conditional name="refGenomeSource.genomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_file" name="bowtie_indices.loc" column="1" offset="0"> + <option type="from_data_table" name="bowtie_indexes" column="1" offset="0"><filter type="param_value" column="0" value="#" compare="startswith" keep="False"/><filter type="param_value" ref="refGenomeSource.index" column="0"/></option></action></when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when></conditional></actions></data> --- a/tools/sr_mapping/mosaik.xml Mon May 09 12:00:05 2011 -0400 +++ b/tools/sr_mapping/mosaik.xml Mon May 09 12:11:54 2011 -0400 @@ -1,5 +1,5 @@ <?xml version="1.0"?> -<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.0021"> +<tool id="mosaik_wrapper" name="Map with Mosaik" version="1.1.1"><description/><requirements><requirement type="package">mosaik</requirement></requirements><command> @@ -38,13 +38,13 @@ <when value="indexed"><param name="indexReference" type="select" label="Select a reference genome"><options from_data_table="mosaik_indexes"> - <filter type="sort_by" column="3"/> - <validator type="no_options" message="No indexes are available for the selected input dataset"/> + <filter type="sort_by" column="2"/> + <validator type="no_options" message="No indexes are available" /></options></param></when><when value="history"> - <param format="fasta" name="historyReference" type="data" label="Select a reference from history"/> + <param format="fasta" name="historyReference" type="data" metadata_name="dbkey" label="Select a reference from history"/></when></conditional><param format="fastq" name="reads" type="data" label="Fastq Reads File"/> @@ -77,9 +77,26 @@ </inputs><outputs><data format="sam" name="output"> - <change_format> - <when input="outFormat" value="bam" format="bam"/> - </change_format> + <change_format> + <when input="outFormat" value="bam" format="bam" /> + </change_format> + <actions> + <conditional name="genomeSource.refGenomeSource"> + <when value="indexed"> + <action type="metadata" name="dbkey"> + <option type="from_data_table" name="mosaik_indexes" column="1"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False" /> + <filter type="param_value" ref="genomeSource.indexReference" column="0" /> + </option> + </action> + </when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="genomeSource.historyReference" param_attribute="dbkey" /> + </action> + </when> + </conditional> + </actions></data></outputs><tests> http://bitbucket.org/galaxy/galaxy-central/changeset/032a24e03862/ changeset: r5528:032a24e03862 user: kellyv date: 2011-05-09 22:37:13 summary: BWA enhancements: added new options to support v. 0.5.9 (-n and -r for samse/sampe and -N for sampe only); fixed dbkey setting; set Sam header suppression off by default affected #: 7 files (16.4 KB) --- a/test-data/bwa_wrapper_out3.sam Mon May 09 12:11:54 2011 -0400 +++ b/test-data/bwa_wrapper_out3.sam Mon May 09 16:37:13 2011 -0400 @@ -1,60 +1,63 @@ -seq1 113 phiX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq1 177 phiX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 -seq10 129 phiX174 4168 37 18M = 4149 -19 AGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq10 65 phiX174 4149 25 18M = 4168 19 ATTCTTTCTTTTCGTATC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:5G11G0 -seq11 129 phiX174 4091 37 18M = 4072 -19 ATCCCCAATGCTTGGCTT IIIII$%*$G$A31I&&B XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq11 65 phiX174 4072 37 18M = 4091 19 GCATTTCTACTCCTTCTC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12T5 -seq12 129 phiX174 5365 25 18M = 5349 -16 GGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9A7 -seq12 65 phiX174 5349 37 18M = 5365 16 CGCGCTTCGATAAAAATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq13 129 phiX174 4093 25 18M = 4074 -19 CCCCAATCCTTGCCTTCC IIIAAIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:7G4G5 -seq13 65 phiX174 4074 37 18M = 4093 19 ATTTCTACTCTTTCTCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17A0 -seq14 129 phiX174 4016 37 3M1D15M = 3998 -18 TGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:3^T15 -seq14 65 phiX174 3998 37 18M = 4016 18 CCCTTTTGAATGTCACGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:5C12 -seq15 129 phiX174 5216 37 5M2I11M = 5198 -18 TTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:2 MD:Z:16 -seq15 65 phiX174 5198 37 18M = 5216 18 CCAACTTACCAAGGTGGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C4 -seq16 129 phiX174 2897 37 18M = 2880 -17 TTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 -seq16 65 phiX174 2880 37 10M1I7M = 2897 17 TCAGGGTATTAAAAGAGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5T11 -seq17 129 phiX174 3053 25 18M = 3034 -19 AAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9G7 -seq17 65 phiX174 3034 37 18M = 3053 19 GTGATGTGCTTGCTACCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq18 133 phiX174 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII -seq18 73 phiX174 4088 37 18M = 4088 0 TCAATCCCCCATGCTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9A8 -seq19 129 phiX174 3324 37 18M = 3304 -20 GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 -seq19 65 phiX174 3304 37 18M = 3324 20 TTCCTGCGCTTAATGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 -seq2 129 phiX174 159 37 18M = 141 -18 CAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq2 65 phiX174 141 37 18M = 159 18 ATTCGACCTATCCTTGCG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq20 129 phiX174 1100 37 18M = 1082 -18 ACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq20 65 phiX174 1082 37 18M = 1100 18 CTTATTACCATTTCAACT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq21 129 phiX174 1363 37 18M = 1344 -19 TAAGCATTTGGTTCAGGG IIIII$%*$G$A31I&&B XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 -seq21 65 phiX174 1344 37 18M = 1363 19 CTGATACCAATAAAACCC II#IIIIIII$5+.(9II XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:15T2 -seq22 137 phiX174 5215 37 18M = 5215 0 GTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq22 69 phiX174 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII -seq23 129 phiX174 4308 25 18M = 4289 -19 TTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0A8A8 -seq23 65 phiX174 4289 37 18M = 4308 19 TGTGCTTCCCCAACTTGA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6C11 -seq24 129 phiX174 4101 37 18M = 4084 -17 CTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 -seq24 65 phiX174 4084 37 18M = 4101 17 TTTCTCAATCCCCAATGC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq25 129 phiX174 537 37 18M = 520 -17 CGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9C8 -seq25 65 phiX174 520 37 18M = 537 17 TTGCTACTGACCGCTCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17C0 -seq26 129 phiX174 1994 37 18M = 1976 -18 AAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq26 65 phiX174 1976 37 18M = 1994 18 CCGCGTGAAATTTCTATG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq27 129 phiX174 2614 37 3M1D15M = 2598 -16 TGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:1C1^G15 -seq27 65 phiX174 2598 37 18M = 2614 16 CGCTAATCAAGTTGTTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9G8 -seq28 129 phiX174 2906 37 18M = 2890 -16 TCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 -seq28 65 phiX174 2890 25 18M = 2906 16 AAAGAGATTATTTGTCGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16T0C0 -seq29 133 phiX174 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII -seq29 73 phiX174 5339 37 18M = 5339 0 CAAATTAATGCGCGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6T11 -seq3 129 phiX174 523 37 18M = 505 -18 CTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq3 65 phiX174 505 37 18M = 523 18 GTAACAAAGTTTGGATTG IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq30 129 phiX174 4108 37 18M = 4091 -17 ACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T17 -seq30 65 phiX174 4091 37 18M = 4108 17 ATCCCCTATGCTTGGCTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 -seq4 137 phiX174 945 37 18M = 945 0 TAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12A5 -seq4 69 phiX174 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII -seq5 129 phiX174 5003 37 18M = 4985 -18 TTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A4 -seq5 65 phiX174 4985 37 18M = 5003 18 CAGTTATATGGCTTTTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13G4 -seq6 129 phiX174 944 37 18M = 925 -19 GTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq6 65 phiX174 925 37 11M1D7M = 944 19 AGGCGCTCGTCTTGGTAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T7 -seq7 129 phiX174 960 37 18M = 943 -17 TTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq7 65 phiX174 943 25 18M = 960 17 TGTAGGTGGTCAACCAAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A1T1 -seq8 137 phiX174 1715 37 18M = 1715 0 ATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 -seq8 69 phiX174 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII -seq9 129 phiX174 2613 37 18M = 2596 -17 TTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIII XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 -seq9 65 phiX174 2596 37 18M = 2613 17 GCCGCTATTCAGGTTGTT IIIIIIIIIIIIIIIIII XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:7A10 +@PG ID:bwa PN:bwa VN:0.5.9-r16 +@RG ID:abcdefg DS:descrip DT:2010-11-01 LB:lib-mom-A PI:400 PL:ILLUMINA SM:mom +@SQ SN:phiX174 LN:5386 +seq1 113 phiX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq1 177 phiX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 +seq10 129 phiX174 4168 37 18M = 4149 -19 AGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq10 65 phiX174 4149 25 18M = 4168 19 ATTCTTTCTTTTCGTATC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:5G11G0 +seq11 129 phiX174 4091 37 18M = 4072 -19 ATCCCCAATGCTTGGCTT IIIII$%*$G$A31I&&B RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq11 65 phiX174 4072 37 18M = 4091 19 GCATTTCTACTCCTTCTC II#IIIIIII$5+.(9II RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12T5 +seq12 129 phiX174 5365 25 18M = 5349 -16 GGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9A7 +seq12 65 phiX174 5349 37 18M = 5365 16 CGCGCTTCGATAAAAATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq13 129 phiX174 4093 25 18M = 4074 -19 CCCCAATCCTTGCCTTCC IIIAAIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:7G4G5 +seq13 65 phiX174 4074 37 18M = 4093 19 ATTTCTACTCTTTCTCAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17A0 +seq14 129 phiX174 4016 37 3M1D15M = 3998 -18 TGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:3^T15 +seq14 65 phiX174 3998 37 18M = 4016 18 CCCTTTTGAATGTCACGC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:5C12 +seq15 129 phiX174 5216 37 5M2I11M = 5198 -18 TTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:2 MD:Z:16 +seq15 65 phiX174 5198 37 18M = 5216 18 CCAACTTACCAAGGTGGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13C4 +seq16 129 phiX174 2897 37 18M = 2880 -17 TTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq16 65 phiX174 2880 37 10M1I7M = 2897 17 TCAGGGTATTAAAAGAGA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5T11 +seq17 129 phiX174 3053 25 18M = 3034 -19 AAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0T9G7 +seq17 65 phiX174 3034 37 18M = 3053 19 GTGATGTGCTTGCTACCG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq18 133 phiX174 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq18 73 phiX174 4088 37 18M = 4088 0 TCAATCCCCCATGCTTGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9A8 +seq19 129 phiX174 3324 37 18M = 3304 -20 GAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6G11 +seq19 65 phiX174 3304 37 18M = 3324 20 TTCCTGCGCTTAATGCTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq2 129 phiX174 159 37 18M = 141 -18 CAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq2 65 phiX174 141 37 18M = 159 18 ATTCGACCTATCCTTGCG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq20 129 phiX174 1100 37 18M = 1082 -18 ACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq20 65 phiX174 1082 37 18M = 1100 18 CTTATTACCATTTCAACT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq21 129 phiX174 1363 37 18M = 1344 -19 TAAGCATTTGGTTCAGGG IIIII$%*$G$A31I&&B RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq21 65 phiX174 1344 37 18M = 1363 19 CTGATACCAATAAAACCC II#IIIIIII$5+.(9II RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:15T2 +seq22 137 phiX174 5215 37 18M = 5215 0 GTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq22 69 phiX174 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq23 129 phiX174 4308 25 18M = 4289 -19 TTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:0A8A8 +seq23 65 phiX174 4289 37 18M = 4308 19 TGTGCTTCCCCAACTTGA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6C11 +seq24 129 phiX174 4101 37 18M = 4084 -17 CTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq24 65 phiX174 4084 37 18M = 4101 17 TTTCTCAATCCCCAATGC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq25 129 phiX174 537 37 18M = 520 -17 CGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9C8 +seq25 65 phiX174 520 37 18M = 537 17 TTGCTACTGACCGCTCTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:17C0 +seq26 129 phiX174 1994 37 18M = 1976 -18 AAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq26 65 phiX174 1976 37 18M = 1994 18 CCGCGTGAAATTTCTATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq27 129 phiX174 2614 37 3M1D15M = 2598 -16 TGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:1C1^G15 +seq27 65 phiX174 2598 37 18M = 2614 16 CGCTAATCAAGTTGTTTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:9G8 +seq28 129 phiX174 2906 37 18M = 2890 -16 TCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:25 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10T7 +seq28 65 phiX174 2890 25 18M = 2906 16 AAAGAGATTATTTGTCGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16T0C0 +seq29 133 phiX174 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq29 73 phiX174 5339 37 18M = 5339 0 CAAATTAATGCGCGCTTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6T11 +seq3 129 phiX174 523 37 18M = 505 -18 CTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq3 65 phiX174 505 37 18M = 523 18 GTAACAAAGTTTGGATTG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq30 129 phiX174 4108 37 18M = 4091 -17 ACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:0T17 +seq30 65 phiX174 4091 37 18M = 4108 17 ATCCCCTATGCTTGGCTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:6A11 +seq4 137 phiX174 945 37 18M = 945 0 TAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:12A5 +seq4 69 phiX174 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq5 129 phiX174 5003 37 18M = 4985 -18 TTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13A4 +seq5 65 phiX174 4985 37 18M = 5003 18 CAGTTATATGGCTTTTGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:13G4 +seq6 129 phiX174 944 37 18M = 925 -19 GTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq6 65 phiX174 925 37 11M1D7M = 944 19 AGGCGCTCGTCTTGGTAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T7 +seq7 129 phiX174 960 37 18M = 943 -17 TTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq7 65 phiX174 943 25 18M = 960 17 TGTAGGTGGTCAACCAAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A1T1 +seq8 137 phiX174 1715 37 18M = 1715 0 ATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:10A7 +seq8 69 phiX174 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII RG:Z:abcdefg +seq9 129 phiX174 2613 37 18M = 2596 -17 TTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq9 65 phiX174 2596 37 18M = 2613 17 GCCGCTATTCAGGTTGTT IIIIIIIIIIIIIIIIII RG:Z:abcdefg XT:A:U NM:i:1 SM:i:37 AM:i:37 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:7A10 --- a/test-data/bwa_wrapper_out4.sam Mon May 09 12:11:54 2011 -0400 +++ b/test-data/bwa_wrapper_out4.sam Mon May 09 16:37:13 2011 -0400 @@ -36,7 +36,7 @@ 427_18_706_F3 4 * 0 0 * * 0 0 CTCTATATGGAAGGTTACTACTCAGTAACCTTAGGGACCAAGAACCGGTT >AAA@B?BAABAAAAA@@@A?B?>=B?@>>B@6??@><@@?:?A;<?=?? 427_18_834_F3 4 * 0 0 * * 0 0 GGGACCCGACCTAGGACGGACAAAGACAGGGACGACAGATATACGATTCA @@@@><?A><@A?@7@A@@6=><?;<;;7@>=?=:<:<;>=6=/:A?B?4 427_18_846_F3 4 * 0 0 * * 0 0 GGACGCGTCACCAGAAAAACTAGGGGACGGTCCACGACCATGACGGGGAG BABB>BBBB7BBA@@ABBB1<BABA<B<A89BB?21A@@22@@A?>A@=? -427_1927_689_F3 0 chrX_part 14818 0 49M * 0 0 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATC ]]ZY]]]Z[]]]ZROQFMVZ]ZYUV]ZXSLTWZUT]]]]]]Z\[ZXW[T XT:A:R CM:i:1 X0:i:3 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:4C44 XA:Z:chrX_part,+12257,49M,2;chrX_part,+26924,49M,2; +427_1927_689_F3 0 chrX_part 26924 0 49M * 0 0 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATC ]]ZY]]]Z[]]]ZROQFMVZ]ZYUV]ZXSLTWZUT]]]]]]Z\[ZXW[T XT:A:R CM:i:1 X0:i:3 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:34T14 XA:Z:chrX_part,+14818,49M,2;chrX_part,+12257,49M,2; 427_19_1049_F3 4 * 0 0 * * 0 0 TCCGCTTGGAACATACTAAAGGAGAGTATATAGATGACCAGGAAAAGCTT ?<>@:A?@B>B=>@@?>AA?B>@@@BB35@B>98<>A5/AB><<BB>8<: 427_19_11_F3 4 * 0 0 * * 0 0 CAGCCCACATGCACCCACTGGGAAGGCCACCCATGAGAAACTCCACGATC =1:<4>?><;=?><1?:>?7>=>=:<=<99:><<55;>>,@=>93>/15: 427_19_137_F3 4 * 0 0 * * 0 0 AAGCTGACGCTACCACGGACAACAGCGGTCAAGGCCGTCAGGCGAAGCGG ?78;?@?<>;=AA=;7?9<8;=<:<8><968;<9;:<:;::<53;=7+85 @@ -131,7 +131,7 @@ 428_628_321_F3 0 chrX_part 28192 37 49M * 0 0 CTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGGT ]]]]]]]]]]]]]]]]]]U]]Z[Y[]]]W\]QO\]\ZYPPVU]XY]\WU XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 428_666_413_F3 0 chrX_part 27425 37 49M * 0 0 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]][]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:40A8 428_912_273_F3 4 * 0 0 * * 0 0 TCCACCGCGAAACGGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGG BAABBBB@@BABA@BB@>??BB@A?@A=@<>@??<ABBA::@A@@@@9>< -429_1074_1497_F3 0 chrX_part 12256 0 49M * 0 0 TAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACAT ]]]]]]]]]]]]VV]]]XZ]]]]]]]]]]]]]YZ]]]]]]]]\[]]][Y XT:A:R CM:i:1 X0:i:2 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:32C16 XA:Z:chrX_part,+26923,49M,3; +429_1074_1497_F3 0 chrX_part 26923 0 49M * 0 0 TAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACAT ]]]]]]]]]]]]VV]]]XZ]]]]]]]]]]]]]YZ]]]]]]]]\[]]][Y XT:A:R CM:i:1 X0:i:2 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:35T13 XA:Z:chrX_part,+12256,49M,3; 429_1244_262_F3 16 chrX_part 27844 23 49M * 0 0 TTTTCCAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCAT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,+15141,49M,2; 429_1264_776_F3 16 chrX_part 27356 37 49M * 0 0 TGGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCC %!X\[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]* XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:49 429_1285_1614_F3 4 * 0 0 * * 0 0 TGTAGTTGCTACCACAGCCTAACAACACACAGACAGCGGAACTGTTACCC A@BB?ABBBBBBBABBBB?AABBA@<BB?A@B>6@=@@;BA@@>@;?B?? @@ -166,7 +166,7 @@ 430_1280_786_F3 0 chrX_part 28246 37 49M * 0 0 AGATATACAATCATGTCATCTGCAAACAGGGACAATTTGACTTCATCTT ]]]]]]]]]]]]]]]]]]]]]]]SX]]]]]]]][]]]\RW]]]SZ]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:44C4 430_1307_10_F3 0 chrX_part 26911 0 49M * 0 0 GAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCT !"]]]]]]]]]]]]]]]]]]]]]]]]]]ZR]]]]]]]]]X[]]]]]]]] XT:A:R CM:i:1 X0:i:2 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:47T1 XA:Z:chrX_part,+12244,49M,3; 430_131_637_F3 4 * 0 0 * * 0 0 ACCAGAGTTAAGGGACCCTGATTGGACGTCCAGCCACCAAGAGCGCGAAA 8??<>>@@8B68>?9=A8?=BB<AAA>0@;@<<A<>A9B@>A8=:@=A?; -430_1403_722_F3 0 chrX_part 14821 0 49M * 0 0 TTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:1 X0:i:3 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:1C47 XA:Z:chrX_part,+12260,49M,2;chrX_part,+26927,49M,2; +430_1403_722_F3 0 chrX_part 12260 0 49M * 0 0 TTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:1 X0:i:3 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:28C20 XA:Z:chrX_part,+14821,49M,2;chrX_part,+26927,49M,2; 430_1406_34_F3 0 chrX_part 26518 37 49M * 0 0 CCTGTGTCCACGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAAC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:10T38 430_1531_1322_F3 0 chrX_part 26775 25 49M * 0 0 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATC ]WP]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\\ XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:46G2 430_1586_641_F3 0 chrX_part 28277 25 49M * 0 0 ACAATTTGACTTCCTCTTTTCCTAATTGAATGCCCTTTATTTCCTTCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:31A17 @@ -180,7 +180,7 @@ 430_491_367_F3 0 chrX_part 27259 37 49M * 0 0 TCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]ZX]]]UU][]]]]]ZHR] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 430_607_895_F3 0 chrX_part 26847 23 49M * 0 0 GGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCG *]]]]]]]]]]]]]]]]]\]]]]]]]]ZZ]]]]\]]]]]]]]]Z[]]]] XT:A:U CM:i:0 X0:i:1 X1:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,+14741,49M,2; 430_688_525_F3 16 chrX_part 27375 37 45M1D4M * 0 0 TGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTATGT WW]]]]]Z]]]]]]]]]]]]\]]]]]]]]]]]]]]]]]]]]]]]]]"!] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:45^A4 -430_691_1191_F3 0 chrX_part 14746 0 49M * 0 0 GCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:0 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,+26852,49M,1; +430_691_1191_F3 0 chrX_part 26852 0 49M * 0 0 GCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:0 X0:i:2 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,+14746,49M,1; 430_693_248_F3 0 chrX_part 14829 37 49M * 0 0 CCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCAC -]]]]]]]]]]]]]]]Z]]]]]]][]]]]]]]]]]]]]]]]]]]]]]]\ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 430_78_1025_F3 0 chrX_part 14935 37 49M * 0 0 TTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]]]]]]]]Z]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 430_821_1672_F3 4 * 0 0 * * 0 0 ATCGGCTGGCGCCAAGAATGTATTTGACGGATGGTCCATCGACGGCAACC A@?AAAAAA@=?:BA>B@>ABA?@A?B>:=@?<<:@>B=74@B;=><@65 @@ -198,3 +198,5 @@ 431_524_1355_F3 16 chrX_part 28191 37 49M * 0 0 GCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 431_753_1184_F3 0 chrX_part 27127 37 49M * 0 0 GAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTG Z]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:23T25 431_933_606_F3 16 chrX_part 27360 37 49M * 0 0 TGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +@PG ID:bwa PN:bwa VN:0.5.9-r16 +@SQ SN:chrX_part LN:37500 --- a/test-data/bwa_wrapper_out6.sam Mon May 09 12:11:54 2011 -0400 +++ b/test-data/bwa_wrapper_out6.sam Mon May 09 16:37:13 2011 -0400 @@ -1,200 +1,203 @@ -427_1253_1057_F3 0 chrX_part 14947 37 49M * 0 0 TTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTCT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]VZ XT:A:U CM:i:0 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:49 -427_1299_965_F3 16 chrX_part 13217 25 49M * 0 0 GGGATGCTCTCTCTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTG ][]]]]Y]]]]Z]]]]]]]]]Z]]]]Y]]]]]]]]Y]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:7C41 -427_12_1018_F3 4 * 0 0 * * 0 0 CTCTTCTCCTCCGGACTAGAGGCCCGGGCAATCAAGGCTGCGTAGACGTA >?<;5@:>>5>7:?<7@><=:>?92<?5>=;@@>?2<?>:?<9<4>56?@ -427_12_390_F3 4 * 0 0 * * 0 0 AAGGGAGTGGTGCTGGTGGGAGGCAATTTGTCGGACCTGGGAAGCGAGTC BBB>=;@@A6<A;=>=A?>??@A58@B>9>>@?70?@<=>>@A9/5?=25 -427_12_550_F3 4 * 0 0 * * 0 0 CGATCTCTGCAACTTCGTGCGCAGGCGATGGGGGGGAAAATGAACGGATA 8A=?<BA@=;?A;?><B?;:5@.<:7?9;6<A62<@;8<==@3:>;=339 -427_12_941_F3 4 * 0 0 * * 0 0 GGGCCAAAGTAAACGCTAATCGAGGAGGACAAAGTAAGGAAGGCGCCTGT B@72=>?A:;<:?>?94B??;3A<?1@<3=<A?8>A6?>=>7A/>=07<@ -427_13_422_F3 4 * 0 0 * * 0 0 AATAACGAAGCGTGTGTGTTAGCGGGAGAGCCGGGCCCCTTCCCGTACGT 9>A2,9@9<8<=;;7=7:>@1<:?37<1>1690>7=<:=A/>53.::<=/ -427_13_494_F3 4 * 0 0 * * 0 0 CGACTACCCCTACCGGTCACCGCTACGGTGAGGCTAAGCTCTTCCAGACG .>>?@;A@?7?@<>39?>=7:==76;=;=65@:::9?8?3=@8=::@2<. -427_13_606_F3 4 * 0 0 * * 0 0 TTTAACGCGATAATCCTTCGAAGGAAAAGAAGTGACTTTCCGTACATACC BB?A?@A??>B@A@<=@A==A>>>>AA@7<?:B=9<@A@A@2@>8><;<= -427_13_861_F3 4 * 0 0 * * 0 0 CGAGGTGCAGGCCTGCTCTGGGGACCCACTGTGACCAGGCGGCCTGCCAC =>>@<@>BB>>58A=@A<BABA:=>@B:==?A9<AA@7::@;??:A?;2> -427_13_961_F3 4 * 0 0 * * 0 0 GACGGGAGACGCTGCGATCGCACCTTAATGGGGGACCGGATGCACAAAAG @BBBBB@BB@B>BBAB@B@AB@ABAABBA?B?B@>@@BA=A?A:<>BBB3 -427_1444_687_F3 16 chrX_part 25682 37 49M * 0 0 TCATTCTCAGCAAACTATCGCAAGGACAAAAAACCAAACACCGCATGTT ]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -427_14_1010_F3 4 * 0 0 * * 0 0 GCTGCTGTGGCCGGGCGCACCCAGACAGGTAGAAAGCCGACTCACCACGT @??A><@=ABA@?A?A@A??AB@AA@=<?B;<@?A<94?A=5;:@@2?@9 -427_14_270_F3 4 * 0 0 * * 0 0 GCAGATGCGTGGAGCAACGGTGGTCTGTAGATCGTCAGGATCTGAAACCA A=A@?BB>@9@BAA89>A@:A@@>2@A;383B><;:;>=1=8B:<>=?8= -427_14_376_F3 4 * 0 0 * * 0 0 TCACACGCAGGGCCCCGTACGGAGAATACTGCTCAATGAAAATGGAGGGG B9??@BA@;?BB@@>AA?:?>A><=<A:4=5<?;=<?;?:95=61;<:<2 -427_14_602_F3 4 * 0 0 * * 0 0 GGCCGGTTGGTCGACTAGGCAGGCCGACAATGCCTGAACATACTAGGGCC ,B=7==A:9;AA45,=:9/.2<;58>9806:=>:<8=877?=9198>:2: -427_14_665_F3 4 * 0 0 * * 0 0 CATACGAGGGAGTCTCTAGCATAAAGCTGGGTCCCCTGACATTGACCTGA <A@@>B7<A5@>@>>>;<@68,9@;<-<<:>9?@?>6.A65=;=8569;5 -427_1522_8_F3 0 chrX_part 12254 0 49M * 0 0 ACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCAC )]]]]]]]]]]]]]PU]]][]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:34C14 XA:Z:chrX_part,+26921,49M,3; -427_15_1039_F3 4 * 0 0 * * 0 0 AGAGTCAACTGAAGCTTCCGAGTCGTGAACGGGGGGAGGAGAGGGAAGGC BBB@@@B?A?ABB><A>?9=:=<:@:?>51:AA>?87>?979<>><>>=< -427_15_1070_F3 4 * 0 0 * * 0 0 CTACTCCCTGCATTAGATACTGGAGCTCGGCTAGAGGGATGGCGTTAAAG =>A<@><?BAA?A?>?4??=;>?@>??=:@<6?98==><<:;<8A:7=@5 -427_15_1081_F3 4 * 0 0 * * 0 0 GCTCCTCCACGATTAATCGTTGGGGTGCAATGAGAAAACAGCCAATGGCC @=AAAB@?@>?B@?=BB@?@B=@>;B@3:?BA39?>@7==<<<A?A<1A? -427_15_423_F3 4 * 0 0 * * 0 0 GCTGGAGGAGAAAGGGGGGACCCGCAATCGAGCGTCCGATAATGAAATGG >/B@=<A=??@B>A>B@@>9?@=A6@B@9?5@6A7A@>@A?=?A/@@A?= -427_15_646_F3 4 * 0 0 * * 0 0 CAGTTCGCTTGGTCAATCAATATAGAGAACCTGGGGAGTAGTGTCCGGAG ?@=?>=A?@??B876:@65.B<914;;<06=?914:67997;5<:/7771 -427_15_872_F3 4 * 0 0 * * 0 0 CGGGTAGACTTTAGTACCTAGACGAAGGGAGTGACATGACGTCGCGTACA <:??A@B@B==>@>A:6=?;5<::30<==63@;;1?=;A5,=7<,4;6@0 -427_16_1107_F3 4 * 0 0 * * 0 0 TGTGTAAGTGAGACACGAGAAGCAAGAACTGATGCCCTGCAGGGTTTAGG <+>B><:;A@B?:>>:A7B5;B@?B>8;:>8=B:B@=;@25A9A=>@1A: -427_16_264_F3 4 * 0 0 * * 0 0 CCCGATCCTAGGCAGAATCGAGAGAGACCACAACCCGCGAAAACCATTGC @<>?@@?AA?@??@>>?;:A>>A=?>=?>?:A>@@@:A8@@@:>/@>A4= -427_16_565_F3 4 * 0 0 * * 0 0 AGCTATGGAATACCAAGACATCCAAGGAACTACTGCCGAAGGTTCCGGAG BB1AABB9@@B>3>=@@,?AB<8A>@@9<=BA8<<>>4A??@:??<?6@< -427_17_1027_F3 4 * 0 0 * * 0 0 CAGTGCAATGGGAGTAAAGCAAATTCGGCAGCCCGTGGCCGAACCGCTTG A@@BAB=>B>BAA?5>=AA8:@B@;=@?@9:>BB::?@A54=B?<0<B@: -427_17_342_F3 4 * 0 0 * * 0 0 AGCTGGAGCTGCTGCCACGGACAAGGTCGGAGCTGAGGCTGGCTGGACTA BA?A?BB>>ABB@;;AA@@>AA>=ABB1??:B6>?>B72>@B49>?@3<< -427_17_446_F3 4 * 0 0 * * 0 0 TATGCCGTGAGACGGGGGGAAACAGACCCTACCCCGATGTATAAGGCCGG =B?>8>BA?=>B;?;>A;:<=?937;?=2;6:==;9=@3?9;51;9:149 -427_17_46_F3 4 * 0 0 * * 0 0 CCAATGAATGAAACAGGGTACCCGCGAGCGCCTGCTGAGCTGACAGTCTC :.>A:@>@?7A@<=2?;6?;>;99=<:8;95>0:><14;@4:><:,;:8? -427_17_917_F3 4 * 0 0 * * 0 0 AAGACTACGCGTTAGGCCAAGAGAAAGACTCAAGAGACGACCTCTAAGAT @@=???A6=-;A:3<@?866@94:20<11@3;19:=:/:9<<45B@:48B -427_1891_897_F3 16 chrX_part 26846 37 49M * 0 0 GGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATC ]]]]]]]]]]]]]]]QW]]]Z]]]]]]]]]PX]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -427_18_267_F3 4 * 0 0 * * 0 0 CTGGCACCGAACGGAGGAAGAAATTGCGTAGATTACAGTAATCAGAAGAC AB@A;>@A@>AAAB:8B<>>@B@A=@?=@;=A<A3>?;@@?<:>+A?;A. -427_18_481_F3 4 * 0 0 * * 0 0 GGCTCGCCCCAGTATCGACGTCGTATGAGAGATGACGAGGCCCGGGCGAG AB>?;B@A>=AAA@@@A?=6B=><=B=<8>=7A2=<==5;@5>7<=3=>; -427_18_706_F3 4 * 0 0 * * 0 0 CTCTATATGGAAGGTTACTACTCAGTAACCTTAGGGACCAAGAACCGGTT >AAA@B?BAABAAAAA@@@A?B?>=B?@>>B@6??@><@@?:?A;<?=?? -427_18_834_F3 4 * 0 0 * * 0 0 GGGACCCGACCTAGGACGGACAAAGACAGGGACGACAGATATACGATTCA @@@@><?A><@A?@7@A@@6=><?;<;;7@>=?=:<:<;>=6=/:A?B?4 -427_18_846_F3 4 * 0 0 * * 0 0 GGACGCGTCACCAGAAAAACTAGGGGACGGTCCACGACCATGACGGGGAG BABB>BBBB7BBA@@ABBB1<BABA<B<A89BB?21A@@22@@A?>A@=? -427_1927_689_F3 0 chrX_part 14818 0 49M * 0 0 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATC ]]ZY]]]Z[]]]ZROQFMVZ]ZYUV]ZXSLTWZUT]]]]]]Z\[ZXW[T XT:A:R CM:i:1 X0:i:3 XM:i:2 XO:i:0 XG:i:0 MD:Z:4C44 XA:Z:chrX_part,+12257,49M,2;chrX_part,+26924,49M,2; -427_19_1049_F3 4 * 0 0 * * 0 0 TCCGCTTGGAACATACTAAAGGAGAGTATATAGATGACCAGGAAAAGCTT ?<>@:A?@B>B=>@@?>AA?B>@@@BB35@B>98<>A5/AB><<BB>8<: -427_19_11_F3 4 * 0 0 * * 0 0 CAGCCCACATGCACCCACTGGGAAGGCCACCCATGAGAAACTCCACGATC =1:<4>?><;=?><1?:>?7>=>=:<=<99:><<55;>>,@=>93>/15: -427_19_137_F3 4 * 0 0 * * 0 0 AAGCTGACGCTACCACGGACAACAGCGGTCAAGGCCGTCAGGCGAAGCGG ?78;?@?<>;=AA=;7?9<8;=<:<8><968;<9;:<:;::<53;=7+85 -427_19_296_F3 4 * 0 0 * * 0 0 CCAGAAACCTCAGCAACACACCACCTAGGCCCCCAGGGTCGGAAGATGCA B@BABBB@BBBBAA@<AAAB>@A@?AA@?@>A=?9>?>?@@@?@=?A<@@ -427_19_324_F3 4 * 0 0 * * 0 0 TGGACGATTTAATGGCAGGGAAGTGAGACAAGACTGGGGTCTGCGAAAAA A;=?3A>>:>>:<87:8483>>627=;40596=885:66>3810/843:9 -427_19_533_F3 4 * 0 0 * * 0 0 GAAAGCTCGATCGTTCGACTTTTCTTCGTCTGAGTCAATCAGACTTGGCA BA@@?>@A?>A@@@@?@<=BAB?>BA?<>3B?<;@?AB?7><@@@AA6?- -427_19_899_F3 4 * 0 0 * * 0 0 CATACCGTAGCCCAGGCAAGGAGACGCTCAGTGTAACAAGACGCAGTCGA @??B>=@<A?;@5AA8=6@B<:3A>6=57@9A2?A=;:A?4>,9A7=48@ -427_20_363_F3 4 * 0 0 * * 0 0 GACGTCGAGATACGGTACCCGGGCTATATTTTAGACGACTTAAAACTAGA AAAA>@B>A+BB@A7B@?<==?>=@.@9?=>A=<<1><>>>=@@?74?.@ -427_20_407_F3 4 * 0 0 * * 0 0 ATAACGGACACCTAAGAAGAGGGAGTTAACATCCAGCGTAGGGCGCGTAC BBBB?BBB?ABBBBABB@>BBB?@?AB?@@2B?@;@94B@AB??;/?@>= -427_20_608_F3 4 * 0 0 * * 0 0 ACAGCACGCGGCTGCAGGAGGGAGAGAGGGGCAAGACGGACGGGCCTGTG B@9<AB?35>@>9?=AB7:@@A6<@A=>=A@@=<=?@<;:=<-<@:=0=: -427_20_892_F3 4 * 0 0 * * 0 0 GACACTCCATGGGTTCGCCGTACGTCAATGCCGACTGAAGAAGCCAGAGG A@A@?A@@>@BA?AA@>@>?B@AABB?AB:@A>?AB<BB@A@>@>>9>?= -427_20_982_F3 4 * 0 0 * * 0 0 TCCCGCGCAAACATCCTGATCAAAACCATCTCCCTGACGGTGGGCTTGAT @??>>>?98@@<36:;=:9=?:89<>9;.:7??/734:40;09.8<1834 -427_21_328_F3 4 * 0 0 * * 0 0 TGTGCGTCTAACCCCCCCCAGGGCGACGAGCTGGGAAGGCGTGAACAAGC B@>>@BB;A?BB?A>AA>;8BB>:<@@<7<AB==>?><>9@A:=7A@/<= -427_21_334_F3 4 * 0 0 * * 0 0 AACAGTAAACAGTAAGGGGGAGAAGGGGCTCTGGACGATGAAGAGGGGGG AB>4>?B@84>@>@;@BA<=<A<3@?A;1=6?=8>@=?7;A=<<?<;<69 -427_21_366_F3 4 * 0 0 * * 0 0 CTACCCCCAGCTTTCCCCGTTGCCTGCGGCCCAGCGGTGGGGCCCATGAG >AA?@@@@>?>B=B><B@?A@AA;B?A=7:<B<>A9>B=@<BA?B>@;?7 -427_21_473_F3 4 * 0 0 * * 0 0 GATGCATGGACGAACCACGCTGGGCAGGACGAATTCTACCGGGCTCGAGA BA?<>>B:>8=B@@8=<==;@A>@;<@;=<69/=<7>5<>4?9;91;36> -427_21_537_F3 4 * 0 0 * * 0 0 AAGCAGTCATAGGGAGCTAGGCGTAGAGAGCGGCTGTGCAAGTCCAGACG AB@@@ABA:A?B@B>>AB=A@@;A?@A@?>8?A<A>=><@@4>=@@7:=9 -427_21_563_F3 4 * 0 0 * * 0 0 CGACAATTCTCGATCGTAGCCAGTATAAGAGACACAAATGCGAGGACTTC >@AAAAA@?=>BAA>=A@@??>=A==@@?@<A:@>:A@@=9>@<@+>=@A -427_22_56_F3 4 * 0 0 * * 0 0 GAGGCACCGTCACAAACTAACTACGTCGCTGGTTGCTCGCGATGAAGGGG ?>=>.?A@?9AB>;?7@A<<=B:;<@7=:?6:B:;3?>0@38A3??<8<< -427_22_692_F3 4 * 0 0 * * 0 0 CGCGATACGAAAGGGGAATCGCCGAACCCGTAAACTAGATTAAGGGAAGA :?;<>B>:@>A>>AAA71@=<?3>2=>?7;9<<7;?7<>9?=+=?-?=7; -427_22_787_F3 4 * 0 0 * * 0 0 CGGTGGCAAGTACGCCGGTAGAGAGGGGGGGGGGGCCGGGGGGCTCATCT <@5>:@@<76@A;;;;A7=;<><;8>A;4;>A<965+;<;<>598;6<82 -427_22_927_F3 4 * 0 0 * * 0 0 TCAAACAGAGTAACTTGATTGGTTCCTAAGTGGTACAAGAGGTCGAGGAA @ABB@>?A??BAB@AB=A?B@@BB@A=@A@B<?9=?>=7<?>><9<>>?; -427_23_177_F3 4 * 0 0 * * 0 0 CTGAACGGTGAACCAAGGCTGCGGCACATGCCAGGCCATTTTTGGTTATC >A@AA@@@A>BA>@=?A@>AA<>>=@@:?=>A<=>>>2BAAA4:,A?6A8 -427_23_740_F3 4 * 0 0 * * 0 0 GCAATCATCAGGTTCGGACTGCCACGCAAACTCTGAGAGGATTTTCTAGA B@@AB@<?@AA@A?@?A@?>A;@>@B;?AA=2>?@A/A=A@A@@B<??7> -427_23_874_F3 4 * 0 0 * * 0 0 GGAGAACTCTAAGAAAGAACTTTAAACCAGTCTTGCCCCCCGATCGTGAA <@ABBBAB=AABAAA@@BA<>A@@B?A??=A@B@@@B<BBB<=<@:>?>: -427_23_986_F3 4 * 0 0 * * 0 0 CGGTCTGTTTTGCGGGACACGAGGTCGTGAACTAGACTGCGGGTGCATCG @6=??@<<><>@A@:<=<;==>@;3=>8=;>::?8@?9=99=4:6@<67; -427_23_993_F3 4 * 0 0 * * 0 0 AGACTCCGGGACAATGAGTCCAGCAGAGGGTGATGAAGGAACGAACGGAA @>BAAA?BBB@?B@BA@ABAB?B?A@A?AAB@<AA?>@=AA<ABB@:@AA -427_24_1040_F3 4 * 0 0 * * 0 0 CCATTTTCCCAGTGAGCACCCTTGCTTCCAATCAGGGGACTGGCTCAGAA 45/2<9A@A93A7<5:;@6=<A:7=:B5740@<698=3<:8:8-:5,220 -427_24_476_F3 4 * 0 0 * * 0 0 CAGCAGGTCCAAACGTGGATCCGCGGGCGGAGAAGGCGACACAGGGCAAA =B>:>>A<<76===6=?;3=;<<45<=6,876968:-256;693464<<< -427_24_880_F3 4 * 0 0 * * 0 0 CGTAGGTAGGCCAGGCGAGGTATTCTATCTGGGCGCAATTACCAGGAACA AAA+AB@?;@AA?;?ABA>AB>B:=BAA+@=A>4?>A?=@4?;2>9A=1? -427_24_952_F3 4 * 0 0 * * 0 0 GGTTTTTCCTTGTTCATGTGTAATCCAGTATGGAGGGCCAAAGAGAGTCC @?B>@9?@-16=9<54:-<53=6>:2;.41/<176,>8137;5:.9=905 -427_25_234_F3 4 * 0 0 * * 0 0 TATCAAGCAACGGGTGTATGGGGGAAGAGAAAGGCGATCCCACCAGATCA 0>@</1A7<+8A64::>4<9<@88=9>94<8@:7<9=>;?8:;195:<5> -427_25_60_F3 4 * 0 0 * * 0 0 TGAGGTATGGGAGTCGTAGGCGCACTCGAGGCGCCTGAGGAAACACCCTC A/>>=?==>:>>8?:>=.=>9>84:@:96<7>6<=<93<<5;>:8==.1< -427_25_854_F3 4 * 0 0 * * 0 0 AGCACTCGCGTAGACAATCGACAGCCCTGACCGAGCGAATAAGGGCTGAA AA@BBB?AB=B@@@>=;B;@4?B9?=@B;@6A?9=<:A@A6:73@55>2> -427_26_256_F3 4 * 0 0 * * 0 0 GAGGGCCGGGGGGCGATCGAAGAGTCTCGAGACGAGGCCGTGTCTCGGAA BB=BAA@@BABB?7A2>-@@@>@?AAB=@8@?9><@>:7>@>:7@@45+8 -427_26_331_F3 4 * 0 0 * * 0 0 TCGCTCGCGCTAAGATACAAGGAAGCTCAACTTTTAGCGCGCATAGGCTG =73:><A;=9?<>;/A;;:<=?276:<19;;A<7<<9<3:9:-.<<>.74 -427_26_583_F3 4 * 0 0 * * 0 0 CACGCGTTATGGAGCTCGGCGAGGGGACTAGGAGCAGAGTCTGCTTAGAT AAA@ABBBB?@B@?=B;>AA?=?@A@>7A@AA>>@==@?A=B==BB7:AA -427_26_646_F3 4 * 0 0 * * 0 0 AGAAACTCTGAGCCGGACCAAAATTAGGAGATCAAGAACCCCGGGAGGCC @@AAA?A>??BB@@A?;A@=BB??:AA7=8AB:><=<==@B;:9:A:>?5 -427_26_857_F3 4 * 0 0 * * 0 0 TTAGCCGTCCGCTGTATCAATCCAGTGTAGTCGTCGTAAACGTAACGTAC >A?=>@@<><=<=><@?7<9@><?:@;@8:@@;6<8>>A9=1/A??5:@. -427_27_1002_F3 4 * 0 0 * * 0 0 GATGCCGATAATTACACACCCCCAAGTGCGAAGGCAAAGGATGGCTTCCC >?<>B<A<=?<B;;9@A9>?@A:A=<A5<3=B:;:AA==0A>3<37A>=5 -427_27_160_F3 4 * 0 0 * * 0 0 TTAAACGTATTCTAGTACCTAAAGGAAGCTGGGCTCACAACGTTTAAAAG >>AA@@-@A?A<>A;@647A=<>9=?;:7@8;3>@2:5@<:7@?A99:?4 -427_27_231_F3 4 * 0 0 * * 0 0 GGCGGGCAAGGGCTGGGGATGGAGACGACTACTTTCCAAAGTCGGCATGC ABAA?AB=>>@B>@?@@6;B@A5;@@@=8=>;:<A?@.?;<@;8=>9<5< -427_27_369_F3 4 * 0 0 * * 0 0 CAATGCCCCTGAAATGGACGTACGCCTAACCGGAGCCGGCTGGGCTACGC ;3:7?@=34?A<3/@A?14<A8;4>7=31<98.0:<<54<77659?4.8< -427_27_778_F3 4 * 0 0 * * 0 0 GCAAATGCCGAAGAAACAGAGAGAGGGCACGGCAGGACACCACCTAGACG AA:=6AB=;=>?;=:@>6=;>>:8=@@=;7A@><?A@?=<???;@?===7 -427_27_939_F3 4 * 0 0 * * 0 0 AAGGAGGGACACAAAACCCCGGCTAATCAGAGAGCAAGGGGAGTCGTCGA 2:53=@:<@9:<?@??28>@<5:A<@>;02=6867A=<<@58->;:72/2 -427_28_1127_F3 4 * 0 0 * * 0 0 GTCCGGGACCTCTTACCCAACACAAAGGCCGAGACCCGTTGCAACTGGCG ??BBBB?@BAB@BABA@?BBA>@BBAA=?>BB>?@A=:?@9@BA@78?B- -427_28_593_F3 4 * 0 0 * * 0 0 TGGCAGAATATTACCATCTAGAGAGAAAAGAGGGTTAGACGCAGGCTAGA 4B;?>@@==;A@=;;A?-;?@@:=?BB95><@<4AA<;>:?97<>@?<89 -427_28_739_F3 4 * 0 0 * * 0 0 CAGCTCCCCGCGAAGCTCTCATTACCTCGGGGTGACTACTAAACGTTGAG 6B=@AA<;=3:B?@65@8@>5A:=>@A859<>99>4A</?:;?596A348 -427_28_798_F3 4 * 0 0 * * 0 0 TACGTAAACCACCTCGCCCGCACTCCAAAACCGAGACCTTCCCACATCAG B@@@@???<36?8:::<=?6-;89<;;:4994<.;5>A5:43>+>0+<11 -427_28_923_F3 4 * 0 0 * * 0 0 CAGCCTTGATCCTACGCTGCGCTGCCGCGAGCGTGGACGATGCTCGAGCC ?B=A?B@>A8BB@>>@>B;6>>AA;A8=:2@:::8?8>66A4?<:?4?;; -427_292_217_F3 0 chrX_part 14846 37 49M * 0 0 GTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTT ]]]]]]]]]]]]]]]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -427_29_521_F3 4 * 0 0 * * 0 0 CTCTGACGTCCCATGAACTTCGCGAAGTCACCCCGGCACAAAACGATTGC >B<@=AA===BB>?<>B:>>@;<6>=?>/;>B?<=3@0;?>><88=;<03 -427_29_911_F3 4 * 0 0 * * 0 0 GTCCGCCAGTCCAGACTGGACAATTCGGACAACGGGCTGAGGCTAGGGAC B?BA@BA@B@?AAB=?@ABB=@BBB@B>A<>@@BA<=?BA>?=@B<B<@= -427_29_95_F3 4 * 0 0 * * 0 0 AGACGAAGTGGTGATGGGTGTAAACGGCCCGGCGTAGAGCACGCTCGAGC ?8?@>A><<:9??5????;;>@@9=<7?8<==>4@-==7;/5>1;4;;24 -427_29_970_F3 4 * 0 0 * * 0 0 GAGCTCGACGCGGGCGAACAAGTGAATGCCTCGAACAGACAGAGCGGCGA A@78BAB:>=BB9;>BA89BAA88AAB-:=@@4<<A@2:>>>.,9>B-78 -427_29_978_F3 4 * 0 0 * * 0 0 ACCCCAAATTTCCGCGCTTACAAACATCTGCGACAAAGATATGGTCCCGG A?@BAB@?B?AA?B?@B@BA>ABB?A?9A@??=7@AB/A?<A?<@@@=@? -427_30_1018_F3 4 * 0 0 * * 0 0 CAGAAAGGCCCCTAAGGCACACACCCGCATGAGGCCAGGCTACCCCAAGC @@@AABB@B?A@;4AAA<;A?A>4AAA98BAA:9A@B=3B;A;:A>A=,B -427_30_1044_F3 4 * 0 0 * * 0 0 CCCTTCGGAGGCGGACCAAGACAGCTAGGGAGGGAGAAAAAAGAAGAAAC ?BA@ABB=;AA><==AB>=@>A@=>=A?=A=A>9A7BABB@A3@A.<76+ -427_30_1053_F3 4 * 0 0 * * 0 0 CGCCGTGCGCTTCTATCGTGGGACGCAAGTTCCGGATGATGACAATACGT <?A=@@ABB>BB@?@;;8A@>@??@>=A<A=9?@?9=9@<.:<BB:9<== -427_30_261_F3 4 * 0 0 * * 0 0 AAGAGCGGCGGCCAAGAGGCTGCTATTGAAGCCTTGCCCGTTCACCACCC A?>??A@@>?@@=@<@<??=A?>@>BA<>>>@7>?<??>>=<=<=>:;?@ -427_30_606_F3 4 * 0 0 * * 0 0 AGTAGGAACCTTACACACGGGAGGCAATCCCTGGCGTGAGGCTCGAGGGA >?@8=@@:<<@A86;A=88>@?8/-<??699A929>>667<9=59>881: -427_30_752_F3 4 * 0 0 * * 0 0 CGGCGGAGGCAGACGCACCATACTGCAACGGAGGAGGGCAAGATGGCGAT @B@=?B?@>=>A.<>>;8;9@@<>;AA:;;??8:3@>:;8<=6=6:0624 -427_30_764_F3 4 * 0 0 * * 0 0 TTGAGACCGAGGGCAGCGCTAGAAAAGCGTGTATTCACGGGGCGAAAGGT BB?A@@=0>3?A:=8?;98??>7=<?@/<9:A3=:=;9=8<<8:?@<9;> -427_30_773_F3 4 * 0 0 * * 0 0 CGTTGCGCAAGAGAAACCGCAGCTACGGCACCGCCGTATACCTAATCCAA <@BBB=BBB@=?@B?=A@@==@@@@=B??===@>>;>A=7A@@8<8<>>? -427_30_959_F3 4 * 0 0 * * 0 0 AGGGAGACATAGCCTGCACTCCCAACCAATTTGCCACGAAATGGTCATAT >=@@?@=?;BA@>9BA=:=BAB=;:AA;9BB?88<==;??=?79;6677@ -427_30_983_F3 4 * 0 0 * * 0 0 CGTCTGACTAGGACTGAGAACCTCACCCTGGGCTCTCTAGAGAGGCTCCG >?@B?BA@A=BAB>@BAAB?B@AA=BB?@?B@A@9A:A<7B<B@>B<@@A -427_31_153_F3 4 * 0 0 * * 0 0 GACAAGGAACTGCCAGGCCGGAGCGGAAGACGTACCATCATCAGCGCGGG ?>=>9AA?@;@A?;9@@:;;>>6<;?@9<<<A@8<><=8@A=>1?9>:9= -427_31_598_F3 4 * 0 0 * * 0 0 GGCAGGGTCTGGCTAGCATCGGTTAAGGATCTGGGGGAAGAGAATCTACG BBA?AB@?/-ABA=9A:1?9BA@@<8@>0<>?=<>@@=?::AA>@::99= -427_71_906_F3 16 chrX_part 28077 25 49M * 0 0 CTTTGAAGCAATTGCGAATGGGAGTTCACTCATGATTTGGCTCTCTGTT []XNU]\]WO\]]]]]\]YX]]]]]]]]]]]]]]]W]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:14T34 -427_794_484_F3 4 * 0 0 * * 0 0 GCTCATACGGACGAGACACCCGTTCCACGATTGAGGCCACCGGGGGGAAT A@BAABBBA=ABBA=@@B?4<BAA4>A@81@B@26>A@+<>=?<;?BB:2 -428_1011_1047_F3 4 * 0 0 * * 0 0 TCGCGCCGCCCTAAAGCCCAGAGTTAAGGGACCCTGAGGGGACGTCCAGC BB?>?BA@<>?B>=?A?>8@AB@A?A@>;=>>??@>A?==@?=6@>7;5> -428_1380_646_F3 16 chrX_part 3496 37 49M * 0 0 ATAAAGAAGGTGGTTTTCAGGTCTATATTCAATGGCTCTGGTGTAATAG ]]]]]]VX][[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 -428_1424_131_F3 4 * 0 0 * * 0 0 CTCTATTAGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCAT 6B7?@BB>:>AB:@BBA>>8B8;:7><<>=9<6<+>8><<?@9>05<46= -428_1495_1538_F3 0 chrX_part 26855 37 49M * 0 0 GGATCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2G46 -428_1562_623_F3 4 * 0 0 * * 0 0 CATGTATTTGACGGATGGTCCAAGGACGATAACCAATAATCCAGGAAAAA ;@A@BABA?AA@A<B?@?==@BA=:?@?><?>?5:==A?4:>?32:=@?< -428_1569_464_F3 0 chrX_part 26911 0 49M * 0 0 GAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCT &)]]]]]]\]]]]]]]]]]]]]]]LS]]YS]]]]Z]]]]X\]]]]]]]] XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:47T1 XA:Z:chrX_part,+12244,49M,3; -428_1573_204_F3 4 * 0 0 * * 0 0 ACAAGTCATGTGACGCAATCACTTAAGGTGCAGGTGGTGAAGCGGAGATG B=;=ABA9:AB@;=AA44>5?;==65=2;978?:;19?/@-1=<==3?:= -428_1632_1017_F3 0 chrX_part 14942 37 49M * 0 0 TTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATG ]]]]]]]]]]]]]]]]]]Z\]]]YU]]]]]]]]RS]]]]]W]]T[TT]] XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 -428_1643_455_F3 4 * 0 0 * * 0 0 TAGTCTAGGATTTCCCACACCACCGGCCAACCGGGGGTACAATGCTCGGC A>>A>AA?;BBBAA>B@@?=AA@@<9>>@@??>A?<=<B@=75<A>;:<@ -428_1684_1168_F3 16 chrX_part 27017 37 49M * 0 0 CTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -428_1691_159_F3 16 chrX_part 14618 37 49M * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGC ]TO]UY]]]]]]]]]]]]VT]]]]]]]]]]]]]]]]]]]]]]]]]]]+/ XT:A:U CM:i:0 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:49 -428_1816_859_F3 0 chrX_part 14837 37 49M * 0 0 AGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\ XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -428_1829_1041_F3 4 * 0 0 * * 0 0 AATAGTGTCACATCGCGAAGGAGCCCGGATACAGAAAAACGTCGAATAAG ,??A@9AB>@5AA>A9A?=?:B=?:5A=;>8@;:89A>=92A96<4@>;9 -428_1841_222_F3 16 chrX_part 26855 37 49M * 0 0 GGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATGGCCACACTG ]\Z]]YV]]]]]]]][S[]]]SQ]]]]]]]]\]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:39C9 -428_1971_118_F3 16 chrX_part 27350 25 49M * 0 0 TGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCC XX]]]]]]][Y]]\]]\]]WX]]]\]]]]\\]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:7G41 -428_1978_162_F3 16 chrX_part 28066 25 49M * 0 0 TATTTTATCCTCTTTGAAGCAATTGTGAATGGGAGTTCACTCATGATTT ]]]]]]]]SS]]]]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:8T40 -428_247_467_F3 4 * 0 0 * * 0 0 CTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCGAACCACACCG ABAABAAAB@AAAA?>>?AA:?@A:9=>A@4;?B@<>8B>.8?A>1:<@> -428_385_1306_F3 0 chrX_part 27180 37 49M * 0 0 TTTCTTGTAAATTTGTTTAAGTTTCTTGTAGATTCTGGATATTAGCCCT ]]]]]]]]]]]]]]YW]]]][]]]MN]]]]]]]]]]]]]]]]]][]]\Z XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:23C25 -428_435_1382_F3 0 chrX_part 14761 0 49M * 0 0 ATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]]ZJ XT:A:R CM:i:1 X0:i:2 XM:i:2 XO:i:0 XG:i:0 MD:Z:35C13 XA:Z:chrX_part,+26867,49M,2; -428_589_1697_F3 4 * 0 0 * * 0 0 CGAGTCTAGAAGAACGAAACGCGCCCCAGGCCGAAGTCTAAGGGGGGCCA @1>B6<<;A?@?B></=B@@/>>B???5?:=<=?9:=12><:>>;:<577 -428_615_1095_F3 16 chrX_part 28737 37 49M * 0 0 ATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTGGTCTAAAATTC ]]Y]]]WY]]]]]]MX]]]]]]]]S\]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -428_628_321_F3 0 chrX_part 28192 37 49M * 0 0 CTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGGT ]]]]]]]]]]]]]]]]]]U]]Z[Y[]]]W\]QO\]\ZYPPVU]XY]\WU XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -428_666_413_F3 0 chrX_part 27425 37 49M * 0 0 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]][]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:40A8 -428_912_273_F3 4 * 0 0 * * 0 0 TCCACCGCGAAACGGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGG BAABBBB@@BABA@BB@>??BB@A?@A=@<>@??<ABBA::@A@@@@9>< -429_1074_1497_F3 0 chrX_part 12256 0 49M * 0 0 TAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACAT ]]]]]]]]]]]]VV]]]XZ]]]]]]]]]]]]]YZ]]]]]]]]\[]]][Y XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:32C16 XA:Z:chrX_part,+26923,49M,3; -429_1244_262_F3 16 chrX_part 27844 37 49M * 0 0 TTTTCCAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCAT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -429_1264_776_F3 16 chrX_part 27356 37 49M * 0 0 TGGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCC %!X\[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]* XT:A:U CM:i:0 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:49 -429_1285_1614_F3 4 * 0 0 * * 0 0 TGTAGTTGCTACCACAGCCTAACAACACACAGACAGCGGAACTGTTACCC A@BB?ABBBBBBBABBBB?AABBA@<BB?A@B>6@=@@;BA@@>@;?B?? -429_1292_826_F3 4 * 0 0 * * 0 0 CGGTGAGGCTCCCGTCAAAGGAATATCACTGCGGGCCGACCGATCACAGT >A@A?AA>?BBB>@@;:?3>A?@??7@@;A=?<<<>=;@??<?9?7<A2A -429_1304_326_F3 0 chrX_part 12249 0 49M * 0 0 GTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTC ]]]]]]]]]]]]]]]]]]]]]]]]\]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:39C9 XA:Z:chrX_part,+26916,49M,3; -429_1398_1503_F3 0 chrX_part 27821 37 49M * 0 0 TCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCAT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y[]]]\]]]]X\]]\U]]] XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 -429_1427_1475_F3 16 chrX_part 27983 25 49M * 0 0 TATCCTCTTTTATTTCATTGAGCAGTGGTTTGTAGTTCTCCTTGAAGAG ]]]TOYT\]]]]]]]]]]]]]X]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:16C32 -429_1568_890_F3 0 chrX_part 13190 25 49M * 0 0 ATTCCCTTTGAAAACTGGCACAAGACAGGGATACCCTCTCTCACCACTC ]]]]]]]]]]]QT]]]PT]]]R]]]]MS]]]]]]]]QT]]]\]]]]QU] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:32G16 -429_1819_792_F3 16 chrX_part 3467 37 49M * 0 0 GTACGAAGAAAACAAAGAGCTCGGTTACCATAAAGAAGGTGGTTTTCAG [UMBRWX]UW]]]]]]]]]]]]]TU]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -429_1854_1258_F3 16 chrX_part 27411 25 49M * 0 0 CTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGT ]]]][[]Z]]]]]]]]]]]]]]]]]Z]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:13T35 -429_1876_126_F3 16 chrX_part 27366 37 49M * 0 0 TGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGA W]Z]]]]\]]]]]]]]]]]]]]]]]]]]]]]][]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 -429_1899_322_F3 0 chrX_part 27853 37 49M * 0 0 TCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCATTGAATCTAT ]]]]]]]]]]]]]]\]]][Z]]]]Z\]]]]]]\\VZ]]]]]]SW]]]Z\ XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:48C0 -429_1905_281_F3 16 chrX_part 26882 37 49M * 0 0 TCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTAC ]]]][X]]]]]]]]]]]]]YX]]]X]]]]]]]]]Y]]]]]]]]]]]]]\ XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:29G19 -429_1921_1124_F3 16 chrX_part 26708 0 49M * 0 0 TTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTG ]]]]]]]]\Y]]]]]]]]]]\]]][]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:0 X0:i:2 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,-14602,49M,1; -429_1925_1090_F3 0 chrX_part 28003 25 49M * 0 0 AGCAGTGGTTTGTAGTTCTCCTTGAAGAGGTCCTTCACATCCCTTGTAA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:45A3 -429_320_1424_F3 4 * 0 0 * * 0 0 ATTGAGCGGGCGAACTGCGAGCACTGATTGCGTGATAGAGGGTAAACAAT BB?9=>B<=><BA<??@=;=:=A5=?@A>==AA48?72:<>>=??@:33= -429_498_1544_F3 0 chrX_part 12236 0 49M * 0 0 GACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:1 X0:i:2 XM:i:2 XO:i:0 XG:i:0 MD:Z:1T47 XA:Z:chrX_part,+26903,49M,2; -429_517_617_F3 0 chrX_part 27136 37 49M * 0 0 CTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 -429_525_1146_F3 16 chrX_part 14836 37 49M * 0 0 CAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGT TTXVUPQYSVYW]]]TT]]]OT]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -429_566_873_F3 16 chrX_part 28192 37 49M * 0 0 CTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGGT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -429_627_1289_F3 4 * 0 0 * * 0 0 TTAGCGCCTACTGAAACTGCAGTGTCACATCGCGAAGGAGCCCGGATACA BBBBBBA?BBBB<BBB@@A@B@?=A@>>@AA??>?>B>:=A>===??<<B -429_641_991_F3 0 chrX_part 27721 37 49M * 0 0 ACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTCCAG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]][ XT:A:U CM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:35C0A12 -429_706_923_F3 0 chrX_part 14842 37 49M * 0 0 AAAAGTGTTCCTATTTCTCCACCTCCTCTCCAGCACCTGTTGTTTCCTG LY]]]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:22A26 -429_820_1223_F3 16 chrX_part 27415 25 49M * 0 0 ATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAA [VUZ]]]]]]]]]]TT]]]]]U]]RZ]]]]]]]]]Y]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:9T39 -429_880_338_F3 4 * 0 0 * * 0 0 GATGTGAACCCGGAATTCCAACGTCACTGCGGGGATTCGTTTAACCCAGG A@A?BBAA@@?B>A@@A=?B?A8?;=A=>@@A?>?@A8;AAA=A<?<;>= -429_899_643_F3 4 * 0 0 * * 0 0 CACAAAATTCACAAATGACGGTACTCAATAGCGGAATATGACTGGACGAT ?AB@6>?AB<=@AA@>@<A>=B@=>3@?@><A@@=>>?A=>;B8=@@6<< -430_1055_244_F3 4 * 0 0 * * 0 0 CGATGTTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCGAACCA ?BBBBBBBBBBBBBABB@BB@=<AB<>>B>9?<AB;:>BB@@<B?>3A@@ -430_1080_625_F3 4 * 0 0 * * 0 0 AGAACTAGGCCTGACACTAGCCAGCCGGGCGTCACTGCAAGGAAACTGCC B=BBBBBBBB>BBBB@?BA@B?@AB>A@AA>A7A@B?+@7A>A?<B-=>@ -430_1105_227_F3 16 chrX_part 27741 37 49M * 0 0 TTTGAAGTCAGGTAGCGTGATGCCTCCAGCTTTGTTCTTTTGGCTTAGG ]]]]]]]][\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16A32 -430_1195_1598_F3 4 * 0 0 * * 0 0 CCTTTTTCAACAAGAGTATTTAATGCTCTGCTGTTTAAGGCCCCTCTCCC @B@BBBBBBABBB@BBBBBBB@AA><6.=>@=5<BA4A5>@8A7B>48:7 -430_1270_1392_F3 0 chrX_part 27268 37 49M * 0 0 GTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGC ]]]]]]]]]]]]]]]]]]]]]]XW]]]SU]]]]]]]]]]]]]QT]]]Q[ XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 -430_1280_786_F3 0 chrX_part 28246 37 49M * 0 0 AGATATACAATCATGTCATCTGCAAACAGGGACAATTTGACTTCATCTT ]]]]]]]]]]]]]]]]]]]]]]]SX]]]]]]]][]]]\RW]]]SZ]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:44C4 -430_1307_10_F3 0 chrX_part 26911 0 49M * 0 0 GAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCT !"]]]]]]]]]]]]]]]]]]]]]]]]]]ZR]]]]]]]]]X[]]]]]]]] XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:47T1 XA:Z:chrX_part,+12244,49M,3; -430_131_637_F3 4 * 0 0 * * 0 0 ACCAGAGTTAAGGGACCCTGATTGGACGTCCAGCCACCAAGAGCGCGAAA 8??<>>@@8B68>?9=A8?=BB<AAA>0@;@<<A<>A9B@>A8=:@=A?; -430_1403_722_F3 0 chrX_part 14821 0 49M * 0 0 TTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:1 X0:i:3 XM:i:2 XO:i:0 XG:i:0 MD:Z:1C47 XA:Z:chrX_part,+12260,49M,2;chrX_part,+26927,49M,2; -430_1406_34_F3 0 chrX_part 26518 37 49M * 0 0 CCTGTGTCCACGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAAC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:10T38 -430_1531_1322_F3 0 chrX_part 26775 25 49M * 0 0 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATC ]WP]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\\ XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:46G2 -430_1586_641_F3 0 chrX_part 28277 25 49M * 0 0 ACAATTTGACTTCCTCTTTTCCTAATTGAATGCCCTTTATTTCCTTCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:31A17 -430_1684_261_F3 16 chrX_part 27257 25 49M * 0 0 TCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGC QS]TU]]]YXVX]XJQX]]]][]YS]]]]\]]]\]]]]\]]]]]]]]], XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:9T39 -430_1726_1548_F3 4 * 0 0 * * 0 0 TTTTCGACGACGAAGCTGCAAAAAGACATAGGCCCGAGGAAGCGCTACAC ;BBB=9@BAA3AA@>4=A>?<A@@=8<?;@8@@>>2=>8A69>5>4<==< -430_1779_172_F3 0 chrX_part 25672 37 49M * 0 0 CTGGAAACCATCATTCTCAGCAAACTATCGCAAGGACAAAAAACCAAAC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]][[]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -430_179_99_F3 0 chrX_part 14832 37 49M * 0 0 CCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -430_1871_988_F3 0 chrX_part 14560 37 49M * 0 0 AAGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCC ]]]]]]]]]]]]]]]]]]]]]]]TO]]]]\]]][T]]]]]]]]]][]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:1T47 -430_1994_1381_F3 4 * 0 0 * * 0 0 GACTCGGTCTCAGATCCAGGAGACTAACCAACCTTGAGGGAAATTAAGAG @BBBABBAB==ABB@>A@A?A@B?A>B@=?@AAAA=AA@8;ABBBAA?@8 -430_392_28_F3 0 chrX_part 12248 0 49M * 0 0 GGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTT ]]]]]]]]]]]]]]]]]]]]]]]]][]]]]]]\]]]]]]]]]]]]]]]] XT:A:R CM:i:1 X0:i:2 XM:i:2 XO:i:0 XG:i:0 MD:Z:40C8 XA:Z:chrX_part,+26915,49M,2; -430_491_367_F3 0 chrX_part 27259 37 49M * 0 0 TCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]ZX]]]UU][]]]]]ZHR] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -430_607_895_F3 0 chrX_part 26847 37 49M * 0 0 GGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCG *]]]]]]]]]]]]]]]]]\]]]]]]]]ZZ]]]]\]]]]]]]]]Z[]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -430_688_525_F3 16 chrX_part 27375 37 45M1D4M * 0 0 TGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTATGT WW]]]]]Z]]]]]]]]]]]]\]]]]]]]]]]]]]]]]]]]]]]]]]"!] XT:A:U CM:i:1 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:45^A4 -430_691_1191_F3 0 chrX_part 14746 0 49M * 0 0 GCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:R CM:i:0 X0:i:2 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,+26852,49M,1; -430_693_248_F3 0 chrX_part 14829 37 49M * 0 0 CCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCAC -]]]]]]]]]]]]]]]Z]]]]]]][]]]]]]]]]]]]]]]]]]]]]]]\ XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -430_78_1025_F3 0 chrX_part 14935 37 49M * 0 0 TTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]]]]]]]]Z]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -430_821_1672_F3 4 * 0 0 * * 0 0 ATCGGCTGGCGCCAAGAATGTATTTGACGGATGGTCCATCGACGGCAACC A@?AAAAAA@=?:BA>B@>ABA?@A?B>:=@?<<:@>B=74@B;=><@65 -430_874_1668_F3 4 * 0 0 * * 0 0 GAGAATTAAGGAAGGGAGCTAGCGTACTAAGCATACGGACGAGACACCCG A@AA>A@AB=@BAA@A@>@?B@=@?B@:A@?>:>A>=69@=@8A@@:/9? -430_89_1672_F3 4 * 0 0 * * 0 0 GGCGGAGATGTTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCG B?B?9@B@>=A@B=>A>?A@B<@==?=?@;>7A?>53A;>32@BAB>6?; -430_900_444_F3 0 chrX_part 26504 37 49M * 0 0 GTGATGTTCCCCTTCCTGTGTCCATGTGTTCTCATTGTTCAATTCCCAC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:11T37 -431_1029_654_F3 0 chrX_part 27939 37 49M * 0 0 GATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTATCC ]]]]]]]]]]]]]]]]]]]]VK]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:17G31 -431_274_859_F3 16 chrX_part 14611 37 49M * 0 0 TCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGA ]]]]XT]]]]]T\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 -431_362_522_F3 4 * 0 0 * * 0 0 CAGCCATAACGCGAGAAAGAAAGAGTATACGATTCAAGAATTAAGAGAGG ?B@?>ABBAA>B?A?@A@A@BA=A<8@>A?2@A@>AA?A?@<@A::779> -431_427_471_F3 0 chrX_part 28034 37 49M * 0 0 CCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]WT]]]TR]]]SU]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A34 -431_436_304_F3 0 chrX_part 26555 37 49M * 0 0 ATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTAC ]]]]]]]]]]]]]]]]]]]U]]]]V[]]]]]]]]X[]]]T]]]]]][]\ XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:11C37 -431_44_655_F3 4 * 0 0 * * 0 0 GCTATTAGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCATC >-<=>@@4:=>@?A:>=9=::::=:5<:<66=7865<9;<59=13:+<;; -431_50_371_F3 4 * 0 0 * * 0 0 CGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGGCTACCAGCATAGA =AA@@AAAABBBAB@=@9@A@A@A?>B<??AA>@;?@?@>B?6=B7@8A@ -431_510_914_F3 16 chrX_part 1438 37 49M * 0 0 TCCTTCTATAGAGTCTAGTTTGTGACCATATTTCTCATTCCAGAGGAAA ]]Z]V[Z]]]]]]WY]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -431_524_1355_F3 16 chrX_part 28191 37 49M * 0 0 GCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 -431_753_1184_F3 0 chrX_part 27127 37 49M * 0 0 GAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTG Z]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:23T25 -431_933_606_F3 16 chrX_part 27360 37 49M * 0 0 TGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +427_1253_1057_F3 0 chrX_part 14947 37 49M * 0 0 TTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATGTGTCT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]VZ RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:49 +427_1299_965_F3 16 chrX_part 13217 25 49M * 0 0 GGGATGCTCTCTCTCACCACTCCTATTCAACATAGTGTTGGAAGTTCTG ][]]]]Y]]]]Z]]]]]]]]]Z]]]]Y]]]]]]]]Y]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:7C41 +427_12_1018_F3 4 * 0 0 * * 0 0 CTCTTCTCCTCCGGACTAGAGGCCCGGGCAATCAAGGCTGCGTAGACGTA >?<;5@:>>5>7:?<7@><=:>?92<?5>=;@@>?2<?>:?<9<4>56?@ RG:Z:474747 +427_12_390_F3 4 * 0 0 * * 0 0 AAGGGAGTGGTGCTGGTGGGAGGCAATTTGTCGGACCTGGGAAGCGAGTC BBB>=;@@A6<A;=>=A?>??@A58@B>9>>@?70?@<=>>@A9/5?=25 RG:Z:474747 +427_12_550_F3 4 * 0 0 * * 0 0 CGATCTCTGCAACTTCGTGCGCAGGCGATGGGGGGGAAAATGAACGGATA 8A=?<BA@=;?A;?><B?;:5@.<:7?9;6<A62<@;8<==@3:>;=339 RG:Z:474747 +427_12_941_F3 4 * 0 0 * * 0 0 GGGCCAAAGTAAACGCTAATCGAGGAGGACAAAGTAAGGAAGGCGCCTGT B@72=>?A:;<:?>?94B??;3A<?1@<3=<A?8>A6?>=>7A/>=07<@ RG:Z:474747 +427_13_422_F3 4 * 0 0 * * 0 0 AATAACGAAGCGTGTGTGTTAGCGGGAGAGCCGGGCCCCTTCCCGTACGT 9>A2,9@9<8<=;;7=7:>@1<:?37<1>1690>7=<:=A/>53.::<=/ RG:Z:474747 +427_13_494_F3 4 * 0 0 * * 0 0 CGACTACCCCTACCGGTCACCGCTACGGTGAGGCTAAGCTCTTCCAGACG .>>?@;A@?7?@<>39?>=7:==76;=;=65@:::9?8?3=@8=::@2<. RG:Z:474747 +427_13_606_F3 4 * 0 0 * * 0 0 TTTAACGCGATAATCCTTCGAAGGAAAAGAAGTGACTTTCCGTACATACC BB?A?@A??>B@A@<=@A==A>>>>AA@7<?:B=9<@A@A@2@>8><;<= RG:Z:474747 +427_13_861_F3 4 * 0 0 * * 0 0 CGAGGTGCAGGCCTGCTCTGGGGACCCACTGTGACCAGGCGGCCTGCCAC =>>@<@>BB>>58A=@A<BABA:=>@B:==?A9<AA@7::@;??:A?;2> RG:Z:474747 +427_13_961_F3 4 * 0 0 * * 0 0 GACGGGAGACGCTGCGATCGCACCTTAATGGGGGACCGGATGCACAAAAG @BBBBB@BB@B>BBAB@B@AB@ABAABBA?B?B@>@@BA=A?A:<>BBB3 RG:Z:474747 +427_1444_687_F3 16 chrX_part 25682 37 49M * 0 0 TCATTCTCAGCAAACTATCGCAAGGACAAAAAACCAAACACCGCATGTT ]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +427_14_1010_F3 4 * 0 0 * * 0 0 GCTGCTGTGGCCGGGCGCACCCAGACAGGTAGAAAGCCGACTCACCACGT @??A><@=ABA@?A?A@A??AB@AA@=<?B;<@?A<94?A=5;:@@2?@9 RG:Z:474747 +427_14_270_F3 4 * 0 0 * * 0 0 GCAGATGCGTGGAGCAACGGTGGTCTGTAGATCGTCAGGATCTGAAACCA A=A@?BB>@9@BAA89>A@:A@@>2@A;383B><;:;>=1=8B:<>=?8= RG:Z:474747 +427_14_376_F3 4 * 0 0 * * 0 0 TCACACGCAGGGCCCCGTACGGAGAATACTGCTCAATGAAAATGGAGGGG B9??@BA@;?BB@@>AA?:?>A><=<A:4=5<?;=<?;?:95=61;<:<2 RG:Z:474747 +427_14_602_F3 4 * 0 0 * * 0 0 GGCCGGTTGGTCGACTAGGCAGGCCGACAATGCCTGAACATACTAGGGCC ,B=7==A:9;AA45,=:9/.2<;58>9806:=>:<8=877?=9198>:2: RG:Z:474747 +427_14_665_F3 4 * 0 0 * * 0 0 CATACGAGGGAGTCTCTAGCATAAAGCTGGGTCCCCTGACATTGACCTGA <A@@>B7<A5@>@>>>;<@68,9@;<-<<:>9?@?>6.A65=;=8569;5 RG:Z:474747 +427_1522_8_F3 0 chrX_part 12254 0 49M * 0 0 ACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCAC )]]]]]]]]]]]]]PU]]][]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:34C14 XA:Z:chrX_part,+26921,49M,3; +427_15_1039_F3 4 * 0 0 * * 0 0 AGAGTCAACTGAAGCTTCCGAGTCGTGAACGGGGGGAGGAGAGGGAAGGC BBB@@@B?A?ABB><A>?9=:=<:@:?>51:AA>?87>?979<>><>>=< RG:Z:474747 +427_15_1070_F3 4 * 0 0 * * 0 0 CTACTCCCTGCATTAGATACTGGAGCTCGGCTAGAGGGATGGCGTTAAAG =>A<@><?BAA?A?>?4??=;>?@>??=:@<6?98==><<:;<8A:7=@5 RG:Z:474747 +427_15_1081_F3 4 * 0 0 * * 0 0 GCTCCTCCACGATTAATCGTTGGGGTGCAATGAGAAAACAGCCAATGGCC @=AAAB@?@>?B@?=BB@?@B=@>;B@3:?BA39?>@7==<<<A?A<1A? RG:Z:474747 +427_15_423_F3 4 * 0 0 * * 0 0 GCTGGAGGAGAAAGGGGGGACCCGCAATCGAGCGTCCGATAATGAAATGG >/B@=<A=??@B>A>B@@>9?@=A6@B@9?5@6A7A@>@A?=?A/@@A?= RG:Z:474747 +427_15_646_F3 4 * 0 0 * * 0 0 CAGTTCGCTTGGTCAATCAATATAGAGAACCTGGGGAGTAGTGTCCGGAG ?@=?>=A?@??B876:@65.B<914;;<06=?914:67997;5<:/7771 RG:Z:474747 +427_15_872_F3 4 * 0 0 * * 0 0 CGGGTAGACTTTAGTACCTAGACGAAGGGAGTGACATGACGTCGCGTACA <:??A@B@B==>@>A:6=?;5<::30<==63@;;1?=;A5,=7<,4;6@0 RG:Z:474747 +427_16_1107_F3 4 * 0 0 * * 0 0 TGTGTAAGTGAGACACGAGAAGCAAGAACTGATGCCCTGCAGGGTTTAGG <+>B><:;A@B?:>>:A7B5;B@?B>8;:>8=B:B@=;@25A9A=>@1A: RG:Z:474747 +427_16_264_F3 4 * 0 0 * * 0 0 CCCGATCCTAGGCAGAATCGAGAGAGACCACAACCCGCGAAAACCATTGC @<>?@@?AA?@??@>>?;:A>>A=?>=?>?:A>@@@:A8@@@:>/@>A4= RG:Z:474747 +427_16_565_F3 4 * 0 0 * * 0 0 AGCTATGGAATACCAAGACATCCAAGGAACTACTGCCGAAGGTTCCGGAG BB1AABB9@@B>3>=@@,?AB<8A>@@9<=BA8<<>>4A??@:??<?6@< RG:Z:474747 +427_17_1027_F3 4 * 0 0 * * 0 0 CAGTGCAATGGGAGTAAAGCAAATTCGGCAGCCCGTGGCCGAACCGCTTG A@@BAB=>B>BAA?5>=AA8:@B@;=@?@9:>BB::?@A54=B?<0<B@: RG:Z:474747 +427_17_342_F3 4 * 0 0 * * 0 0 AGCTGGAGCTGCTGCCACGGACAAGGTCGGAGCTGAGGCTGGCTGGACTA BA?A?BB>>ABB@;;AA@@>AA>=ABB1??:B6>?>B72>@B49>?@3<< RG:Z:474747 +427_17_446_F3 4 * 0 0 * * 0 0 TATGCCGTGAGACGGGGGGAAACAGACCCTACCCCGATGTATAAGGCCGG =B?>8>BA?=>B;?;>A;:<=?937;?=2;6:==;9=@3?9;51;9:149 RG:Z:474747 +427_17_46_F3 4 * 0 0 * * 0 0 CCAATGAATGAAACAGGGTACCCGCGAGCGCCTGCTGAGCTGACAGTCTC :.>A:@>@?7A@<=2?;6?;>;99=<:8;95>0:><14;@4:><:,;:8? RG:Z:474747 +427_17_917_F3 4 * 0 0 * * 0 0 AAGACTACGCGTTAGGCCAAGAGAAAGACTCAAGAGACGACCTCTAAGAT @@=???A6=-;A:3<@?866@94:20<11@3;19:=:/:9<<45B@:48B RG:Z:474747 +427_1891_897_F3 16 chrX_part 26846 37 49M * 0 0 GGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATC ]]]]]]]]]]]]]]]QW]]]Z]]]]]]]]]PX]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +427_18_267_F3 4 * 0 0 * * 0 0 CTGGCACCGAACGGAGGAAGAAATTGCGTAGATTACAGTAATCAGAAGAC AB@A;>@A@>AAAB:8B<>>@B@A=@?=@;=A<A3>?;@@?<:>+A?;A. RG:Z:474747 +427_18_481_F3 4 * 0 0 * * 0 0 GGCTCGCCCCAGTATCGACGTCGTATGAGAGATGACGAGGCCCGGGCGAG AB>?;B@A>=AAA@@@A?=6B=><=B=<8>=7A2=<==5;@5>7<=3=>; RG:Z:474747 +427_18_706_F3 4 * 0 0 * * 0 0 CTCTATATGGAAGGTTACTACTCAGTAACCTTAGGGACCAAGAACCGGTT >AAA@B?BAABAAAAA@@@A?B?>=B?@>>B@6??@><@@?:?A;<?=?? RG:Z:474747 +427_18_834_F3 4 * 0 0 * * 0 0 GGGACCCGACCTAGGACGGACAAAGACAGGGACGACAGATATACGATTCA @@@@><?A><@A?@7@A@@6=><?;<;;7@>=?=:<:<;>=6=/:A?B?4 RG:Z:474747 +427_18_846_F3 4 * 0 0 * * 0 0 GGACGCGTCACCAGAAAAACTAGGGGACGGTCCACGACCATGACGGGGAG BABB>BBBB7BBA@@ABBB1<BABA<B<A89BB?21A@@22@@A?>A@=? RG:Z:474747 +427_1927_689_F3 0 chrX_part 26924 0 49M * 0 0 AGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATC ]]ZY]]]Z[]]]ZROQFMVZ]ZYUV]ZXSLTWZUT]]]]]]Z\[ZXW[T RG:Z:474747 XT:A:R CM:i:1 X0:i:3 XM:i:2 XO:i:0 XG:i:0 MD:Z:34T14 XA:Z:chrX_part,+14818,49M,2;chrX_part,+12257,49M,2; +427_19_1049_F3 4 * 0 0 * * 0 0 TCCGCTTGGAACATACTAAAGGAGAGTATATAGATGACCAGGAAAAGCTT ?<>@:A?@B>B=>@@?>AA?B>@@@BB35@B>98<>A5/AB><<BB>8<: RG:Z:474747 +427_19_11_F3 4 * 0 0 * * 0 0 CAGCCCACATGCACCCACTGGGAAGGCCACCCATGAGAAACTCCACGATC =1:<4>?><;=?><1?:>?7>=>=:<=<99:><<55;>>,@=>93>/15: RG:Z:474747 +427_19_137_F3 4 * 0 0 * * 0 0 AAGCTGACGCTACCACGGACAACAGCGGTCAAGGCCGTCAGGCGAAGCGG ?78;?@?<>;=AA=;7?9<8;=<:<8><968;<9;:<:;::<53;=7+85 RG:Z:474747 +427_19_296_F3 4 * 0 0 * * 0 0 CCAGAAACCTCAGCAACACACCACCTAGGCCCCCAGGGTCGGAAGATGCA B@BABBB@BBBBAA@<AAAB>@A@?AA@?@>A=?9>?>?@@@?@=?A<@@ RG:Z:474747 +427_19_324_F3 4 * 0 0 * * 0 0 TGGACGATTTAATGGCAGGGAAGTGAGACAAGACTGGGGTCTGCGAAAAA A;=?3A>>:>>:<87:8483>>627=;40596=885:66>3810/843:9 RG:Z:474747 +427_19_533_F3 4 * 0 0 * * 0 0 GAAAGCTCGATCGTTCGACTTTTCTTCGTCTGAGTCAATCAGACTTGGCA BA@@?>@A?>A@@@@?@<=BAB?>BA?<>3B?<;@?AB?7><@@@AA6?- RG:Z:474747 +427_19_899_F3 4 * 0 0 * * 0 0 CATACCGTAGCCCAGGCAAGGAGACGCTCAGTGTAACAAGACGCAGTCGA @??B>=@<A?;@5AA8=6@B<:3A>6=57@9A2?A=;:A?4>,9A7=48@ RG:Z:474747 +427_20_363_F3 4 * 0 0 * * 0 0 GACGTCGAGATACGGTACCCGGGCTATATTTTAGACGACTTAAAACTAGA AAAA>@B>A+BB@A7B@?<==?>=@.@9?=>A=<<1><>>>=@@?74?.@ RG:Z:474747 +427_20_407_F3 4 * 0 0 * * 0 0 ATAACGGACACCTAAGAAGAGGGAGTTAACATCCAGCGTAGGGCGCGTAC BBBB?BBB?ABBBBABB@>BBB?@?AB?@@2B?@;@94B@AB??;/?@>= RG:Z:474747 +427_20_608_F3 4 * 0 0 * * 0 0 ACAGCACGCGGCTGCAGGAGGGAGAGAGGGGCAAGACGGACGGGCCTGTG B@9<AB?35>@>9?=AB7:@@A6<@A=>=A@@=<=?@<;:=<-<@:=0=: RG:Z:474747 +427_20_892_F3 4 * 0 0 * * 0 0 GACACTCCATGGGTTCGCCGTACGTCAATGCCGACTGAAGAAGCCAGAGG A@A@?A@@>@BA?AA@>@>?B@AABB?AB:@A>?AB<BB@A@>@>>9>?= RG:Z:474747 +427_20_982_F3 4 * 0 0 * * 0 0 TCCCGCGCAAACATCCTGATCAAAACCATCTCCCTGACGGTGGGCTTGAT @??>>>?98@@<36:;=:9=?:89<>9;.:7??/734:40;09.8<1834 RG:Z:474747 +427_21_328_F3 4 * 0 0 * * 0 0 TGTGCGTCTAACCCCCCCCAGGGCGACGAGCTGGGAAGGCGTGAACAAGC B@>>@BB;A?BB?A>AA>;8BB>:<@@<7<AB==>?><>9@A:=7A@/<= RG:Z:474747 +427_21_334_F3 4 * 0 0 * * 0 0 AACAGTAAACAGTAAGGGGGAGAAGGGGCTCTGGACGATGAAGAGGGGGG AB>4>?B@84>@>@;@BA<=<A<3@?A;1=6?=8>@=?7;A=<<?<;<69 RG:Z:474747 +427_21_366_F3 4 * 0 0 * * 0 0 CTACCCCCAGCTTTCCCCGTTGCCTGCGGCCCAGCGGTGGGGCCCATGAG >AA?@@@@>?>B=B><B@?A@AA;B?A=7:<B<>A9>B=@<BA?B>@;?7 RG:Z:474747 +427_21_473_F3 4 * 0 0 * * 0 0 GATGCATGGACGAACCACGCTGGGCAGGACGAATTCTACCGGGCTCGAGA BA?<>>B:>8=B@@8=<==;@A>@;<@;=<69/=<7>5<>4?9;91;36> RG:Z:474747 +427_21_537_F3 4 * 0 0 * * 0 0 AAGCAGTCATAGGGAGCTAGGCGTAGAGAGCGGCTGTGCAAGTCCAGACG AB@@@ABA:A?B@B>>AB=A@@;A?@A@?>8?A<A>=><@@4>=@@7:=9 RG:Z:474747 +427_21_563_F3 4 * 0 0 * * 0 0 CGACAATTCTCGATCGTAGCCAGTATAAGAGACACAAATGCGAGGACTTC >@AAAAA@?=>BAA>=A@@??>=A==@@?@<A:@>:A@@=9>@<@+>=@A RG:Z:474747 +427_22_56_F3 4 * 0 0 * * 0 0 GAGGCACCGTCACAAACTAACTACGTCGCTGGTTGCTCGCGATGAAGGGG ?>=>.?A@?9AB>;?7@A<<=B:;<@7=:?6:B:;3?>0@38A3??<8<< RG:Z:474747 +427_22_692_F3 4 * 0 0 * * 0 0 CGCGATACGAAAGGGGAATCGCCGAACCCGTAAACTAGATTAAGGGAAGA :?;<>B>:@>A>>AAA71@=<?3>2=>?7;9<<7;?7<>9?=+=?-?=7; RG:Z:474747 +427_22_787_F3 4 * 0 0 * * 0 0 CGGTGGCAAGTACGCCGGTAGAGAGGGGGGGGGGGCCGGGGGGCTCATCT <@5>:@@<76@A;;;;A7=;<><;8>A;4;>A<965+;<;<>598;6<82 RG:Z:474747 +427_22_927_F3 4 * 0 0 * * 0 0 TCAAACAGAGTAACTTGATTGGTTCCTAAGTGGTACAAGAGGTCGAGGAA @ABB@>?A??BAB@AB=A?B@@BB@A=@A@B<?9=?>=7<?>><9<>>?; RG:Z:474747 +427_23_177_F3 4 * 0 0 * * 0 0 CTGAACGGTGAACCAAGGCTGCGGCACATGCCAGGCCATTTTTGGTTATC >A@AA@@@A>BA>@=?A@>AA<>>=@@:?=>A<=>>>2BAAA4:,A?6A8 RG:Z:474747 +427_23_740_F3 4 * 0 0 * * 0 0 GCAATCATCAGGTTCGGACTGCCACGCAAACTCTGAGAGGATTTTCTAGA B@@AB@<?@AA@A?@?A@?>A;@>@B;?AA=2>?@A/A=A@A@@B<??7> RG:Z:474747 +427_23_874_F3 4 * 0 0 * * 0 0 GGAGAACTCTAAGAAAGAACTTTAAACCAGTCTTGCCCCCCGATCGTGAA <@ABBBAB=AABAAA@@BA<>A@@B?A??=A@B@@@B<BBB<=<@:>?>: RG:Z:474747 +427_23_986_F3 4 * 0 0 * * 0 0 CGGTCTGTTTTGCGGGACACGAGGTCGTGAACTAGACTGCGGGTGCATCG @6=??@<<><>@A@:<=<;==>@;3=>8=;>::?8@?9=99=4:6@<67; RG:Z:474747 +427_23_993_F3 4 * 0 0 * * 0 0 AGACTCCGGGACAATGAGTCCAGCAGAGGGTGATGAAGGAACGAACGGAA @>BAAA?BBB@?B@BA@ABAB?B?A@A?AAB@<AA?>@=AA<ABB@:@AA RG:Z:474747 +427_24_1040_F3 4 * 0 0 * * 0 0 CCATTTTCCCAGTGAGCACCCTTGCTTCCAATCAGGGGACTGGCTCAGAA 45/2<9A@A93A7<5:;@6=<A:7=:B5740@<698=3<:8:8-:5,220 RG:Z:474747 +427_24_476_F3 4 * 0 0 * * 0 0 CAGCAGGTCCAAACGTGGATCCGCGGGCGGAGAAGGCGACACAGGGCAAA =B>:>>A<<76===6=?;3=;<<45<=6,876968:-256;693464<<< RG:Z:474747 +427_24_880_F3 4 * 0 0 * * 0 0 CGTAGGTAGGCCAGGCGAGGTATTCTATCTGGGCGCAATTACCAGGAACA AAA+AB@?;@AA?;?ABA>AB>B:=BAA+@=A>4?>A?=@4?;2>9A=1? RG:Z:474747 +427_24_952_F3 4 * 0 0 * * 0 0 GGTTTTTCCTTGTTCATGTGTAATCCAGTATGGAGGGCCAAAGAGAGTCC @?B>@9?@-16=9<54:-<53=6>:2;.41/<176,>8137;5:.9=905 RG:Z:474747 +427_25_234_F3 4 * 0 0 * * 0 0 TATCAAGCAACGGGTGTATGGGGGAAGAGAAAGGCGATCCCACCAGATCA 0>@</1A7<+8A64::>4<9<@88=9>94<8@:7<9=>;?8:;195:<5> RG:Z:474747 +427_25_60_F3 4 * 0 0 * * 0 0 TGAGGTATGGGAGTCGTAGGCGCACTCGAGGCGCCTGAGGAAACACCCTC A/>>=?==>:>>8?:>=.=>9>84:@:96<7>6<=<93<<5;>:8==.1< RG:Z:474747 +427_25_854_F3 4 * 0 0 * * 0 0 AGCACTCGCGTAGACAATCGACAGCCCTGACCGAGCGAATAAGGGCTGAA AA@BBB?AB=B@@@>=;B;@4?B9?=@B;@6A?9=<:A@A6:73@55>2> RG:Z:474747 +427_26_256_F3 4 * 0 0 * * 0 0 GAGGGCCGGGGGGCGATCGAAGAGTCTCGAGACGAGGCCGTGTCTCGGAA BB=BAA@@BABB?7A2>-@@@>@?AAB=@8@?9><@>:7>@>:7@@45+8 RG:Z:474747 +427_26_331_F3 4 * 0 0 * * 0 0 TCGCTCGCGCTAAGATACAAGGAAGCTCAACTTTTAGCGCGCATAGGCTG =73:><A;=9?<>;/A;;:<=?276:<19;;A<7<<9<3:9:-.<<>.74 RG:Z:474747 +427_26_583_F3 4 * 0 0 * * 0 0 CACGCGTTATGGAGCTCGGCGAGGGGACTAGGAGCAGAGTCTGCTTAGAT AAA@ABBBB?@B@?=B;>AA?=?@A@>7A@AA>>@==@?A=B==BB7:AA RG:Z:474747 +427_26_646_F3 4 * 0 0 * * 0 0 AGAAACTCTGAGCCGGACCAAAATTAGGAGATCAAGAACCCCGGGAGGCC @@AAA?A>??BB@@A?;A@=BB??:AA7=8AB:><=<==@B;:9:A:>?5 RG:Z:474747 +427_26_857_F3 4 * 0 0 * * 0 0 TTAGCCGTCCGCTGTATCAATCCAGTGTAGTCGTCGTAAACGTAACGTAC >A?=>@@<><=<=><@?7<9@><?:@;@8:@@;6<8>>A9=1/A??5:@. RG:Z:474747 +427_27_1002_F3 4 * 0 0 * * 0 0 GATGCCGATAATTACACACCCCCAAGTGCGAAGGCAAAGGATGGCTTCCC >?<>B<A<=?<B;;9@A9>?@A:A=<A5<3=B:;:AA==0A>3<37A>=5 RG:Z:474747 +427_27_160_F3 4 * 0 0 * * 0 0 TTAAACGTATTCTAGTACCTAAAGGAAGCTGGGCTCACAACGTTTAAAAG >>AA@@-@A?A<>A;@647A=<>9=?;:7@8;3>@2:5@<:7@?A99:?4 RG:Z:474747 +427_27_231_F3 4 * 0 0 * * 0 0 GGCGGGCAAGGGCTGGGGATGGAGACGACTACTTTCCAAAGTCGGCATGC ABAA?AB=>>@B>@?@@6;B@A5;@@@=8=>;:<A?@.?;<@;8=>9<5< RG:Z:474747 +427_27_369_F3 4 * 0 0 * * 0 0 CAATGCCCCTGAAATGGACGTACGCCTAACCGGAGCCGGCTGGGCTACGC ;3:7?@=34?A<3/@A?14<A8;4>7=31<98.0:<<54<77659?4.8< RG:Z:474747 +427_27_778_F3 4 * 0 0 * * 0 0 GCAAATGCCGAAGAAACAGAGAGAGGGCACGGCAGGACACCACCTAGACG AA:=6AB=;=>?;=:@>6=;>>:8=@@=;7A@><?A@?=<???;@?===7 RG:Z:474747 +427_27_939_F3 4 * 0 0 * * 0 0 AAGGAGGGACACAAAACCCCGGCTAATCAGAGAGCAAGGGGAGTCGTCGA 2:53=@:<@9:<?@??28>@<5:A<@>;02=6867A=<<@58->;:72/2 RG:Z:474747 +427_28_1127_F3 4 * 0 0 * * 0 0 GTCCGGGACCTCTTACCCAACACAAAGGCCGAGACCCGTTGCAACTGGCG ??BBBB?@BAB@BABA@?BBA>@BBAA=?>BB>?@A=:?@9@BA@78?B- RG:Z:474747 +427_28_593_F3 4 * 0 0 * * 0 0 TGGCAGAATATTACCATCTAGAGAGAAAAGAGGGTTAGACGCAGGCTAGA 4B;?>@@==;A@=;;A?-;?@@:=?BB95><@<4AA<;>:?97<>@?<89 RG:Z:474747 +427_28_739_F3 4 * 0 0 * * 0 0 CAGCTCCCCGCGAAGCTCTCATTACCTCGGGGTGACTACTAAACGTTGAG 6B=@AA<;=3:B?@65@8@>5A:=>@A859<>99>4A</?:;?596A348 RG:Z:474747 +427_28_798_F3 4 * 0 0 * * 0 0 TACGTAAACCACCTCGCCCGCACTCCAAAACCGAGACCTTCCCACATCAG B@@@@???<36?8:::<=?6-;89<;;:4994<.;5>A5:43>+>0+<11 RG:Z:474747 +427_28_923_F3 4 * 0 0 * * 0 0 CAGCCTTGATCCTACGCTGCGCTGCCGCGAGCGTGGACGATGCTCGAGCC ?B=A?B@>A8BB@>>@>B;6>>AA;A8=:2@:::8?8>66A4?<:?4?;; RG:Z:474747 +427_292_217_F3 0 chrX_part 14846 37 49M * 0 0 GTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTT ]]]]]]]]]]]]]]]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +427_29_521_F3 4 * 0 0 * * 0 0 CTCTGACGTCCCATGAACTTCGCGAAGTCACCCCGGCACAAAACGATTGC >B<@=AA===BB>?<>B:>>@;<6>=?>/;>B?<=3@0;?>><88=;<03 RG:Z:474747 +427_29_911_F3 4 * 0 0 * * 0 0 GTCCGCCAGTCCAGACTGGACAATTCGGACAACGGGCTGAGGCTAGGGAC B?BA@BA@B@?AAB=?@ABB=@BBB@B>A<>@@BA<=?BA>?=@B<B<@= RG:Z:474747 +427_29_95_F3 4 * 0 0 * * 0 0 AGACGAAGTGGTGATGGGTGTAAACGGCCCGGCGTAGAGCACGCTCGAGC ?8?@>A><<:9??5????;;>@@9=<7?8<==>4@-==7;/5>1;4;;24 RG:Z:474747 +427_29_970_F3 4 * 0 0 * * 0 0 GAGCTCGACGCGGGCGAACAAGTGAATGCCTCGAACAGACAGAGCGGCGA A@78BAB:>=BB9;>BA89BAA88AAB-:=@@4<<A@2:>>>.,9>B-78 RG:Z:474747 +427_29_978_F3 4 * 0 0 * * 0 0 ACCCCAAATTTCCGCGCTTACAAACATCTGCGACAAAGATATGGTCCCGG A?@BAB@?B?AA?B?@B@BA>ABB?A?9A@??=7@AB/A?<A?<@@@=@? RG:Z:474747 +427_30_1018_F3 4 * 0 0 * * 0 0 CAGAAAGGCCCCTAAGGCACACACCCGCATGAGGCCAGGCTACCCCAAGC @@@AABB@B?A@;4AAA<;A?A>4AAA98BAA:9A@B=3B;A;:A>A=,B RG:Z:474747 +427_30_1044_F3 4 * 0 0 * * 0 0 CCCTTCGGAGGCGGACCAAGACAGCTAGGGAGGGAGAAAAAAGAAGAAAC ?BA@ABB=;AA><==AB>=@>A@=>=A?=A=A>9A7BABB@A3@A.<76+ RG:Z:474747 +427_30_1053_F3 4 * 0 0 * * 0 0 CGCCGTGCGCTTCTATCGTGGGACGCAAGTTCCGGATGATGACAATACGT <?A=@@ABB>BB@?@;;8A@>@??@>=A<A=9?@?9=9@<.:<BB:9<== RG:Z:474747 +427_30_261_F3 4 * 0 0 * * 0 0 AAGAGCGGCGGCCAAGAGGCTGCTATTGAAGCCTTGCCCGTTCACCACCC A?>??A@@>?@@=@<@<??=A?>@>BA<>>>@7>?<??>>=<=<=>:;?@ RG:Z:474747 +427_30_606_F3 4 * 0 0 * * 0 0 AGTAGGAACCTTACACACGGGAGGCAATCCCTGGCGTGAGGCTCGAGGGA >?@8=@@:<<@A86;A=88>@?8/-<??699A929>>667<9=59>881: RG:Z:474747 +427_30_752_F3 4 * 0 0 * * 0 0 CGGCGGAGGCAGACGCACCATACTGCAACGGAGGAGGGCAAGATGGCGAT @B@=?B?@>=>A.<>>;8;9@@<>;AA:;;??8:3@>:;8<=6=6:0624 RG:Z:474747 +427_30_764_F3 4 * 0 0 * * 0 0 TTGAGACCGAGGGCAGCGCTAGAAAAGCGTGTATTCACGGGGCGAAAGGT BB?A@@=0>3?A:=8?;98??>7=<?@/<9:A3=:=;9=8<<8:?@<9;> RG:Z:474747 +427_30_773_F3 4 * 0 0 * * 0 0 CGTTGCGCAAGAGAAACCGCAGCTACGGCACCGCCGTATACCTAATCCAA <@BBB=BBB@=?@B?=A@@==@@@@=B??===@>>;>A=7A@@8<8<>>? RG:Z:474747 +427_30_959_F3 4 * 0 0 * * 0 0 AGGGAGACATAGCCTGCACTCCCAACCAATTTGCCACGAAATGGTCATAT >=@@?@=?;BA@>9BA=:=BAB=;:AA;9BB?88<==;??=?79;6677@ RG:Z:474747 +427_30_983_F3 4 * 0 0 * * 0 0 CGTCTGACTAGGACTGAGAACCTCACCCTGGGCTCTCTAGAGAGGCTCCG >?@B?BA@A=BAB>@BAAB?B@AA=BB?@?B@A@9A:A<7B<B@>B<@@A RG:Z:474747 +427_31_153_F3 4 * 0 0 * * 0 0 GACAAGGAACTGCCAGGCCGGAGCGGAAGACGTACCATCATCAGCGCGGG ?>=>9AA?@;@A?;9@@:;;>>6<;?@9<<<A@8<><=8@A=>1?9>:9= RG:Z:474747 +427_31_598_F3 4 * 0 0 * * 0 0 GGCAGGGTCTGGCTAGCATCGGTTAAGGATCTGGGGGAAGAGAATCTACG BBA?AB@?/-ABA=9A:1?9BA@@<8@>0<>?=<>@@=?::AA>@::99= RG:Z:474747 +427_71_906_F3 16 chrX_part 28077 25 49M * 0 0 CTTTGAAGCAATTGCGAATGGGAGTTCACTCATGATTTGGCTCTCTGTT []XNU]\]WO\]]]]]\]YX]]]]]]]]]]]]]]]W]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:14T34 +427_794_484_F3 4 * 0 0 * * 0 0 GCTCATACGGACGAGACACCCGTTCCACGATTGAGGCCACCGGGGGGAAT A@BAABBBA=ABBA=@@B?4<BAA4>A@81@B@26>A@+<>=?<;?BB:2 RG:Z:474747 +428_1011_1047_F3 4 * 0 0 * * 0 0 TCGCGCCGCCCTAAAGCCCAGAGTTAAGGGACCCTGAGGGGACGTCCAGC BB?>?BA@<>?B>=?A?>8@AB@A?A@>;=>>??@>A?==@?=6@>7;5> RG:Z:474747 +428_1380_646_F3 16 chrX_part 3496 37 49M * 0 0 ATAAAGAAGGTGGTTTTCAGGTCTATATTCAATGGCTCTGGTGTAATAG ]]]]]]VX][[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 +428_1424_131_F3 4 * 0 0 * * 0 0 CTCTATTAGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCAT 6B7?@BB>:>AB:@BBA>>8B8;:7><<>=9<6<+>8><<?@9>05<46= RG:Z:474747 +428_1495_1538_F3 0 chrX_part 26855 37 49M * 0 0 GGATCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2G46 +428_1562_623_F3 4 * 0 0 * * 0 0 CATGTATTTGACGGATGGTCCAAGGACGATAACCAATAATCCAGGAAAAA ;@A@BABA?AA@A<B?@?==@BA=:?@?><?>?5:==A?4:>?32:=@?< RG:Z:474747 +428_1569_464_F3 0 chrX_part 26911 0 49M * 0 0 GAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCT &)]]]]]]\]]]]]]]]]]]]]]]LS]]YS]]]]Z]]]]X\]]]]]]]] RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:47T1 XA:Z:chrX_part,+12244,49M,3; +428_1573_204_F3 4 * 0 0 * * 0 0 ACAAGTCATGTGACGCAATCACTTAAGGTGCAGGTGGTGAAGCGGAGATG B=;=ABA9:AB@;=AA44>5?;==65=2;978?:;19?/@-1=<==3?:= RG:Z:474747 +428_1632_1017_F3 0 chrX_part 14942 37 49M * 0 0 TTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTTTTTCATG ]]]]]]]]]]]]]]]]]]Z\]]]YU]]]]]]]]RS]]]]]W]]T[TT]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 +428_1643_455_F3 4 * 0 0 * * 0 0 TAGTCTAGGATTTCCCACACCACCGGCCAACCGGGGGTACAATGCTCGGC A>>A>AA?;BBBAA>B@@?=AA@@<9>>@@??>A?<=<B@=75<A>;:<@ RG:Z:474747 +428_1684_1168_F3 16 chrX_part 27017 37 49M * 0 0 CTAACTGGTGTGAGATGGTATCTCATTGTGGTTTTGATTTGCATTTCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +428_1691_159_F3 16 chrX_part 14618 37 49M * 0 0 TTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGC ]TO]UY]]]]]]]]]]]]VT]]]]]]]]]]]]]]]]]]]]]]]]]]]+/ RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:49 +428_1816_859_F3 0 chrX_part 14837 37 49M * 0 0 AGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\ RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +428_1829_1041_F3 4 * 0 0 * * 0 0 AATAGTGTCACATCGCGAAGGAGCCCGGATACAGAAAAACGTCGAATAAG ,??A@9AB>@5AA>A9A?=?:B=?:5A=;>8@;:89A>=92A96<4@>;9 RG:Z:474747 +428_1841_222_F3 16 chrX_part 26855 37 49M * 0 0 GGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATGGCCACACTG ]\Z]]YV]]]]]]]][S[]]]SQ]]]]]]]]\]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:39C9 +428_1971_118_F3 16 chrX_part 27350 25 49M * 0 0 TGGCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCC XX]]]]]]][Y]]\]]\]]WX]]]\]]]]\\]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:7G41 +428_1978_162_F3 16 chrX_part 28066 25 49M * 0 0 TATTTTATCCTCTTTGAAGCAATTGTGAATGGGAGTTCACTCATGATTT ]]]]]]]]SS]]]]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:8T40 +428_247_467_F3 4 * 0 0 * * 0 0 CTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCGAACCACACCG ABAABAAAB@AAAA?>>?AA:?@A:9=>A@4;?B@<>8B>.8?A>1:<@> RG:Z:474747 +428_385_1306_F3 0 chrX_part 27180 37 49M * 0 0 TTTCTTGTAAATTTGTTTAAGTTTCTTGTAGATTCTGGATATTAGCCCT ]]]]]]]]]]]]]]YW]]]][]]]MN]]]]]]]]]]]]]]]]]][]]\Z RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:23C25 +428_435_1382_F3 0 chrX_part 14761 0 49M * 0 0 ATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]]ZJ RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:2 XO:i:0 XG:i:0 MD:Z:35C13 XA:Z:chrX_part,+26867,49M,2; +428_589_1697_F3 4 * 0 0 * * 0 0 CGAGTCTAGAAGAACGAAACGCGCCCCAGGCCGAAGTCTAAGGGGGGCCA @1>B6<<;A?@?B></=B@@/>>B???5?:=<=?9:=12><:>>;:<577 RG:Z:474747 +428_615_1095_F3 16 chrX_part 28737 37 49M * 0 0 ATTGAGGATTTTTGCATCAATGTTCATCAAGGATATTGGTCTAAAATTC ]]Y]]]WY]]]]]]MX]]]]]]]]S\]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +428_628_321_F3 0 chrX_part 28192 37 49M * 0 0 CTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGGT ]]]]]]]]]]]]]]]]]]U]]Z[Y[]]]W\]QO\]\ZYPPVU]XY]\WU RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +428_666_413_F3 0 chrX_part 27425 37 49M * 0 0 CTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAACGTTTAAGTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]][]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:40A8 +428_912_273_F3 4 * 0 0 * * 0 0 TCCACCGCGAAACGGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGG BAABBBB@@BABA@BB@>??BB@A?@A=@<>@??<ABBA::@A@@@@9>< RG:Z:474747 +429_1074_1497_F3 0 chrX_part 26923 0 49M * 0 0 TAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACAT ]]]]]]]]]]]]VV]]]XZ]]]]]]]]]]]]]YZ]]]]]]]]\[]]][Y RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:35T13 XA:Z:chrX_part,+12256,49M,3; +429_1244_262_F3 16 chrX_part 27844 37 49M * 0 0 TTTTCCAATTCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCAT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +429_1264_776_F3 16 chrX_part 27356 37 49M * 0 0 TGGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCC %!X\[]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]* RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:49 +429_1285_1614_F3 4 * 0 0 * * 0 0 TGTAGTTGCTACCACAGCCTAACAACACACAGACAGCGGAACTGTTACCC A@BB?ABBBBBBBABBBB?AABBA@<BB?A@B>6@=@@;BA@@>@;?B?? RG:Z:474747 +429_1292_826_F3 4 * 0 0 * * 0 0 CGGTGAGGCTCCCGTCAAAGGAATATCACTGCGGGCCGACCGATCACAGT >A@A?AA>?BBB>@@;:?3>A?@??7@@;A=?<<<>=;@??<?9?7<A2A RG:Z:474747 +429_1304_326_F3 0 chrX_part 12249 0 49M * 0 0 GTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTC ]]]]]]]]]]]]]]]]]]]]]]]]\]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:39C9 XA:Z:chrX_part,+26916,49M,3; +429_1398_1503_F3 0 chrX_part 27821 37 49M * 0 0 TCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGTCAT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y[]]]\]]]]X\]]\U]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 +429_1427_1475_F3 16 chrX_part 27983 25 49M * 0 0 TATCCTCTTTTATTTCATTGAGCAGTGGTTTGTAGTTCTCCTTGAAGAG ]]]TOYT\]]]]]]]]]]]]]X]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:16C32 +429_1568_890_F3 0 chrX_part 13190 25 49M * 0 0 ATTCCCTTTGAAAACTGGCACAAGACAGGGATACCCTCTCTCACCACTC ]]]]]]]]]]]QT]]]PT]]]R]]]]MS]]]]]]]]QT]]]\]]]]QU] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:32G16 +429_1819_792_F3 16 chrX_part 3467 37 49M * 0 0 GTACGAAGAAAACAAAGAGCTCGGTTACCATAAAGAAGGTGGTTTTCAG [UMBRWX]UW]]]]]]]]]]]]]TU]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +429_1854_1258_F3 16 chrX_part 27411 25 49M * 0 0 CTGAATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGT ]]]][[]Z]]]]]]]]]]]]]]]]]Z]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:13T35 +429_1876_126_F3 16 chrX_part 27366 37 49M * 0 0 TGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGA W]Z]]]]\]]]]]]]]]]]]]]]]]]]]]]]][]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 +429_1899_322_F3 0 chrX_part 27853 37 49M * 0 0 TCTGTGAAGAAAGTCATTGGTAGCTTGATGGGGATGGCATTGAATCTAT ]]]]]]]]]]]]]]\]]][Z]]]]Z\]]]]]]\\VZ]]]]]]SW]]]Z\ RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:48C0 +429_1905_281_F3 16 chrX_part 26882 37 49M * 0 0 TCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTAC ]]]][X]]]]]]]]]]]]]YX]]]X]]]]]]]]]Y]]]]]]]]]]]]]\ RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:29G19 +429_1921_1124_F3 16 chrX_part 26708 0 49M * 0 0 TTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTG ]]]]]]]]\Y]]]]]]]]]]\]]][]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:R CM:i:0 X0:i:2 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,-14602,49M,1; +429_1925_1090_F3 0 chrX_part 28003 25 49M * 0 0 AGCAGTGGTTTGTAGTTCTCCTTGAAGAGGTCCTTCACATCCCTTGTAA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:45A3 +429_320_1424_F3 4 * 0 0 * * 0 0 ATTGAGCGGGCGAACTGCGAGCACTGATTGCGTGATAGAGGGTAAACAAT BB?9=>B<=><BA<??@=;=:=A5=?@A>==AA48?72:<>>=??@:33= RG:Z:474747 +429_498_1544_F3 0 chrX_part 12236 0 49M * 0 0 GACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:2 XO:i:0 XG:i:0 MD:Z:1T47 XA:Z:chrX_part,+26903,49M,2; +429_517_617_F3 0 chrX_part 27136 37 49M * 0 0 CTGTTCATGTCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 +429_525_1146_F3 16 chrX_part 14836 37 49M * 0 0 CAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGT TTXVUPQYSVYW]]]TT]]]OT]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +429_566_873_F3 16 chrX_part 28192 37 49M * 0 0 CTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGGT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +429_627_1289_F3 4 * 0 0 * * 0 0 TTAGCGCCTACTGAAACTGCAGTGTCACATCGCGAAGGAGCCCGGATACA BBBBBBA?BBBB<BBB@@A@B@?=A@>>@AA??>?>B>:=A>===??<<B RG:Z:474747 +429_641_991_F3 0 chrX_part 27721 37 49M * 0 0 ACTGTAGCCTTGTAGTATAGTTTGAAGTCAGGTAGTGTGATGCCTCCAG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]][ RG:Z:474747 XT:A:U CM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:35C0A12 +429_706_923_F3 0 chrX_part 14842 37 49M * 0 0 AAAAGTGTTCCTATTTCTCCACCTCCTCTCCAGCACCTGTTGTTTCCTG LY]]]\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:22A26 +429_820_1223_F3 16 chrX_part 27415 25 49M * 0 0 ATGGTAATGCCTAGGTTTTCTTCTAGGGTTTTTATGGTTTTAGGTCTAA [VUZ]]]]]]]]]]TT]]]]]U]]RZ]]]]]]]]]Y]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:9T39 +429_880_338_F3 4 * 0 0 * * 0 0 GATGTGAACCCGGAATTCCAACGTCACTGCGGGGATTCGTTTAACCCAGG A@A?BBAA@@?B>A@@A=?B?A8?;=A=>@@A?>?@A8;AAA=A<?<;>= RG:Z:474747 +429_899_643_F3 4 * 0 0 * * 0 0 CACAAAATTCACAAATGACGGTACTCAATAGCGGAATATGACTGGACGAT ?AB@6>?AB<=@AA@>@<A>=B@=>3@?@><A@@=>>?A=>;B8=@@6<< RG:Z:474747 +430_1055_244_F3 4 * 0 0 * * 0 0 CGATGTTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCGAACCA ?BBBBBBBBBBBBBABB@BB@=<AB<>>B>9?<AB;:>BB@@<B?>3A@@ RG:Z:474747 +430_1080_625_F3 4 * 0 0 * * 0 0 AGAACTAGGCCTGACACTAGCCAGCCGGGCGTCACTGCAAGGAAACTGCC B=BBBBBBBB>BBBB@?BA@B?@AB>A@AA>A7A@B?+@7A>A?<B-=>@ RG:Z:474747 +430_1105_227_F3 16 chrX_part 27741 37 49M * 0 0 TTTGAAGTCAGGTAGCGTGATGCCTCCAGCTTTGTTCTTTTGGCTTAGG ]]]]]]]][\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:16A32 +430_1195_1598_F3 4 * 0 0 * * 0 0 CCTTTTTCAACAAGAGTATTTAATGCTCTGCTGTTTAAGGCCCCTCTCCC @B@BBBBBBABBB@BBBBBBB@AA><6.=>@=5<BA4A5>@8A7B>48:7 RG:Z:474747 +430_1270_1392_F3 0 chrX_part 27268 37 49M * 0 0 GTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGC ]]]]]]]]]]]]]]]]]]]]]]XW]]]SU]]]]]]]]]]]]]QT]]]Q[ RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 +430_1280_786_F3 0 chrX_part 28246 37 49M * 0 0 AGATATACAATCATGTCATCTGCAAACAGGGACAATTTGACTTCATCTT ]]]]]]]]]]]]]]]]]]]]]]]SX]]]]]]]][]]]\RW]]]SZ]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:44C4 +430_1307_10_F3 0 chrX_part 26911 0 49M * 0 0 GAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCT !"]]]]]]]]]]]]]]]]]]]]]]]]]]ZR]]]]]]]]]X[]]]]]]]] RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:3 XO:i:0 XG:i:0 MD:Z:47T1 XA:Z:chrX_part,+12244,49M,3; +430_131_637_F3 4 * 0 0 * * 0 0 ACCAGAGTTAAGGGACCCTGATTGGACGTCCAGCCACCAAGAGCGCGAAA 8??<>>@@8B68>?9=A8?=BB<AAA>0@;@<<A<>A9B@>A8=:@=A?; RG:Z:474747 +430_1403_722_F3 0 chrX_part 12260 0 49M * 0 0 TTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:R CM:i:1 X0:i:3 XM:i:2 XO:i:0 XG:i:0 MD:Z:28C20 XA:Z:chrX_part,+14821,49M,2;chrX_part,+26927,49M,2; +430_1406_34_F3 0 chrX_part 26518 37 49M * 0 0 CCTGTGTCCACGTGTTCTCATTGTTCAATTCCCACCTATGAGTGAGAAC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:10T38 +430_1531_1322_F3 0 chrX_part 26775 25 49M * 0 0 CAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATAATC ]WP]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\\ RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:46G2 +430_1586_641_F3 0 chrX_part 28277 25 49M * 0 0 ACAATTTGACTTCCTCTTTTCCTAATTGAATGCCCTTTATTTCCTTCTC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:31A17 +430_1684_261_F3 16 chrX_part 27257 25 49M * 0 0 TCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGC QS]TU]]]YXVX]XJQX]]]][]YS]]]]\]]]\]]]]\]]]]]]]]], RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:9T39 +430_1726_1548_F3 4 * 0 0 * * 0 0 TTTTCGACGACGAAGCTGCAAAAAGACATAGGCCCGAGGAAGCGCTACAC ;BBB=9@BAA3AA@>4=A>?<A@@=8<?;@8@@>>2=>8A69>5>4<==< RG:Z:474747 +430_1779_172_F3 0 chrX_part 25672 37 49M * 0 0 CTGGAAACCATCATTCTCAGCAAACTATCGCAAGGACAAAAAACCAAAC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]][[]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +430_179_99_F3 0 chrX_part 14832 37 49M * 0 0 CCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +430_1871_988_F3 0 chrX_part 14560 37 49M * 0 0 AAGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCC ]]]]]]]]]]]]]]]]]]]]]]]TO]]]]\]]][T]]]]]]]]]][]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:1T47 +430_1994_1381_F3 4 * 0 0 * * 0 0 GACTCGGTCTCAGATCCAGGAGACTAACCAACCTTGAGGGAAATTAAGAG @BBBABBAB==ABB@>A@A?A@B?A>B@=?@AAAA=AA@8;ABBBAA?@8 RG:Z:474747 +430_392_28_F3 0 chrX_part 12248 0 49M * 0 0 GGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTT ]]]]]]]]]]]]]]]]]]]]]]]]][]]]]]]\]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:R CM:i:1 X0:i:2 XM:i:2 XO:i:0 XG:i:0 MD:Z:40C8 XA:Z:chrX_part,+26915,49M,2; +430_491_367_F3 0 chrX_part 27259 37 49M * 0 0 TCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]ZX]]]UU][]]]]]ZHR] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +430_607_895_F3 0 chrX_part 26847 37 49M * 0 0 GGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCG *]]]]]]]]]]]]]]]]]\]]]]]]]]ZZ]]]]\]]]]]]]]]Z[]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +430_688_525_F3 16 chrX_part 27375 37 45M1D4M * 0 0 TGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTATGT WW]]]]]Z]]]]]]]]]]]]\]]]]]]]]]]]]]]]]]]]]]]]]]"!] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:45^A4 +430_691_1191_F3 0 chrX_part 26852 0 49M * 0 0 GCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:R CM:i:0 X0:i:2 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 XA:Z:chrX_part,+14746,49M,1; +430_693_248_F3 0 chrX_part 14829 37 49M * 0 0 CCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCAC -]]]]]]]]]]]]]]]Z]]]]]]][]]]]]]]]]]]]]]]]]]]]]]]\ RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +430_78_1025_F3 0 chrX_part 14935 37 49M * 0 0 TTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTT ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\]]]]]]]]]]Z]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +430_821_1672_F3 4 * 0 0 * * 0 0 ATCGGCTGGCGCCAAGAATGTATTTGACGGATGGTCCATCGACGGCAACC A@?AAAAAA@=?:BA>B@>ABA?@A?B>:=@?<<:@>B=74@B;=><@65 RG:Z:474747 +430_874_1668_F3 4 * 0 0 * * 0 0 GAGAATTAAGGAAGGGAGCTAGCGTACTAAGCATACGGACGAGACACCCG A@AA>A@AB=@BAA@A@>@?B@=@?B@:A@?>:>A>=69@=@8A@@:/9? RG:Z:474747 +430_89_1672_F3 4 * 0 0 * * 0 0 GGCGGAGATGTTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCG B?B?9@B@>=A@B=>A>?A@B<@==?=?@;>7A?>53A;>32@BAB>6?; RG:Z:474747 +430_900_444_F3 0 chrX_part 26504 37 49M * 0 0 GTGATGTTCCCCTTCCTGTGTCCATGTGTTCTCATTGTTCAATTCCCAC ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:11T37 +431_1029_654_F3 0 chrX_part 27939 37 49M * 0 0 GATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTATCC ]]]]]]]]]]]]]]]]]]]]VK]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:17G31 +431_274_859_F3 16 chrX_part 14611 37 49M * 0 0 TCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGA ]]]]XT]]]]]T\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:49 +431_362_522_F3 4 * 0 0 * * 0 0 CAGCCATAACGCGAGAAAGAAAGAGTATACGATTCAAGAATTAAGAGAGG ?B@?>ABBAA>B?A?@A@A@BA=A<8@>A?2@A@>AA?A?@<@A::779> RG:Z:474747 +431_427_471_F3 0 chrX_part 28034 37 49M * 0 0 CCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGA ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]WT]]]TR]]]SU]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:14A34 +431_436_304_F3 0 chrX_part 26555 37 49M * 0 0 ATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTAC ]]]]]]]]]]]]]]]]]]]U]]]]V[]]]]]]]]X[]]]T]]]]]][]\ RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:11C37 +431_44_655_F3 4 * 0 0 * * 0 0 GCTATTAGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCATC >-<=>@@4:=>@?A:>=9=::::=:5<:<66=7865<9;<59=13:+<;; RG:Z:474747 +431_50_371_F3 4 * 0 0 * * 0 0 CGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGGCTACCAGCATAGA =AA@@AAAABBBAB@=@9@A@A@A?>B<??AA>@;?@?@>B?6=B7@8A@ RG:Z:474747 +431_510_914_F3 16 chrX_part 1438 37 49M * 0 0 TCCTTCTATAGAGTCTAGTTTGTGACCATATTTCTCATTCCAGAGGAAA ]]Z]V[Z]]]]]]WY]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +431_524_1355_F3 16 chrX_part 28191 37 49M * 0 0 GCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +431_753_1184_F3 0 chrX_part 27127 37 49M * 0 0 GAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTG Z]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:1 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:23T25 +431_933_606_F3 16 chrX_part 27360 37 49M * 0 0 TGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATG ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]] RG:Z:474747 XT:A:U CM:i:0 X0:i:1 XM:i:1 XO:i:0 XG:i:0 MD:Z:49 +@PG ID:bwa PN:bwa VN:0.5.9-r16 +@RG ID:474747 DS:description DT:2011-03-14 LB:lib-child-1-A PI:400 PL:SOLID SM:child-1 +@SQ SN:chrX_part LN:37500 --- a/test-data/bwa_wrapper_out7.sam Mon May 09 12:11:54 2011 -0400 +++ b/test-data/bwa_wrapper_out7.sam Mon May 09 16:37:13 2011 -0400 @@ -418,3 +418,5 @@ 853_996_488 77 * 0 0 * * 0 0 TGCCCCGTCCACAAAACTCTAGACACACGCCGACCTTGGCAAAAGAAGAA .&'6,#*<(%'8('(,8.4'.1*9)81-0(*0$&2+-)5,0/,1*21#%* 853_997_740 141 * 0 0 * * 0 0 GTTATCGGGGGTTTTCGCAACATAGCTTTGGTAAGCATTTCTGCACCCCT (=('(,(,+<=3?<;::97<;::9<;8:4;<;9::=38:;?=;1<99087 853_997_740 77 * 0 0 * * 0 0 GGGGGGAGATCGGTCGTCCTCGCGATTCGACGTAGGGAAGGAAACCGAAC 9&5;'.1')&(4&2&(,'))=&,,-.&+,&)(.,7/2)(4/-'95,4,<3 +@PG ID:bwa PN:bwa VN:0.5.9-r16 +@SQ SN:chrM LN:16660 --- a/tools/sr_mapping/bwa_color_wrapper.xml Mon May 09 12:11:54 2011 -0400 +++ b/tools/sr_mapping/bwa_color_wrapper.xml Mon May 09 16:37:13 2011 -0400 @@ -1,5 +1,5 @@ -<tool id="bwa_color_wrapper" name="Map with BWA" version="1.0.0"> - <description>for SOLiD</description> +<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.1"> + <description></description><parallelism method="basic"></parallelism><command interpreter="python"> bwa_wrapper.py @@ -45,15 +45,30 @@ --suboptAlign=$params.suboptAlign --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN + --outputTopNDisc=$params.outputTopNDisc --maxInsertSize=$params.maxInsertSize --maxOccurPairing=$params.maxOccurPairing + #if $params.readGroup.specReadGroup == "yes" + --rgid="$params.readGroup.rgid" + --rgcn="$params.readGroup.rgcn" + --rgds="$params.readGroup.rgds" + --rgdt="$params.readGroup.rgdt" + --rgfo="$params.readGroup.rgfo" + --rgks="$params.readGroup.rgks" + --rglb="$params.readGroup.rglb" + --rgpg="$params.readGroup.rgpg" + --rgpi="$params.readGroup.rgpi" + --rgpl="$params.readGroup.rgpl" + --rgpu="$params.readGroup.rgpu" + --rgsm="$params.readGroup.rgsm" + #end if #end if ## suppress output SAM header --suppressHeader=$suppressHeader </command><requirements> - <requirement type='package'>bwa</requirement> + <requirement type="package">bwa</requirement></requirements><inputs><conditional name="genomeSource"> @@ -64,7 +79,7 @@ <when value="indexed"><param name="indices" type="select" label="Select a reference genome"><options from_data_table="bwa_indexes_color"> - <filter type="sort_by" column="3" /> + <filter type="sort_by" column="2" /><validator type="no_options" message="No indexes are available for the selected input dataset" /></options></param> @@ -99,25 +114,52 @@ </param><when value="pre_set" /><when value="full"> - <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance (-n)" help="Enter this value OR a fraction of missing alignments, not both" /> - <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate (-n)" help="Enter this value OR maximum edit distance, not both" /> - <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (-o)" /> - <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (-e)" help="-1 for k-difference mode (disallowing long gaps)" /> - <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (-d)" /> - <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (-i)" /> - <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (-l)" help="Enter -1 for infinity" /> - <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (-k)" /> - <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (-M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /> - <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (-O)" /> - <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (-E)" /> - <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp) (-R)" /> - <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default (-N)" /> - <param name="outputTopN" type="integer" value="-1" label="Output top [value] hits" help="For single-end reads only. Enter -1 to disable outputting multiple hits. NOTE: If you put in a positive value here, your output will NOT be in SAM format (-n)" /> - <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes (-a)" /> - <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing (-o)" /> + <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance (aln -n)" help="Enter this value OR a fraction of missing alignments, not both" /> + <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate (aln -n)" help="Enter this value OR maximum edit distance, not both" /> + <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (aln -o)" /> + <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (aln -e)" help="-1 for k-difference mode (disallowing long gaps)" /> + <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (aln -d)" /> + <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (aln -i)" /> + <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (aln -l)" help="Enter -1 for infinity" /> + <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (aln -k)" /> + <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /> + <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /> + <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> + <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> + <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /> + <param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /> + <param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> + <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly (sampe -a)" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes" /> + <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing (sampe -o)" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" /> + <conditional name="readGroup"> + <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="rgid" type="text" size="25" label="Read group identiﬁer. Each @RG line must have a unique ID. The value of ID is used in the RG +tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group +IDs may be modiﬁed when merging SAM ﬁles in order to handle collisions." /> + <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read" help="Optional" /> + <param name="rgds" type="text" size="25" label="Description" help="Optional" /> + <param name="rgdt" type="text" size="25" label="Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)" help="Optional" /> + <param name="rgfo" type="text" size="25" label="Flow order. The array of nucleotide bases that correspond to the nucleotides used for each +flow of each read." help="Optional. Multi-base flows are encoded in IUPAC format, and non-nucleotide flows by +various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" /> + <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read" help="Optional" /> + <param name="rglb" type="text" size="25" label="Library name" help="Required if RG specified" /> + <param name="rgpg" type="text" size="25" label="Programs used for processing the read group" help="Optional" /> + <param name="rgpi" type="text" size="25" label="Predicted median insert size" help="Optional" /> + <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads. Valid values : CAPILLARY, LS454, ILLUMINA, +SOLID, HELICOS, IONTORRENT and PACBIO" help="Required if RG specified" /> + <param name="rgpu" type="text" size="25" label="Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD). Unique identiﬁer." help="Optional" /> + <param name="rgsm" type="text" size="25" label="Sample. Use pool name where a pool is being sequenced" help="Required if RG specified" /> + </when> + <when value="no" /> + </conditional></when></conditional> - <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /> + <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /></inputs><outputs><data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> @@ -125,11 +167,17 @@ <conditional name="genomeSource.refGenomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="bwa_indexes_color" column="0"> - <filter type="param_value" ref="genomeSource.indices" column="1" /> + <option type="from_data_table" name="bwa_indexes_color" column="1"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="genomeSource.indices" column="0" /></option></action></when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when></conditional></actions></data> @@ -144,7 +192,6 @@ bwa samse hg19chrX_midpart.fasta bwa_wrapper_out4.sai test-data/bwa_wrapper_in4.fastqcssanger > bwa_wrapper_out4.u.sam hg19chrX_midpart.fasta is the prefix for the reference files (hg19chrX_midpart.fasta.amb, hg19chrX_midpart.fasta.ann, hg19chrX_midpart.fasta.bwt, ...) It's just part of hg19 chrX, from the middle of the chromosome - remove the comment lines (beginning with '@') from the resulting sam file plain old sort doesn't handle underscores like python: python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out4.u.sam bwa_wrapper_out4.sam --> @@ -153,8 +200,8 @@ <param name="sPaired" value="single" /><param name="input1" value="bwa_wrapper_in4.fastqcssanger" ftype="fastqcssanger" /><param name="source_select" value="pre_set" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out4.sam" ftype="sam" sort="True" /> + <param name="suppressHeader" value="false" /> + <output name="output" file="bwa_wrapper_out4.sam" ftype="sam" sort="True" lines_diff="2" /></test><test> @@ -205,11 +251,25 @@ <param name="gapExtensPenalty" value="4" /><param name="suboptAlign" value="true" /><param name="noIterSearch" value="true" /> - <param name="outputTopN" value="-1" /> + <param name="outputTopN" value="3" /> + <param name="outputTopNDisc" value="10" /><param name="maxInsertSize" value="500" /><param name="maxOccurPairing" value="100000" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out6.sam" ftype="sam" sort="True" /> + <param name="specReadGroup" value="yes" /> + <param name="rgid" value="474747" /> + <param name="rgcn" value="" /> + <param name="rgds" value="description" /> + <param name="rgdt" value="2011-03-14" /> + <param name="rgfo" value="" /> + <param name="rgks" value="" /> + <param name="rglb" value="lib-child-1-A" /> + <param name="rgpg" value="" /> + <param name="rgpi" value="200" /> + <param name="rgpl" value="SOLID" /> + <param name="rgpu" value="" /> + <param name="rgsm" value="child-1" /> + <param name="suppressHeader" value="false" /> + <output name="output" file="bwa_wrapper_out6.sam" ftype="sam" sort="True" lines_diff="2" /></test><test> @@ -243,14 +302,14 @@ <param name="gapExtensPenalty" value="4" /><param name="suboptAlign" value="true" /><param name="noIterSearch" value="true" /> - <param name="outputTopN" value="-1" /> + <param name="outputTopN" value="3" /> + <param name="outputTopNDisc" value="10" /><param name="maxInsertSize" value="100" /><param name="maxOccurPairing" value="2" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out7.sam" ftype="sam" sort="True" /> + <param name="specReadGroup" value="no" /> + <param name="suppressHeader" value="false" /> + <output name="output" file="bwa_wrapper_out7.sam" ftype="sam" sort="True" lines_diff="2" /></test> - - </tests><help> @@ -371,11 +430,10 @@ For **samse**:: - -n INT Output up to INT top hits. Value -1 to disable outputting multiple - hits. NOTE: Entering a value other than -1 will result in output that - is not in SAM format, and therefore not usable further down the - pipeline. Check the BWA documentation for details on the format of - the output. [-1] + -n INT Maximum number of alignments to output in the XA tag for reads paired + properly. If a read has more than INT hits, the XA tag will not be + written. [3] + -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null] For **sampe**:: @@ -383,9 +441,40 @@ properly. Since version 0.4.5, this option is only used when there are not enough good alignment to infer the distribution of insert sizes. [500] + -n INT Maximum number of alignments to output in the XA tag for reads paired + properly. If a read has more than INT hits, the XA tag will not be + written. [3] + -N INT Maximum number of alignments to output in the XA tag for disconcordant + read pairs (excluding singletons). If a read has more than INT hits, + the XA tag will not be written. [10] -o INT Maximum occurrences of a read for pairing. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing. [100000] + -r STR Specify the read group in a format like '@RG\tID:foo\tSM:bar' [null] + +For specifying the read group in **samse** or **sampe**, use the following:: + + @RG Read group. Unordered multiple @RG lines are allowed. + ID Read group identiﬁer. Each @RG line must have a unique ID. The value of + ID is used in the RG tags of alignment records. Must be unique among all + read groups in header section. Read group IDs may be modiﬁed when + merging SAM ﬁles in order to handle collisions. + CN Name of sequencing center producing the read. + DS Description. + DT Date the run was produced (ISO8601 date or date/time). + FO Flow order. The array of nucleotide bases that correspond to the + nucleotides used for each flow of each read. Multi-base flows are encoded + in IUPAC format, and non-nucleotide flows by various other characters. + Format : /\*|[ACMGRSVTWYHKDBN]+/ + KS The array of nucleotide bases that correspond to the key sequence of each read. + LB Library. + PG Programs used for processing the read group. + PI Predicted median insert size. + PL Platform/technology used to produce the reads. Valid values : CAPILLARY, + LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO. + PU Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for + SOLiD). Unique identiﬁer. + SM Sample. Use pool name where a pool is being sequenced. </help></tool> --- a/tools/sr_mapping/bwa_wrapper.py Mon May 09 12:11:54 2011 -0400 +++ b/tools/sr_mapping/bwa_wrapper.py Mon May 09 16:37:13 2011 -0400 @@ -3,36 +3,11 @@ """ Runs BWA on single-end or paired-end data. Produces a SAM file containing the mappings. -Works with BWA version 0.5.3-0.5.5. +Works with BWA version 0.5.9. usage: bwa_wrapper.py [options] - -t, --threads=t: The number of threads to use - -r, --ref=r: The reference genome to use or index - -f, --fastq=f: The (forward) fastq file to use for the mapping - -F, --rfastq=F: The reverse fastq file to use for mapping if paired-end data - -u, --output=u: The file to save the output (SAM format) - -g, --genAlignType=g: The type of pairing (single or paired) - -p, --params=p: Parameter setting to use (pre_set or full) - -s, --fileSource=s: Whether to use a previously indexed reference sequence or one from history (indexed or history) - -n, --maxEditDist=n: Maximum edit distance if integer - -m, --fracMissingAligns=m: Fraction of missing alignments given 2% uniform base error rate if fraction - -o, --maxGapOpens=o: Maximum number of gap opens - -e, --maxGapExtens=e: Maximum number of gap extensions - -d, --disallowLongDel=d: Disallow a long deletion within specified bps - -i, --disallowIndel=i: Disallow indel within specified bps - -l, --seed=l: Take the first specified subsequences - -k, --maxEditDistSeed=k: Maximum edit distance to the seed - -M, --mismatchPenalty=M: Mismatch penalty - -O, --gapOpenPenalty=O: Gap open penalty - -E, --gapExtensPenalty=E: Gap extension penalty - -R, --suboptAlign=R: Proceed with suboptimal alignments even if the top hit is a repeat - -N, --noIterSearch=N: Disable iterative search - -T, --outputTopN=T: Output top specified hits - -S, --maxInsertSize=S: Maximum insert size for a read pair to be considered mapped good - -P, --maxOccurPairing=P: Maximum occurrences of a read for pairings - -H, --suppressHeader=h: Suppress header - -D, --dbkey=D: Dbkey for reference genome - -X, --do_not_build_index: Flag to specify that provided file is already indexed and to just use 'as is' + +See below for options """ import optparse, os, shutil, subprocess, sys, tempfile @@ -81,9 +56,22 @@ parser.add_option( '-E', '--gapExtensPenalty', dest='gapExtensPenalty', help='Gap extension penalty' ) parser.add_option( '-R', '--suboptAlign', dest='suboptAlign', help='Proceed with suboptimal alignments even if the top hit is a repeat' ) parser.add_option( '-N', '--noIterSearch', dest='noIterSearch', help='Disable iterative search' ) - parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Output top specified hits' ) + parser.add_option( '-T', '--outputTopN', dest='outputTopN', help='Maximum number of alignments to output in the XA tag for reads paired properly' ) + parser.add_option( '', '--outputTopNDisc', dest='outputTopNDisc', help='Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons)' ) parser.add_option( '-S', '--maxInsertSize', dest='maxInsertSize', help='Maximum insert size for a read pair to be considered mapped good' ) parser.add_option( '-P', '--maxOccurPairing', dest='maxOccurPairing', help='Maximum occurrences of a read for pairings' ) + parser.add_option( '', '--rgid', dest='rgid', help='Read group identifier' ) + parser.add_option( '', '--rgcn', dest='rgcn', help='Sequencing center that produced the read' ) + parser.add_option( '', '--rgds', dest='rgds', help='Description' ) + parser.add_option( '', '--rgdt', dest='rgdt', help='Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)' ) + parser.add_option( '', '--rgfo', dest='rgfo', help='Flow order' ) + parser.add_option( '', '--rgks', dest='rgks', help='The array of nucleotide bases that correspond to the key sequence of each read' ) + parser.add_option( '', '--rglb', dest='rglb', help='Library name' ) + parser.add_option( '', '--rgpg', dest='rgpg', help='Programs used for processing the read group' ) + parser.add_option( '', '--rgpi', dest='rgpi', help='Predicted median insert size' ) + parser.add_option( '', '--rgpl', dest='rgpl', choices=[ 'CAPILLARY', 'LS454', 'ILLUMINA', 'SOLID', 'HELICOS', 'IONTORRENT' and 'PACBIO' ], help='Platform/technology used to produce the reads' ) + parser.add_option( '', '--rgpu', dest='rgpu', help='Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for SOLiD)' ) + parser.add_option( '', '--rgsm', dest='rgsm', help='Sample' ) parser.add_option( '-D', '--dbkey', dest='dbkey', help='Dbkey for reference genome' ) parser.add_option( '-X', '--do_not_build_index', dest='do_not_build_index', action='store_true', help="Don't build index" ) parser.add_option( '-H', '--suppressHeader', dest='suppressHeader', help='Suppress header' ) @@ -202,13 +190,35 @@ options.disallowIndel, seed, options.maxEditDistSeed, options.threads, options.mismatchPenalty, options.gapOpenPenalty, options.gapExtensPenalty, suboptAlign, noIterSearch, color_space ) - if options.genAlignType == 'single': - if options.outputTopN != '-1': - gen_alignment_cmds = '-n %s' % options.outputTopN - else: - gen_alignment_cmds = '' - elif options.genAlignType == 'paired': + if options.genAlignType == 'paired': gen_alignment_cmds = '-a %s -o %s' % ( options.maxInsertSize, options.maxOccurPairing ) + if options.outputTopNDisc: + gen_alignment_cmds += ' -N %s' % options.outputTopNDisc + else: + gen_alignment_cmds = '' + if options.rgid: + if not options.rglb or not options.rgpl or not options.rgsm: + stop_err( 'If you want to specify read groups, you must include the ID, LB, PL, and SM tags.' ) + readGroup = '@RG\tID:%s\tLB:%s\tPL:%s\tSM:%s' % ( options.rgid, options.rglb, options.rgpl, options.rgsm ) + if options.rgcn: + readGroup += '\tCN:%s' % options.rgcn + if options.rgds: + readGroup += '\tDS:%s' % options.rgds + if options.rgdt: + readGroup += '\tDT:%s' % options.rgdt + if options.rgfo: + readGroup += '\tFO:%s' % options.rgfo + if options.rgks: + readGroup += '\tKS:%s' % options.rgks + if options.rgpg: + readGroup += '\tPG:%s' % options.rgpg + if options.rgpi: + readGroup += '\tPI:%s' % options.rgpi + if options.rgpu: + readGroup += '\tPU:%s' % options.rgpu + gen_alignment_cmds += ' -r "%s"' % readGroup + if options.outputTopN: + gen_alignment_cmds += ' -n %s' % options.outputTopN # set up output files tmp_align_out = tempfile.NamedTemporaryFile( dir=tmp_dir ) tmp_align_out_name = tmp_align_out.name --- a/tools/sr_mapping/bwa_wrapper.xml Mon May 09 12:11:54 2011 -0400 +++ b/tools/sr_mapping/bwa_wrapper.xml Mon May 09 16:37:13 2011 -0400 @@ -1,5 +1,5 @@ -<tool id="bwa_wrapper" name="Map with BWA" version="1.2.1"> - <description>for Illumina</description> +<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.2"> + <description></description><parallelism method="basic"></parallelism><command interpreter="python"> bwa_wrapper.py @@ -44,15 +44,30 @@ --suboptAlign=$params.suboptAlign --noIterSearch=$params.noIterSearch --outputTopN=$params.outputTopN + --outputTopNDisc=$params.outputTopNDisc --maxInsertSize=$params.maxInsertSize --maxOccurPairing=$params.maxOccurPairing + #if $params.readGroup.specReadGroup == "yes" + --rgid="$params.readGroup.rgid" + --rgcn="$params.readGroup.rgcn" + --rgds="$params.readGroup.rgds" + --rgdt="$params.readGroup.rgdt" + --rgfo="$params.readGroup.rgfo" + --rgks="$params.readGroup.rgks" + --rglb="$params.readGroup.rglb" + --rgpg="$params.readGroup.rgpg" + --rgpi="$params.readGroup.rgpi" + --rgpl="$params.readGroup.rgpl" + --rgpu="$params.readGroup.rgpu" + --rgsm="$params.readGroup.rgsm" + #end if #end if ## suppress output SAM header --suppressHeader=$suppressHeader </command><requirements> - <requirement type='package'>bwa</requirement> + <requirement type="package">bwa</requirement></requirements><inputs><conditional name="genomeSource"> @@ -63,8 +78,8 @@ <when value="indexed"><param name="indices" type="select" label="Select a reference genome"><options from_data_table="bwa_indexes"> - <filter type="sort_by" column="3" /> - <validator type="no_options" message="No indexes are available for the selected input dataset" /> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /></options></param></when> @@ -92,25 +107,52 @@ </param><when value="pre_set" /><when value="full"> - <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance (-n)" help="Enter this value OR a fraction of missing alignments, not both" /> - <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate (-n)" help="Enter this value OR maximum edit distance, not both" /> - <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (-o)" /> - <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (-e)" help="-1 for k-difference mode (disallowing long gaps)" /> - <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (-d)" /> - <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (-i)" /> - <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (-l)" help="Enter -1 for infinity" /> - <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (-k)" /> - <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (-M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /> - <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (-O)" /> - <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (-E)" /> - <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat" help="By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp) (-R)" /> - <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default (-N)" /> - <param name="outputTopN" type="integer" value="-1" label="Output top [value] hits" help="For single-end reads only. Enter -1 to disable outputting multiple hits. NOTE: If you put in a positive value here, your output will NOT be in SAM format (-n)" /> - <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes (-a)" /> - <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing (-o)" /> + <param name="maxEditDist" type="integer" value="0" label="Maximum edit distance (aln -n)" help="Enter this value OR a fraction of missing alignments, not both" /> + <param name="fracMissingAligns" type="float" value="0.04" label="Fraction of missing alignments given 2% uniform base error rate (aln -n)" help="Enter this value OR maximum edit distance, not both" /> + <param name="maxGapOpens" type="integer" value="1" label="Maximum number of gap opens (aln -o)" /> + <param name="maxGapExtens" type="integer" value="-1" label="Maximum number of gap extensions (aln -e)" help="-1 for k-difference mode (disallowing long gaps)" /> + <param name="disallowLongDel" type="integer" value="16" label="Disallow long deletion within [value] bp towards the 3'-end (aln -d)" /> + <param name="disallowIndel" type="integer" value="5" label="Disallow insertion/deletion within [value] bp towards the end (aln -i)" /> + <param name="seed" type="integer" value="-1" label="Number of first subsequences to take as seed (aln -l)" help="Enter -1 for infinity" /> + <param name="maxEditDistSeed" type="integer" value="2" label="Maximum edit distance in the seed (aln -k)" /> + <param name="mismatchPenalty" type="integer" value="3" label="Mismatch penalty (aln -M)" help="BWA will not search for suboptimal hits with a score lower than [value]" /> + <param name="gapOpenPenalty" type="integer" value="11" label="Gap open penalty (aln -O)" /> + <param name="gapExtensPenalty" type="integer" value="4" label="Gap extension penalty (aln -E)" /> + <param name="suboptAlign" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Proceed with suboptimal alignments even if the top hit is a repeat (aln -R)" help="For paired-end reads only. By default, BWA only searches for suboptimal alignments if the top hit is unique. Using this option has no effect on accuracy for single-end reads. It is mainly designed for improving the alignment accuracy of paired-end reads. However, the pairing procedure will be slowed down, especially for very short reads (~32bp)" /> + <param name="noIterSearch" type="boolean" truevalue="true" falsevalue="false" checked="no" label="Disable iterative search (aln -N)" help="All hits with no more than maxDiff differences will be found. This mode is much slower than the default" /> + <param name="outputTopN" type="integer" value="3" label="Maximum number of alignments to output in the XA tag for reads paired properly (samse/sampe -n)" help="If a read has more than INT hits, the XA tag will not be written" /> + <param name="outputTopNDisc" type="integer" value="10" label="Maximum number of alignments to output in the XA tag for disconcordant read pairs (excluding singletons) (sampe -N)" help="For paired-end reads only. If a read has more than INT hits, the XA tag will not be written" /> + <param name="maxInsertSize" type="integer" value="500" label="Maximum insert size for a read pair to be considered as being mapped properly (sampe -a)" help="For paired-end reads only. Only used when there are not enough good alignments to infer the distribution of insert sizes" /> + <param name="maxOccurPairing" type="integer" value="100000" label="Maximum occurrences of a read for pairing (sampe -o)" help="For paired-end reads only. A read with more occurrences will be treated as a single-end read. Reducing this parameter helps faster pairing" /> + <conditional name="readGroup"> + <param name="specReadGroup" type="select" label="Specify the read group for this file? (samse/sampe -r)"> + <option value="yes">Yes</option> + <option value="no">No</option> + </param> + <when value="yes"> + <param name="rgid" type="text" size="25" label="Read group identiﬁer. Each @RG line must have a unique ID. The value of ID is used in the RG +tags of alignment records. Must be unique among all read groups in header section." help="Required if RG specified. Read group +IDs may be modiﬁed when merging SAM ﬁles in order to handle collisions." /> + <param name="rgcn" type="text" size="25" label="Sequencing center that produced the read" help="Optional" /> + <param name="rgds" type="text" size="25" label="Description" help="Optional" /> + <param name="rgdt" type="text" size="25" label="Date that run was produced (ISO8601 format date or date/time, like YYYY-MM-DD)" help="Optional" /> + <param name="rgfo" type="text" size="25" label="Flow order. The array of nucleotide bases that correspond to the nucleotides used for each +ﬂow of each read." help="Optional. Multi-base ﬂows are encoded in IUPAC format, and non-nucleotide ﬂows by +various other characters. Format : /\*|[ACMGRSVTWYHKDBN]+/" /> + <param name="rgks" type="text" size="25" label="The array of nucleotide bases that correspond to the key sequence of each read" help="Optional" /> + <param name="rglb" type="text" size="25" label="Library name" help="Required if RG specified" /> + <param name="rgpg" type="text" size="25" label="Programs used for processing the read group" help="Optional" /> + <param name="rgpi" type="text" size="25" label="Predicted median insert size" help="Optional" /> + <param name="rgpl" type="text" size="25" label="Platform/technology used to produce the reads. Valid values : CAPILLARY, LS454, ILLUMINA, +SOLID, HELICOS, IONTORRENT and PACBIO" help="Required if RG specified" /> + <param name="rgpu" type="text" size="25" label="Platform unit (e.g. ﬂowcell-barcode.lane for Illumina or slide for SOLiD). Unique identiﬁer." help="Optional" /> + <param name="rgsm" type="text" size="25" label="Sample. Use pool name where a pool is being sequenced" help="Required if RG specified" /> + </when> + <when value="no" /> + </conditional></when></conditional> - <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /> + <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /></inputs><outputs><data format="sam" name="output" label="${tool.name} on ${on_string}: mapped reads"> @@ -118,11 +160,17 @@ <conditional name="genomeSource.refGenomeSource"><when value="indexed"><action type="metadata" name="dbkey"> - <option type="from_data_table" name="bwa_indexes" column="0"> - <filter type="param_value" ref="genomeSource.indices" column="1"/> + <option type="from_data_table" name="bwa_indexes" column="1"> + <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/> + <filter type="param_value" ref="genomeSource.indices" column="0"/></option></action></when> + <when value="history"> + <action type="metadata" name="dbkey"> + <option type="from_param" name="genomeSource.ownFile" param_attribute="dbkey" /> + </action> + </when></conditional></actions></data> @@ -152,7 +200,7 @@ cp test-data/phiX.fasta phiX.fasta bwa index -a is phiX.fasta bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fasta test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out2.sai - bwa samse phiX.fasta bwa_wrapper_out2.sai test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out2.u.sam + bwa samse -n 3 phiX.fasta bwa_wrapper_out2.sai test-data/bwa_wrapper_in1.fastqsanger > bwa_wrapper_out2.u.sam phiX.fasta is the prefix for the reference files (phiX.fasta.amb, phiX.fasta.ann, phiX.fasta.bwt, ...) remove the comment lines (beginning with '@') from the resulting sam file plain old sort doesn't handle underscores like python: @@ -176,9 +224,11 @@ <param name="gapExtensPenalty" value="4" /><param name="suboptAlign" value="true" /><param name="noIterSearch" value="true" /> - <param name="outputTopN" value="-1" /> + <param name="outputTopN" value="3" /> + <param name="outputTopNDisc" value="10" /><param name="maxInsertSize" value="500" /><param name="maxOccurPairing" value="100000" /> + <param name="specReadGroup" value="no" /><param name="suppressHeader" value="true" /><output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="True" /></test> @@ -187,9 +237,8 @@ BWA commands: bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fasta test-data/bwa_wrapper_in2.fastqsanger > bwa_wrapper_out3a.sai bwa aln -n 0.04 -o 1 -e -1 -d 16 -i 5 -k 2 -t 4 -M 3 -O 11 -E 4 -R -N phiX.fasta test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out3b.sai - bwa sampe -a 500 -o 100000 phiX.fasta bwa_wrapper_out3a.sai bwa_wrapper_out3b.sai test-data/bwa_wrapper_in2.fastqsanger test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out3.u.sam + bwa sampe -a 500 -o 100000 -n 3 -N 10 -r "@RG\tID:abcdefg\tDS:descrip\tDT:2010-11-01\tLB:lib-mom-A\tPI:400\tPL:ILLUMINA\tSM:mom" phiX.fasta bwa_wrapper_out3a.sai bwa_wrapper_out3b.sai test-data/bwa_wrapper_in2.fastqsanger test-data/bwa_wrapper_in3.fastqsanger > bwa_wrapper_out3.u.sam phiX.fasta is the prefix for the reference - remove the comment lines (beginning with '@') from the resulting sam file plain old sort doesn't handle underscores like python: python -c "import sys; lines=file(sys.argv[1],'rb').readlines(); lines.sort(); file(sys.argv[2],'wb').write(''.join(lines))" bwa_wrapper_out3.u.sam bwa_wrapper_out3.sam --> @@ -212,11 +261,25 @@ <param name="gapExtensPenalty" value="4" /><param name="suboptAlign" value="true" /><param name="noIterSearch" value="true" /> - <param name="outputTopN" value="-1" /> + <param name="outputTopN" value="3" /> + <param name="outputTopNDisc" value="10" /><param name="maxInsertSize" value="500" /><param name="maxOccurPairing" value="100000" /> - <param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" sort="True" /> + <param name="specReadGroup" value="yes" /> + <param name="rgid" value="abcdefg" /> + <param name="rgcn" value="" /> + <param name="rgds" value="descrip" /> + <param name="rgdt" value="2010-11-01" /> + <param name="rgfo" value="" /> + <param name="rgks" value="" /> + <param name="rglb" value="lib-mom-A" /> + <param name="rgpg" value="" /> + <param name="rgpi" value="400" /> + <param name="rgpl" value="ILLUMINA" /> + <param name="rgpu" value="" /> + <param name="rgsm" value="mom" /> + <param name="suppressHeader" value="false" /> + <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" sort="True" lines_diff="2" /></test><test> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="10"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="56"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="30"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/><output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="16"/> @@ -238,7 +236,6 @@ -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 16:40:44 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 16:51:14 2011 -0400 @@ -209,7 +209,6 @@ -I INT The minimum intron length. Cufflinks will not report transcripts with introns longer than this, and will ignore SAM alignments with REF_SKIP CIGAR operations longer than this. The default is 300,000. -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene. -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript. -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. </help> --- a/tools/picard/rgPicardASMetrics.xml Mon May 09 16:40:44 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Mon May 09 16:51:14 2011 -0400 @@ -70,8 +70,8 @@ <param name="adaptors" value="" /><param name="maxinsert" value="100000" /><param name="refGenomeSource" value="indexed" /> - <param name="index" value="hg18" /> - <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg18" /> + <param name="index" value="hg19" /> + <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg19" /><output name="html_file" file="picard_output_AsMetrics_indexed_hg18_sorted_pair.html" ftype="html" lines_diff="50"/></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 09 May '11

09 May '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/91251384e091/ changeset: r5524:91251384e091 user: fubar date: 2011-05-09 19:11:45 summary: small changes to fix test outputs for insertsize and bamindex affected #: 2 files (68 bytes) --- a/test-data/picard_BIS_output1.txt Mon May 09 11:07:01 2011 -0400 +++ b/test-data/picard_BIS_output1.txt Mon May 09 13:11:45 2011 -0400 @@ -6,16 +6,17 @@ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<meta name="generator" content="Galaxy BamIndexStats tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output picard_wrapper run at 26/04/2011 14:12:45</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +Galaxy tool wrapper picard_wrapper at 09/05/2011 13:04:11</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table><tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr> +<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr></table><p/> -<b>Picard on line resources</b><ul> +<b>Picard on line resources:</b><ul><li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li><li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/><b>Picard output</b><hr/> @@ -26,9 +27,9 @@ <tr class="d1"><td>NoCoordinateCount= 1</td></tr></table><b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/rgalaxy/database/job_working_directory/94/dataset_96_files/tmpvRqH6t.bam returned status 0 and stderr: -[Tue Apr 26 14:12:45 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/rgalaxy/database/job_working_directory/94/dataset_96_files/tmpvRqH6t.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Tue Apr 26 14:12:45 EDT 2011] net.sf.picard.sam.BamIndexStats done. +<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/2/dataset_2_files/tmpMiaCgO.bam returned status 0 and stderr: +[Mon May 09 13:04:11 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/2/dataset_2_files/tmpMiaCgO.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Mon May 09 13:04:11 EDT 2011] net.sf.picard.sam.BamIndexStats done. Runtime.totalMemory()=9109504 --- a/test-data/picard_BIS_output2.txt Mon May 09 11:07:01 2011 -0400 +++ b/test-data/picard_BIS_output2.txt Mon May 09 13:11:45 2011 -0400 @@ -6,16 +6,17 @@ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<meta name="generator" content="Galaxy BamIndexStats tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output picard_wrapper run at 26/04/2011 14:13:02</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +Galaxy tool wrapper picard_wrapper at 09/05/2011 13:04:21</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table><tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr> +<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr></table><p/> -<b>Picard on line resources</b><ul> +<b>Picard on line resources:</b><ul><li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li><li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/><b>Picard output</b><hr/> @@ -28,9 +29,9 @@ <tr class="d1"><td>NoCoordinateCount= 1</td></tr></table><b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/rgalaxy/database/job_working_directory/96/dataset_98_files/tmp3cpQkW.bam returned status 0 and stderr: -[Tue Apr 26 14:13:02 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/rgalaxy/database/job_working_directory/96/dataset_98_files/tmp3cpQkW.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Tue Apr 26 14:13:02 EDT 2011] net.sf.picard.sam.BamIndexStats done. +<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/4/dataset_4_files/tmpB_J8W5.bam returned status 0 and stderr: +[Mon May 09 13:04:21 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/4/dataset_4_files/tmpB_J8W5.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Mon May 09 13:04:21 EDT 2011] net.sf.picard.sam.BamIndexStats done. Runtime.totalMemory()=9109504 http://bitbucket.org/galaxy/galaxy-central/changeset/9f48de75b63b/ changeset: r5525:9f48de75b63b user: fubar date: 2011-05-09 19:28:26 summary: branch merge affected #: 15 files (12.0 KB) --- a/buildbot_setup.sh Mon May 09 13:11:45 2011 -0400 +++ b/buildbot_setup.sh Mon May 09 13:28:26 2011 -0400 @@ -53,6 +53,7 @@ /galaxy/data/location/perm_base_index.loc /galaxy/data/location/perm_color_index.loc /galaxy/data/location/phastOdds.loc +/galaxy/data/location/picard_index.loc /galaxy/data/location/quality_scores.loc /galaxy/data/location/regions.loc /galaxy/data/location/sam_fa_indices.loc --- a/test-data/cuffdiff_out1.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out1.txt Mon May 09 13:28:26 2011 -0400 @@ -1,99 +1,99 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant -TCONS_00000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no -TCONS_00000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no -TCONS_00000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no -TCONS_00000004 - chr1:3189810-3190789 q1 q2 OK 0 645918 6.95322e-310 1.79769e+308 0 yes -TCONS_00000005 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no -TCONS_00000006 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no -TCONS_00000007 - chr1:3191512-3192077 q1 q2 OK 0 704881 6.95322e-310 1.79769e+308 0 yes -TCONS_00000008 - chr1:3191512-3192077 q1 q2 OK 0 0 0 0 1 no -TCONS_00000009 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no -TCONS_00000010 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no -TCONS_00000011 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no -TCONS_00000012 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no -TCONS_00000013 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no -TCONS_00000014 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no -TCONS_00000015 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no -TCONS_00000016 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no -TCONS_00000017 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no -TCONS_00000018 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000019 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no -TCONS_00000020 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no -TCONS_00000021 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no -TCONS_00000022 - chr1:3201077-3201481 q1 q2 OK 0 155328 0 1.79769e+308 0 yes -TCONS_00000023 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no -TCONS_00000024 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no -TCONS_00000025 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no -TCONS_00000026 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no -TCONS_00000027 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no -TCONS_00000028 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no -TCONS_00000029 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no -TCONS_00000030 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no -TCONS_00000031 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no -TCONS_00000032 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 no -TCONS_00000033 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no -TCONS_00000034 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no -TCONS_00000035 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000036 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000037 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -TCONS_00000038 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no -TCONS_00000039 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no -TCONS_00000040 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -TCONS_00000041 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no -TCONS_00000042 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no -TCONS_00000043 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no -TCONS_00000044 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no -TCONS_00000045 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no -TCONS_00000046 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no -TCONS_00000047 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no -TCONS_00000048 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no -TCONS_00000049 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no -TCONS_00000050 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no -TCONS_00000051 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no -TCONS_00000052 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no -TCONS_00000053 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no -TCONS_00000054 - chr1:3189810-3190789 q1 q2 OK 343500 303241 -0.124659 2.28891 0.0220846 no -TCONS_00000055 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes -TCONS_00000056 - chr1:3191512-3192077 q1 q2 OK 345096 376320 0.0866161 -1.17079 0.241685 no -TCONS_00000057 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no -TCONS_00000058 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no -TCONS_00000059 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no -TCONS_00000060 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no -TCONS_00000061 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no -TCONS_00000062 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no -TCONS_00000063 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 no -TCONS_00000064 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no -TCONS_00000065 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no -TCONS_00000066 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no -TCONS_00000067 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no -TCONS_00000068 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no -TCONS_00000069 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no -TCONS_00000070 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no -TCONS_00000071 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no -TCONS_00000072 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no -TCONS_00000073 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no -TCONS_00000074 - chr1:3277913-3278390 q1 q2 OK 165459 0 0 2.22507e-308 0 yes -TCONS_00000075 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no -TCONS_00000076 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no -TCONS_00000077 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no -TCONS_00000078 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no -TCONS_00000079 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no -TCONS_00000080 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no -TCONS_00000081 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no -TCONS_00000082 - chr1:3290919-3291273 q1 q2 OK 163613 0 0 2.22507e-308 0 yes -TCONS_00000083 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -TCONS_00000084 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no -TCONS_00000085 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no -TCONS_00000086 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no -TCONS_00000087 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no -TCONS_00000088 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no -TCONS_00000089 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -TCONS_00000090 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no -TCONS_00000091 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no -TCONS_00000092 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no -TCONS_00000093 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no -TCONS_00000094 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no -TCONS_00000095 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no -TCONS_00000096 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no -TCONS_00000097 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no -TCONS_00000098 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant +TCONS_00000001 XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.550547 no +TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.777411 no +TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 1.24051 no +TCONS_00000004 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 2.49256e+06 5.29759e+06 0.753941 -1.11223 0.266041 0.790061 no +TCONS_00000005 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 1.25641 no +TCONS_00000006 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 1.27273 no +TCONS_00000007 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 2.77423e+06 6.7156e+06 0.88406 -1.27269 0.203128 0.663553 no +TCONS_00000008 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 1.11098e+07 3.03942e+07 1.00642 -0.806752 0.419809 1.17547 no +TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.56023e+07 1.79769e+308 1.79769e+308 0.0416323 0.582852 no +TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 2.71123e+06 1.79769e+308 1.79769e+308 0.158655 0.598008 no +TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 1.28947 no +TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 3.93442e+06 1.79769e+308 1.79769e+308 0.0416319 0.679987 no +TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.818327 no +TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 1.30667 no +TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 1.32432 no +TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 1.34247 no +TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 1.36111 no +TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 1.38028 no +TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 1.4 no +TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 460348 460348 0 0 1 1.42029 no +TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 1.44118 no +TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 37206.6 186033 1.60944 -2.18263 0.0290634 2.84821 no +TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 1.46269 no +TCONS_00000024 XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.642305 no +TCONS_00000025 XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 1.60978e+07 1.79769e+308 1.79769e+308 0.0416319 1.35997 no +TCONS_00000026 XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 2.38694e+06 1.19347e+06 -0.693147 0.565952 0.571426 1.55555 no +TCONS_00000027 XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 27029.9 243269 2.19722 -1.95282 0.0508409 0.553601 no +TCONS_00000028 XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 1.73712e+07 1.79769e+308 1.79769e+308 0.0786496 0.700696 no +TCONS_00000029 XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 3.32455e+07 1.79769e+308 1.79769e+308 0.0786496 0.770766 no +TCONS_00000030 XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 1.34946e+09 1.79769e+308 1.79769e+308 0.0786496 0.481729 no +TCONS_00000031 XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 1.48485 no +TCONS_00000032 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 1.50769 no +TCONS_00000033 XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 1.49798e+07 1.79769e+308 1.79769e+308 0.158655 0.86379 no +TCONS_00000034 XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 6.39146e+06 1.79769e+308 1.79769e+308 0.158655 0.676009 no +TCONS_00000035 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 6.40392e+06 0 -1.79769e+308 -1.79769e+308 0.0814259 0.469396 no +TCONS_00000036 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 1.2964e+06 1.46758e+06 0.124018 -0.0764318 0.939076 2.42183 no +TCONS_00000037 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 1.53125 no +TCONS_00000038 XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 1.55556 no +TCONS_00000039 XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 1.58065 no +TCONS_00000040 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 1 no +TCONS_00000041 XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 1.01031 no +TCONS_00000042 XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 1.02083 no +TCONS_00000043 XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 1.03158 no +TCONS_00000044 XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 1.04255 no +TCONS_00000045 XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 1.05376 no +TCONS_00000046 XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 1.06522 no +TCONS_00000047 XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 1.07692 no +TCONS_00000048 XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 1.08889 no +TCONS_00000049 XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 1.10112 no +TCONS_00000050 XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 1.11364 no +TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 1.12644 no +TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 1.13953 no +TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 1.15294 no +TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 171639 239968 0.335111 -1.01532 0.309956 0.893401 no +TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 227564 240951 0.0571584 -0.115428 0.908106 2.40525 no +TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 175955 319423 0.596288 -1.18662 0.235378 0.720847 no +TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 1.91712e+06 1.91712e+06 0 0 1 1.16667 no +TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 1.18072 no +TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 1.19512 no +TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 1.20988 no +TCONS_00000061 XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 1.225 no +TCONS_00000062 XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 2.27907 no +TCONS_00000063 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 2.51282 no +TCONS_00000064 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 9.11292e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.513844 no +TCONS_00000065 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 8.43162e+06 0 -1.79769e+308 -1.79769e+308 0.0416319 0.815985 no +TCONS_00000066 XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 2.13043 no +TCONS_00000067 XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 2.10791e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.647842 no +TCONS_00000068 XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 2.45 no +TCONS_00000069 XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 2.39024 no +TCONS_00000070 XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 2.33333 no +TCONS_00000071 XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 4.79961e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.740391 no +TCONS_00000072 XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 2.22727 no +TCONS_00000073 XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 2.17778 no +TCONS_00000074 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 127495 27320.3 -1.54045 2.07809 0.037701 1.84735 no +TCONS_00000075 XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 2.08511 no +TCONS_00000076 XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 2.04167 no +TCONS_00000077 XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 2 no +TCONS_00000078 XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 1.96 no +TCONS_00000079 XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 1.92157 no +TCONS_00000080 XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 1.88462 no +TCONS_00000081 XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 8.68561e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.706737 no +TCONS_00000082 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 95795.4 28263.3 -1.22065 1.20083 0.229815 0.726513 no +TCONS_00000083 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 449954 89990.7 -1.60944 1.40539 0.159905 0.540368 no +TCONS_00000084 XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 1.84906 no +TCONS_00000085 XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 1.81481 no +TCONS_00000086 XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 1.78182 no +TCONS_00000087 XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 1.75 no +TCONS_00000088 XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 4.27915e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.555293 no +TCONS_00000089 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 281197 0 -1.79769e+308 -1.79769e+308 0.0416319 1.01998 no +TCONS_00000090 XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 5.72196e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.57586 no +TCONS_00000091 XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 2.1224e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.592897 no +TCONS_00000092 XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 3.08417e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.509995 no +TCONS_00000093 XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 3.50371e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.621929 no +TCONS_00000094 XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 1.7193 no +TCONS_00000095 XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 1.68966 no +TCONS_00000096 XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 1.66102 no +TCONS_00000097 XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 1.63333 no +TCONS_00000098 XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 1.60656 no --- a/test-data/cuffdiff_out10.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out10.txt Mon May 09 13:28:26 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant --- a/test-data/cuffdiff_out11.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out11.txt Mon May 09 13:28:26 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant --- a/test-data/cuffdiff_out2.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out2.txt Mon May 09 13:28:26 2011 -0400 @@ -1,88 +1,88 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant -XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no -XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no -XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no -XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no -XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no -XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no -XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 343500 949159 1.01639 -7.54436 4.55191e-14 yes -XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes -XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 345096 1.0812e+06 1.142 -9.91597 0 yes -XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no -XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no -XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no -XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no -XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no -XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no -XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no -XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no -XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no -XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no -XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no -XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no -XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no -XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no -XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no -XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no -XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no -XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no -XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no -XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 155328 6.95322e-310 1.79769e+308 0 yes -XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no -XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no -XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no -XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no -XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no -XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no -XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no -XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no -XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no -XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no -XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no -XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no -XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no -XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no -XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no -XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no -XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no -XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no -XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no -XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 165459 0 6.95322e-310 2.22507e-308 0 yes -XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no -XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no -XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no -XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no -XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no -XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no -XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no -XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no -XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no -XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 163613 0 6.95322e-310 2.22507e-308 0 yes -XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no -XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no -XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no -XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no -XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no -XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no -XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no -XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no -XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no -XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no -XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no -XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no -XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no -XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no -XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no -XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no -XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no -XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no -XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no -XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no -XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no -XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no -XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no -XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no -XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no -XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant +XLOC_000001 XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.456168 no +XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.726474 no +XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 1.8125 no +XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 1.07407 no +XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 1.12987 no +XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 1.14474 no +XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 2.6642e+06 5.53756e+06 0.731649 -1.14241 0.253284 0.734525 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 227564 240951 0.0571584 -0.115428 0.908106 2.3941 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 1.406e+07 3.74293e+07 0.979119 -0.979283 0.32744 0.918944 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 1.91712e+06 1.91712e+06 0 0 1 1.22535 no +XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.56023e+07 1.79769e+308 1.79769e+308 0.0416323 0.452751 no +XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 2.71123e+06 1.79769e+308 1.79769e+308 0.158655 0.55212 no +XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 1.26087 no +XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 1.55357 no +XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 3.93442e+06 1.79769e+308 1.79769e+308 0.0416319 0.603662 no +XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.811942 no +XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 1.52632 no +XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 1.5 no +XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 1.47458 no +XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 1.45 no +XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 1.42623 no +XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 1.40323 no +XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 1.38095 no +XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 1.35938 no +XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 460348 460348 0 0 1 1.33846 no +XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 1.31818 no +XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 1.29851 no +XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 1.27941 no +XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 37206.6 186033 1.60944 -2.18263 0.0290634 2.52852 no +XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 9.11292e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.488751 no +XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 1.24286 no +XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 8.43162e+06 0 -1.79769e+308 -1.79769e+308 0.0416319 0.724395 no +XLOC_000033 XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 1.20833 no +XLOC_000034 XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.526347 no +XLOC_000035 XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 1.60978e+07 1.79769e+308 1.79769e+308 0.0416319 0.905494 no +XLOC_000036 XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 2.10791e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.530885 no +XLOC_000037 XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 2.38694e+06 1.19347e+06 -0.693147 0.565952 0.571426 1.55356 no +XLOC_000038 XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 1.19178 no +XLOC_000039 XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 1.17568 no +XLOC_000040 XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 27029.9 243269 2.19722 -1.95282 0.0508409 0.491462 no +XLOC_000041 XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 1.16 no +XLOC_000042 XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 1.73712e+07 1.79769e+308 1.79769e+308 0.0786496 0.57021 no +XLOC_000043 XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 4.79961e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.627409 no +XLOC_000044 XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 3.32455e+07 1.79769e+308 1.79769e+308 0.0786496 0.622047 no +XLOC_000045 XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 1.11538 no +XLOC_000046 XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 1.34946e+09 1.79769e+308 1.79769e+308 0.0786496 0.427657 no +XLOC_000047 XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 1.10127 no +XLOC_000048 XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 1.0875 no +XLOC_000049 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 127495 27320.3 -1.54045 2.07809 0.037701 1.63999 no +XLOC_000050 XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 1.06098 no +XLOC_000051 XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 1.04819 no +XLOC_000052 XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 1.49798e+07 1.79769e+308 1.79769e+308 0.158655 0.766834 no +XLOC_000053 XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 1.03571 no +XLOC_000054 XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 1.02353 no +XLOC_000055 XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 1.01163 no +XLOC_000056 XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 1 no +XLOC_000057 XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 6.39146e+06 1.79769e+308 1.79769e+308 0.158655 0.69015 no +XLOC_000058 XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 8.68561e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.657286 no +XLOC_000059 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 7.79612e+06 1.49584e+06 -1.65094 1.39409 0.16329 0.48987 no +XLOC_000060 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 449954 89990.7 -1.60944 1.40539 0.159905 0.496847 no +XLOC_000061 XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 2.23077 no +XLOC_000062 XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 2.175 no +XLOC_000063 XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 2.12195 no +XLOC_000064 XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 2.07143 no +XLOC_000065 XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 1.97727 no +XLOC_000066 XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 1.93333 no +XLOC_000067 XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 4.27915e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.600131 no +XLOC_000068 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 281197 0 -1.79769e+308 -1.79769e+308 0.0416319 1.20732 no +XLOC_000069 XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 5.72196e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.575125 no +XLOC_000070 XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 2.1224e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.684252 no +XLOC_000071 XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 1.58182 no +XLOC_000072 XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 3.08417e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.517429 no +XLOC_000073 XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 1.61111 no +XLOC_000074 XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 3.50371e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.511222 no +XLOC_000075 XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 1.64151 no +XLOC_000076 XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 1.67308 no +XLOC_000077 XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 1.70588 no +XLOC_000078 XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 1.74 no +XLOC_000079 XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 1.77551 no +XLOC_000080 XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 1.85106 no +XLOC_000081 XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 1.8913 no +XLOC_000082 XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 2.02326 no +XLOC_000083 XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 2.28947 no +XLOC_000084 XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 2.35135 no +XLOC_000085 XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 2.41667 no +XLOC_000086 XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 2.48571 no +XLOC_000087 XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 2.55882 no --- a/test-data/cuffdiff_out3.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out3.txt Mon May 09 13:28:26 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant --- a/test-data/cuffdiff_out4.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out4.txt Mon May 09 13:28:26 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant --- a/test-data/cuffdiff_out5.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out5.txt Mon May 09 13:28:26 2011 -0400 @@ -1,99 +1,99 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 0 0 0 -TCONS_00000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 -TCONS_00000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 -TCONS_00000004 - - - - chr1:3189810-3190789 0 0 0 645918 357201 934636 -TCONS_00000005 - - - - chr1:3189810-3190789 0 0 0 0 0 0 -TCONS_00000006 - - - - chr1:3189810-3190789 0 0 0 0 0 0 -TCONS_00000007 - - - - chr1:3191512-3192077 0 0 0 704881 400219 1.00954e+06 -TCONS_00000008 - - - - chr1:3191512-3192077 0 0 0 0 0 0 -TCONS_00000009 - - - - chr1:3192441-3192494 0 0 0 0 0 0 -TCONS_00000010 - - - - chr1:3192550-3192629 0 0 0 0 0 0 -TCONS_00000011 - - - - chr1:3192731-3192811 0 0 0 0 0 0 -TCONS_00000012 - - - - chr1:3192940-3193042 0 0 0 0 0 0 -TCONS_00000013 - - - - chr1:3194185-3194226 0 0 0 0 0 0 -TCONS_00000014 - - - - chr1:3194302-3194329 0 0 0 0 0 0 -TCONS_00000015 - - - - chr1:3195083-3195110 0 0 0 0 0 0 -TCONS_00000016 - - - - chr1:3195450-3195477 0 0 0 0 0 0 -TCONS_00000017 - - - - chr1:3197089-3197116 0 0 0 0 0 0 -TCONS_00000018 - - - - chr1:3197246-3197273 0 0 0 0 0 0 -TCONS_00000019 - - - - chr1:3197346-3197373 0 0 0 0 0 0 -TCONS_00000020 - - - - chr1:3200022-3200191 0 0 0 0 0 0 -TCONS_00000021 - - - - chr1:3200325-3200352 0 0 0 0 0 0 -TCONS_00000022 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 -TCONS_00000023 - - - - chr1:3201672-3201699 0 0 0 0 0 0 -TCONS_00000024 i Xkr4 - - chr1:3212213-3212292 0 0 0 0 0 0 -TCONS_00000025 i Xkr4 - - chr1:3212367-3212439 0 0 0 0 0 0 -TCONS_00000026 i Xkr4 - - chr1:3213095-3213192 0 0 0 0 0 0 -TCONS_00000027 i Xkr4 - - chr1:3242633-3242923 0 0 0 0 0 0 -TCONS_00000028 i Xkr4 - - chr1:3243018-3243079 0 0 0 0 0 0 -TCONS_00000029 i Xkr4 - - chr1:3243347-3243401 0 0 0 0 0 0 -TCONS_00000030 i Xkr4 - - chr1:3256974-3257011 0 0 0 0 0 0 -TCONS_00000031 i Xkr4 - - chr1:3277190-3277218 0 0 0 0 0 0 -TCONS_00000032 i Xkr4 - - chr1:3277913-3278390 0 0 0 0 0 0 -TCONS_00000033 i Xkr4 - - chr1:3280686-3280741 0 0 0 0 0 0 -TCONS_00000034 i Xkr4 - - chr1:3290488-3290553 0 0 0 0 0 0 -TCONS_00000035 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 -TCONS_00000036 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 -TCONS_00000037 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 -TCONS_00000038 i Xkr4 - - chr1:3300051-3300078 0 0 0 0 0 0 -TCONS_00000039 i Xkr4 - - chr1:3318999-3319051 0 0 0 0 0 0 -TCONS_00000040 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 -TCONS_00000041 i Xkr4 - - chr1:3363214-3363278 0 0 0 0 0 0 -TCONS_00000042 i Xkr4 - - chr1:3363753-3363849 0 0 0 0 0 0 -TCONS_00000043 i Xkr4 - - chr1:3367135-3367162 0 0 0 0 0 0 -TCONS_00000044 i Xkr4 - - chr1:3367333-3367382 0 0 0 0 0 0 -TCONS_00000045 i Xkr4 - - chr1:3377211-3377262 0 0 0 0 0 0 -TCONS_00000046 i Xkr4 - - chr1:3391325-3391352 0 0 0 0 0 0 -TCONS_00000047 i Xkr4 - - chr1:3435841-3435880 0 0 0 0 0 0 -TCONS_00000048 i Xkr4 - - chr1:3447761-3447788 0 0 0 0 0 0 -TCONS_00000049 i Xkr4 - - chr1:3450906-3450965 0 0 0 0 0 0 -TCONS_00000050 i Xkr4 - - chr1:3451051-3451109 0 0 0 0 0 0 -TCONS_00000051 - - - - chr1:3174765-3174792 0 0 0 0 0 0 -TCONS_00000052 - - - - chr1:3187401-3187428 0 0 0 0 0 0 -TCONS_00000053 - - - - chr1:3188521-3188548 0 0 0 0 0 0 -TCONS_00000054 - - - - chr1:3189810-3190789 343500 342328 344672 303241 270227 336255 -TCONS_00000055 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 -TCONS_00000056 - - - - chr1:3191512-3192077 345096 343921 346271 376320 320653 431986 -TCONS_00000057 - - - - chr1:3192250-3192336 0 0 0 0 0 0 -TCONS_00000058 - - - - chr1:3192649-3192676 0 0 0 0 0 0 -TCONS_00000059 - - - - chr1:3194706-3194733 0 0 0 0 0 0 -TCONS_00000060 - - - - chr1:3197425-3197452 0 0 0 0 0 0 -TCONS_00000061 - - - - chr1:3200430-3200457 0 0 0 0 0 0 -TCONS_00000062 - - - - chr1:3201007-3201039 0 0 0 0 0 0 -TCONS_00000063 - - - - chr1:3201077-3201481 0 0 0 0 0 0 -TCONS_00000064 - - - - chr1:3201596-3201666 0 0 0 0 0 0 -TCONS_00000065 - - - - chr1:3201725-3201809 0 0 0 0 0 0 -TCONS_00000066 i Xkr4 - - chr1:3211521-3211561 0 0 0 0 0 0 -TCONS_00000067 i Xkr4 - - chr1:3212717-3212801 0 0 0 0 0 0 -TCONS_00000068 i Xkr4 - - chr1:3240606-3240633 0 0 0 0 0 0 -TCONS_00000069 i Xkr4 - - chr1:3242479-3242512 0 0 0 0 0 0 -TCONS_00000070 i Xkr4 - - chr1:3242924-3243005 0 0 0 0 0 0 -TCONS_00000071 i Xkr4 - - chr1:3243108-3243154 0 0 0 0 0 0 -TCONS_00000072 i Xkr4 - - chr1:3254079-3254106 0 0 0 0 0 0 -TCONS_00000073 i Xkr4 - - chr1:3277155-3277182 0 0 0 0 0 0 -TCONS_00000074 i Xkr4 - - chr1:3277913-3278390 165459 164646 166273 0 0 0 -TCONS_00000075 i Xkr4 - - chr1:3280117-3280144 0 0 0 0 0 0 -TCONS_00000076 i Xkr4 - - chr1:3280498-3280525 0 0 0 0 0 0 -TCONS_00000077 i Xkr4 - - chr1:3282504-3282531 0 0 0 0 0 0 -TCONS_00000078 i Xkr4 - - chr1:3282650-3282677 0 0 0 0 0 0 -TCONS_00000079 i Xkr4 - - chr1:3282760-3282832 0 0 0 0 0 0 -TCONS_00000080 i Xkr4 - - chr1:3284966-3284993 0 0 0 0 0 0 -TCONS_00000081 i Xkr4 - - chr1:3290798-3290859 0 0 0 0 0 0 -TCONS_00000082 i Xkr4 - - chr1:3290919-3291273 163613 162804 164422 0 0 0 -TCONS_00000083 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 -TCONS_00000084 i Xkr4 - - chr1:3299691-3299733 0 0 0 0 0 0 -TCONS_00000085 i Xkr4 - - chr1:3307748-3307775 0 0 0 0 0 0 -TCONS_00000086 i Xkr4 - - chr1:3318620-3318647 0 0 0 0 0 0 -TCONS_00000087 i Xkr4 - - chr1:3330527-3330554 0 0 0 0 0 0 -TCONS_00000088 i Xkr4 - - chr1:3351240-3351311 0 0 0 0 0 0 -TCONS_00000089 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 -TCONS_00000090 i Xkr4 - - chr1:3356180-3356225 0 0 0 0 0 0 -TCONS_00000091 i Xkr4 - - chr1:3363076-3363176 0 0 0 0 0 0 -TCONS_00000092 i Xkr4 - - chr1:3363387-3363446 0 0 0 0 0 0 -TCONS_00000093 i Xkr4 - - chr1:3364871-3364919 0 0 0 0 0 0 -TCONS_00000094 i Xkr4 - - chr1:3367210-3367237 0 0 0 0 0 0 -TCONS_00000095 i Xkr4 - - chr1:3369580-3369607 0 0 0 0 0 0 -TCONS_00000096 i Xkr4 - - chr1:3375001-3375028 0 0 0 0 0 0 -TCONS_00000097 i Xkr4 - - chr1:3379888-3379915 0 0 0 0 0 0 -TCONS_00000098 i Xkr4 - - chr1:3386739-3386836 0 0 0 0 0 0 +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +TCONS_00000001 c Xkr4 XLOC_000001 - - chr1:3204754-3204833 79 - OK 0 0 0 5.42247e+06 0 1.3091e+07 +TCONS_00000002 - - XLOC_000002 - - chr1:3111449-3111490 41 - OK 0 0 0 1.39654e+08 0 4.18963e+08 +TCONS_00000003 - - XLOC_000003 - - chr1:3111545-3111576 31 - OK 0 0 0 0 0 0 +TCONS_00000004 - - XLOC_000007 - - chr1:3189810-3190789 142 - OK 2.49256e+06 0 5.08341e+06 5.29759e+06 686576 9.90861e+06 +TCONS_00000005 - - XLOC_000007 - - chr1:3189810-3190789 31 - OK 0 0 0 0 0 0 +TCONS_00000006 - - XLOC_000007 - - chr1:3189810-3190789 27 - OK 0 0 0 0 0 0 +TCONS_00000007 - - XLOC_000009 - - chr1:3191512-3192077 131 - OK 2.77423e+06 0 5.7461e+06 6.7156e+06 774909 1.26563e+07 +TCONS_00000008 - - XLOC_000009 - - chr1:3191512-3192077 69 - OK 1.11098e+07 0 3.60229e+07 3.03942e+07 0 6.3641e+07 +TCONS_00000009 - - XLOC_000011 - - chr1:3192441-3192494 53 - OK 0 0 0 5.56023e+07 0 1.19806e+08 +TCONS_00000010 - - XLOC_000012 - - chr1:3192550-3192629 79 - OK 0 0 0 2.71123e+06 0 8.1337e+06 +TCONS_00000011 - - XLOC_000014 - - chr1:3192731-3192811 80 - OK 0 0 0 0 0 0 +TCONS_00000012 - - XLOC_000015 - - chr1:3192940-3193042 102 - OK 0 0 0 3.93442e+06 0 8.47748e+06 +TCONS_00000013 - - XLOC_000016 - - chr1:3194185-3194226 41 - OK 0 0 0 1.39654e+08 0 4.18963e+08 +TCONS_00000014 - - XLOC_000017 - - chr1:3194302-3194329 27 - OK 0 0 0 0 0 0 +TCONS_00000015 - - XLOC_000019 - - chr1:3195083-3195110 27 - OK 0 0 0 0 0 0 +TCONS_00000016 - - XLOC_000020 - - chr1:3195450-3195477 27 - OK 0 0 0 0 0 0 +TCONS_00000017 - - XLOC_000021 - - chr1:3197089-3197116 27 - OK 0 0 0 0 0 0 +TCONS_00000018 - - XLOC_000022 - - chr1:3197246-3197273 27 - OK 0 0 0 0 0 0 +TCONS_00000019 - - XLOC_000023 - - chr1:3197346-3197373 27 - OK 0 0 0 0 0 0 +TCONS_00000020 - - XLOC_000025 - - chr1:3200022-3200191 169 - OK 460348 0 991912 460348 0 991912 +TCONS_00000021 - - XLOC_000026 - - chr1:3200325-3200352 27 - OK 0 0 0 0 0 0 +TCONS_00000022 - - XLOC_000029 - - chr1:3201077-3201481 404 - OK 37206.6 0 80169.2 186033 15366.6 356700 +TCONS_00000023 - - XLOC_000031 - - chr1:3201672-3201699 27 - OK 0 0 0 0 0 0 +TCONS_00000024 i Xkr4 XLOC_000034 - - chr1:3212213-3212292 79 - OK 0 0 0 5.42247e+06 0 1.3091e+07 +TCONS_00000025 i Xkr4 XLOC_000035 - - chr1:3212367-3212439 72 - OK 0 0 0 1.60978e+07 0 3.46859e+07 +TCONS_00000026 i Xkr4 XLOC_000037 - - chr1:3213095-3213192 97 - OK 2.38694e+06 0 5.76259e+06 1.19347e+06 0 3.58042e+06 +TCONS_00000027 i Xkr4 XLOC_000040 - - chr1:3242633-3242923 290 - OK 27029.9 0 81089.8 243269 0 494190 +TCONS_00000028 i Xkr4 XLOC_000042 - - chr1:3243018-3243079 61 - OK 0 0 0 1.73712e+07 0 4.19378e+07 +TCONS_00000029 i Xkr4 XLOC_000044 - - chr1:3243347-3243401 54 - OK 0 0 0 3.32455e+07 0 8.02618e+07 +TCONS_00000030 i Xkr4 XLOC_000046 - - chr1:3256974-3257011 37 - OK 0 0 0 1.34946e+09 0 3.25789e+09 +TCONS_00000031 i Xkr4 XLOC_000048 - - chr1:3277190-3277218 28 - OK 0 0 0 0 0 0 +TCONS_00000032 i Xkr4 XLOC_000049 - - chr1:3277913-3278390 27 - OK 0 0 0 0 0 0 +TCONS_00000033 i Xkr4 XLOC_000052 - - chr1:3280686-3280741 55 - OK 0 0 0 1.49798e+07 0 4.49395e+07 +TCONS_00000034 i Xkr4 XLOC_000057 - - chr1:3290488-3290553 65 - OK 0 0 0 6.39146e+06 0 1.91744e+07 +TCONS_00000035 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 84 - OK 6.40392e+06 0 1.55816e+07 0 0 0 +TCONS_00000036 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 98 - OK 1.2964e+06 0 4.55711e+06 1.46758e+06 0 4.47705e+06 +TCONS_00000037 i Xkr4 XLOC_000060 - - chr1:3299443-3299664 55 - OK 0 0 0 0 0 0 +TCONS_00000038 i Xkr4 XLOC_000062 - - chr1:3300051-3300078 27 - OK 0 0 0 0 0 0 +TCONS_00000039 i Xkr4 XLOC_000065 - - chr1:3318999-3319051 52 - OK 0 0 0 0 0 0 +TCONS_00000040 i Xkr4 XLOC_000068 - - chr1:3355887-3356119 27 - OK 0 0 0 0 0 0 +TCONS_00000041 i Xkr4 XLOC_000071 - - chr1:3363214-3363278 64 - OK 0 0 0 0 0 0 +TCONS_00000042 i Xkr4 XLOC_000073 - - chr1:3363753-3363849 96 - OK 0 0 0 0 0 0 +TCONS_00000043 i Xkr4 XLOC_000075 - - chr1:3367135-3367162 27 - OK 0 0 0 0 0 0 +TCONS_00000044 i Xkr4 XLOC_000077 - - chr1:3367333-3367382 49 - OK 0 0 0 0 0 0 +TCONS_00000045 i Xkr4 XLOC_000080 - - chr1:3377211-3377262 51 - OK 0 0 0 0 0 0 +TCONS_00000046 i Xkr4 XLOC_000083 - - chr1:3391325-3391352 27 - OK 0 0 0 0 0 0 +TCONS_00000047 i Xkr4 XLOC_000084 - - chr1:3435841-3435880 39 - OK 0 0 0 0 0 0 +TCONS_00000048 i Xkr4 XLOC_000085 - - chr1:3447761-3447788 27 - OK 0 0 0 0 0 0 +TCONS_00000049 i Xkr4 XLOC_000086 - - chr1:3450906-3450965 59 - OK 0 0 0 0 0 0 +TCONS_00000050 i Xkr4 XLOC_000087 - - chr1:3451051-3451109 58 - OK 0 0 0 0 0 0 +TCONS_00000051 - - XLOC_000004 - - chr1:3174765-3174792 27 - OK 0 0 0 0 0 0 +TCONS_00000052 - - XLOC_000005 - - chr1:3187401-3187428 27 - OK 0 0 0 0 0 0 +TCONS_00000053 - - XLOC_000006 - - chr1:3188521-3188548 27 - OK 0 0 0 0 0 0 +TCONS_00000054 - - XLOC_000007 - - chr1:3189810-3190789 979 - OK 171639 69105.7 274173 239968 172568 307367 +TCONS_00000055 - - XLOC_000008 - - chr1:3190858-3191434 576 - OK 227564 66605.9 388523 240951 73918.5 407983 +TCONS_00000056 - - XLOC_000009 - - chr1:3191512-3192077 565 - OK 175955 38281.8 313628 319423 117942 520904 +TCONS_00000057 - - XLOC_000010 - - chr1:3192250-3192336 86 - OK 1.91712e+06 0 5.75136e+06 1.91712e+06 0 5.75136e+06 +TCONS_00000058 - - XLOC_000013 - - chr1:3192649-3192676 27 - OK 0 0 0 0 0 0 +TCONS_00000059 - - XLOC_000018 - - chr1:3194706-3194733 27 - OK 0 0 0 0 0 0 +TCONS_00000060 - - XLOC_000024 - - chr1:3197425-3197452 27 - OK 0 0 0 0 0 0 +TCONS_00000061 - - XLOC_000027 - - chr1:3200430-3200457 27 - OK 0 0 0 0 0 0 +TCONS_00000062 - - XLOC_000028 - - chr1:3201007-3201039 32 - OK 0 0 0 0 0 0 +TCONS_00000063 - - XLOC_000029 - - chr1:3201077-3201481 27 - OK 0 0 0 0 0 0 +TCONS_00000064 - - XLOC_000030 - - chr1:3201596-3201666 70 - OK 9.11292e+06 0 2.20005e+07 0 0 0 +TCONS_00000065 - - XLOC_000032 - - chr1:3201725-3201809 84 - OK 8.43162e+06 0 1.81676e+07 0 0 0 +TCONS_00000066 i Xkr4 XLOC_000033 - - chr1:3211521-3211561 40 - OK 0 0 0 0 0 0 +TCONS_00000067 i Xkr4 XLOC_000036 - - chr1:3212717-3212801 84 - OK 2.10791e+06 0 6.32372e+06 0 0 0 +TCONS_00000068 i Xkr4 XLOC_000038 - - chr1:3240606-3240633 27 - OK 0 0 0 0 0 0 +TCONS_00000069 i Xkr4 XLOC_000039 - - chr1:3242479-3242512 33 - OK 0 0 0 0 0 0 +TCONS_00000070 i Xkr4 XLOC_000041 - - chr1:3242924-3243005 81 - OK 0 0 0 0 0 0 +TCONS_00000071 i Xkr4 XLOC_000043 - - chr1:3243108-3243154 46 - OK 4.79961e+07 0 1.43988e+08 0 0 0 +TCONS_00000072 i Xkr4 XLOC_000045 - - chr1:3254079-3254106 27 - OK 0 0 0 0 0 0 +TCONS_00000073 i Xkr4 XLOC_000047 - - chr1:3277155-3277182 27 - OK 0 0 0 0 0 0 +TCONS_00000074 i Xkr4 XLOC_000049 - - chr1:3277913-3278390 477 - OK 127495 8942.18 246048 27320.3 0 58867.2 +TCONS_00000075 i Xkr4 XLOC_000050 - - chr1:3280117-3280144 27 - OK 0 0 0 0 0 0 +TCONS_00000076 i Xkr4 XLOC_000051 - - chr1:3280498-3280525 27 - OK 0 0 0 0 0 0 +TCONS_00000077 i Xkr4 XLOC_000053 - - chr1:3282504-3282531 27 - OK 0 0 0 0 0 0 +TCONS_00000078 i Xkr4 XLOC_000054 - - chr1:3282650-3282677 27 - OK 0 0 0 0 0 0 +TCONS_00000079 i Xkr4 XLOC_000055 - - chr1:3282760-3282832 72 - OK 0 0 0 0 0 0 +TCONS_00000080 i Xkr4 XLOC_000056 - - chr1:3284966-3284993 27 - OK 0 0 0 0 0 0 +TCONS_00000081 i Xkr4 XLOC_000058 - - chr1:3290798-3290859 61 - OK 8.68561e+06 0 2.60568e+07 0 0 0 +TCONS_00000082 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 354 - OK 95795.4 0 201253 28263.3 0 76569.5 +TCONS_00000083 i Xkr4 XLOC_000060 - - chr1:3299443-3299664 197 - OK 449954 0 952175 89990.7 0 269972 +TCONS_00000084 i Xkr4 XLOC_000061 - - chr1:3299691-3299733 42 - OK 0 0 0 0 0 0 +TCONS_00000085 i Xkr4 XLOC_000063 - - chr1:3307748-3307775 27 - OK 0 0 0 0 0 0 +TCONS_00000086 i Xkr4 XLOC_000064 - - chr1:3318620-3318647 27 - OK 0 0 0 0 0 0 +TCONS_00000087 i Xkr4 XLOC_000066 - - chr1:3330527-3330554 27 - OK 0 0 0 0 0 0 +TCONS_00000088 i Xkr4 XLOC_000067 - - chr1:3351240-3351311 71 - OK 4.27915e+06 0 1.28374e+07 0 0 0 +TCONS_00000089 i Xkr4 XLOC_000068 - - chr1:3355887-3356119 212 - OK 281197 0 605895 0 0 0 +TCONS_00000090 i Xkr4 XLOC_000069 - - chr1:3356180-3356225 45 - OK 5.72196e+07 0 1.71659e+08 0 0 0 +TCONS_00000091 i Xkr4 XLOC_000070 - - chr1:3363076-3363176 100 - OK 2.1224e+06 0 5.12392e+06 0 0 0 +TCONS_00000092 i Xkr4 XLOC_000072 - - chr1:3363387-3363446 59 - OK 3.08417e+07 0 6.64547e+07 0 0 0 +TCONS_00000093 i Xkr4 XLOC_000074 - - chr1:3364871-3364919 48 - OK 3.50371e+07 0 1.05111e+08 0 0 0 +TCONS_00000094 i Xkr4 XLOC_000076 - - chr1:3367210-3367237 27 - OK 0 0 0 0 0 0 +TCONS_00000095 i Xkr4 XLOC_000078 - - chr1:3369580-3369607 27 - OK 0 0 0 0 0 0 +TCONS_00000096 i Xkr4 XLOC_000079 - - chr1:3375001-3375028 27 - OK 0 0 0 0 0 0 +TCONS_00000097 i Xkr4 XLOC_000081 - - chr1:3379888-3379915 27 - OK 0 0 0 0 0 0 +TCONS_00000098 i Xkr4 XLOC_000082 - - chr1:3386739-3386836 97 - OK 0 0 0 0 0 0 --- a/test-data/cuffdiff_out6.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out6.txt Mon May 09 13:28:26 2011 -0400 @@ -1,88 +1,88 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -XLOC_000001 - - - - chr1:3204754-3204833 0 0 0 0 0 0 -XLOC_000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 -XLOC_000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 -XLOC_000004 - - - - chr1:3174765-3174792 0 0 0 0 0 0 -XLOC_000005 - - - - chr1:3187401-3187428 0 0 0 0 0 0 -XLOC_000006 - - - - chr1:3188521-3188548 0 0 0 0 0 0 -XLOC_000007 - - - - chr1:3189810-3190789 343500 342328 344672 947555 680603 1.21451e+06 -XLOC_000008 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 -XLOC_000009 - - - - chr1:3191512-3192077 345096 343921 346271 1.07827e+06 822433 1.33412e+06 -XLOC_000010 - - - - chr1:3192250-3192336 0 0 0 0 0 0 -XLOC_000011 - - - - chr1:3192441-3192494 0 0 0 0 0 0 -XLOC_000012 - - - - chr1:3192550-3192629 0 0 0 0 0 0 -XLOC_000013 - - - - chr1:3192649-3192676 0 0 0 0 0 0 -XLOC_000014 - - - - chr1:3192731-3192811 0 0 0 0 0 0 -XLOC_000015 - - - - chr1:3192940-3193042 0 0 0 0 0 0 -XLOC_000016 - - - - chr1:3194185-3194226 0 0 0 0 0 0 -XLOC_000017 - - - - chr1:3194302-3194329 0 0 0 0 0 0 -XLOC_000018 - - - - chr1:3194706-3194733 0 0 0 0 0 0 -XLOC_000019 - - - - chr1:3195083-3195110 0 0 0 0 0 0 -XLOC_000020 - - - - chr1:3195450-3195477 0 0 0 0 0 0 -XLOC_000021 - - - - chr1:3197089-3197116 0 0 0 0 0 0 -XLOC_000022 - - - - chr1:3197246-3197273 0 0 0 0 0 0 -XLOC_000023 - - - - chr1:3197346-3197373 0 0 0 0 0 0 -XLOC_000024 - - - - chr1:3197425-3197452 0 0 0 0 0 0 -XLOC_000025 - - - - chr1:3200022-3200191 0 0 0 0 0 0 -XLOC_000026 - - - - chr1:3200325-3200352 0 0 0 0 0 0 -XLOC_000027 - - - - chr1:3200430-3200457 0 0 0 0 0 0 -XLOC_000028 - - - - chr1:3201007-3201039 0 0 0 0 0 0 -XLOC_000029 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 -XLOC_000030 - - - - chr1:3201596-3201666 0 0 0 0 0 0 -XLOC_000031 - - - - chr1:3201672-3201699 0 0 0 0 0 0 -XLOC_000032 - - - - chr1:3201725-3201809 0 0 0 0 0 0 -XLOC_000033 - - - - chr1:3211521-3211561 0 0 0 0 0 0 -XLOC_000034 - - - - chr1:3212213-3212292 0 0 0 0 0 0 -XLOC_000035 - - - - chr1:3212367-3212439 0 0 0 0 0 0 -XLOC_000036 - - - - chr1:3212717-3212801 0 0 0 0 0 0 -XLOC_000037 - - - - chr1:3213095-3213192 0 0 0 0 0 0 -XLOC_000038 - - - - chr1:3240606-3240633 0 0 0 0 0 0 -XLOC_000039 - - - - chr1:3242479-3242512 0 0 0 0 0 0 -XLOC_000040 - - - - chr1:3242633-3242923 0 0 0 0 0 0 -XLOC_000041 - - - - chr1:3242924-3243005 0 0 0 0 0 0 -XLOC_000042 - - - - chr1:3243018-3243079 0 0 0 0 0 0 -XLOC_000043 - - - - chr1:3243108-3243154 0 0 0 0 0 0 -XLOC_000044 - - - - chr1:3243347-3243401 0 0 0 0 0 0 -XLOC_000045 - - - - chr1:3254079-3254106 0 0 0 0 0 0 -XLOC_000046 - - - - chr1:3256974-3257011 0 0 0 0 0 0 -XLOC_000047 - - - - chr1:3277155-3277182 0 0 0 0 0 0 -XLOC_000048 - - - - chr1:3277190-3277218 0 0 0 0 0 0 -XLOC_000049 - - - - chr1:3277913-3278390 165459 164646 166273 0 0 0 -XLOC_000050 - - - - chr1:3280117-3280144 0 0 0 0 0 0 -XLOC_000051 - - - - chr1:3280498-3280525 0 0 0 0 0 0 -XLOC_000052 - - - - chr1:3280686-3280741 0 0 0 0 0 0 -XLOC_000053 - - - - chr1:3282504-3282531 0 0 0 0 0 0 -XLOC_000054 - - - - chr1:3282650-3282677 0 0 0 0 0 0 -XLOC_000055 - - - - chr1:3282760-3282832 0 0 0 0 0 0 -XLOC_000056 - - - - chr1:3284966-3284993 0 0 0 0 0 0 -XLOC_000057 - - - - chr1:3290488-3290553 0 0 0 0 0 0 -XLOC_000058 - - - - chr1:3290798-3290859 0 0 0 0 0 0 -XLOC_000059 - - - - chr1:3290919-3291273 163613 162804 164422 0 0 0 -XLOC_000060 - - - - chr1:3299443-3299664 0 0 0 0 0 0 -XLOC_000061 - - - - chr1:3299691-3299733 0 0 0 0 0 0 -XLOC_000062 - - - - chr1:3300051-3300078 0 0 0 0 0 0 -XLOC_000063 - - - - chr1:3307748-3307775 0 0 0 0 0 0 -XLOC_000064 - - - - chr1:3318620-3318647 0 0 0 0 0 0 -XLOC_000065 - - - - chr1:3318999-3319051 0 0 0 0 0 0 -XLOC_000066 - - - - chr1:3330527-3330554 0 0 0 0 0 0 -XLOC_000067 - - - - chr1:3351240-3351311 0 0 0 0 0 0 -XLOC_000068 - - - - chr1:3355887-3356119 0 0 0 0 0 0 -XLOC_000069 - - - - chr1:3356180-3356225 0 0 0 0 0 0 -XLOC_000070 - - - - chr1:3363076-3363176 0 0 0 0 0 0 -XLOC_000071 - - - - chr1:3363214-3363278 0 0 0 0 0 0 -XLOC_000072 - - - - chr1:3363387-3363446 0 0 0 0 0 0 -XLOC_000073 - - - - chr1:3363753-3363849 0 0 0 0 0 0 -XLOC_000074 - - - - chr1:3364871-3364919 0 0 0 0 0 0 -XLOC_000075 - - - - chr1:3367135-3367162 0 0 0 0 0 0 -XLOC_000076 - - - - chr1:3367210-3367237 0 0 0 0 0 0 -XLOC_000077 - - - - chr1:3367333-3367382 0 0 0 0 0 0 -XLOC_000078 - - - - chr1:3369580-3369607 0 0 0 0 0 0 -XLOC_000079 - - - - chr1:3375001-3375028 0 0 0 0 0 0 -XLOC_000080 - - - - chr1:3377211-3377262 0 0 0 0 0 0 -XLOC_000081 - - - - chr1:3379888-3379915 0 0 0 0 0 0 -XLOC_000082 - - - - chr1:3386739-3386836 0 0 0 0 0 0 -XLOC_000083 - - - - chr1:3391325-3391352 0 0 0 0 0 0 -XLOC_000084 - - - - chr1:3435841-3435880 0 0 0 0 0 0 -XLOC_000085 - - - - chr1:3447761-3447788 0 0 0 0 0 0 -XLOC_000086 - - - - chr1:3450906-3450965 0 0 0 0 0 0 -XLOC_000087 - - - - chr1:3451051-3451109 0 0 0 0 0 0 +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +XLOC_000001 - - XLOC_000001 - - chr1:3204754-3204833 - - OK 0 0 0 5.42247e+06 0 1.3091e+07 +XLOC_000002 - - XLOC_000002 - - chr1:3111449-3111490 - - OK 0 0 0 1.39654e+08 0 4.18963e+08 +XLOC_000003 - - XLOC_000003 - - chr1:3111545-3111576 - - OK 0 0 0 0 0 0 +XLOC_000004 - - XLOC_000004 - - chr1:3174765-3174792 - - OK 0 0 0 0 0 0 +XLOC_000005 - - XLOC_000005 - - chr1:3187401-3187428 - - OK 0 0 0 0 0 0 +XLOC_000006 - - XLOC_000006 - - chr1:3188521-3188548 - - OK 0 0 0 0 0 0 +XLOC_000007 - - XLOC_000007 - - chr1:3189810-3190789 - - OK 2.6642e+06 71325.8 5.25708e+06 5.53756e+06 926051 1.01491e+07 +XLOC_000008 - - XLOC_000008 - - chr1:3190858-3191434 - - OK 227564 66605.9 388523 240951 73918.5 407983 +XLOC_000009 - - XLOC_000009 - - chr1:3191512-3192077 - - OK 1.406e+07 0 3.91501e+07 3.74293e+07 3.65533e+06 7.12032e+07 +XLOC_000010 - - XLOC_000010 - - chr1:3192250-3192336 - - OK 1.91712e+06 0 5.75136e+06 1.91712e+06 0 5.75136e+06 +XLOC_000011 - - XLOC_000011 - - chr1:3192441-3192494 - - OK 0 0 0 5.56023e+07 0 1.19806e+08 +XLOC_000012 - - XLOC_000012 - - chr1:3192550-3192629 - - OK 0 0 0 2.71123e+06 0 8.1337e+06 +XLOC_000013 - - XLOC_000013 - - chr1:3192649-3192676 - - OK 0 0 0 0 0 0 +XLOC_000014 - - XLOC_000014 - - chr1:3192731-3192811 - - OK 0 0 0 0 0 0 +XLOC_000015 - - XLOC_000015 - - chr1:3192940-3193042 - - OK 0 0 0 3.93442e+06 0 8.47748e+06 +XLOC_000016 - - XLOC_000016 - - chr1:3194185-3194226 - - OK 0 0 0 1.39654e+08 0 4.18963e+08 +XLOC_000017 - - XLOC_000017 - - chr1:3194302-3194329 - - OK 0 0 0 0 0 0 +XLOC_000018 - - XLOC_000018 - - chr1:3194706-3194733 - - OK 0 0 0 0 0 0 +XLOC_000019 - - XLOC_000019 - - chr1:3195083-3195110 - - OK 0 0 0 0 0 0 +XLOC_000020 - - XLOC_000020 - - chr1:3195450-3195477 - - OK 0 0 0 0 0 0 +XLOC_000021 - - XLOC_000021 - - chr1:3197089-3197116 - - OK 0 0 0 0 0 0 +XLOC_000022 - - XLOC_000022 - - chr1:3197246-3197273 - - OK 0 0 0 0 0 0 +XLOC_000023 - - XLOC_000023 - - chr1:3197346-3197373 - - OK 0 0 0 0 0 0 +XLOC_000024 - - XLOC_000024 - - chr1:3197425-3197452 - - OK 0 0 0 0 0 0 +XLOC_000025 - - XLOC_000025 - - chr1:3200022-3200191 - - OK 460348 0 991912 460348 0 991912 +XLOC_000026 - - XLOC_000026 - - chr1:3200325-3200352 - - OK 0 0 0 0 0 0 +XLOC_000027 - - XLOC_000027 - - chr1:3200430-3200457 - - OK 0 0 0 0 0 0 +XLOC_000028 - - XLOC_000028 - - chr1:3201007-3201039 - - OK 0 0 0 0 0 0 +XLOC_000029 - - XLOC_000029 - - chr1:3201077-3201481 - - OK 37206.6 0 80169.2 186033 15366.6 356700 +XLOC_000030 - - XLOC_000030 - - chr1:3201596-3201666 - - OK 9.11292e+06 0 2.20005e+07 0 0 0 +XLOC_000031 - - XLOC_000031 - - chr1:3201672-3201699 - - OK 0 0 0 0 0 0 +XLOC_000032 - - XLOC_000032 - - chr1:3201725-3201809 - - OK 8.43162e+06 0 1.81676e+07 0 0 0 +XLOC_000033 - - XLOC_000033 - - chr1:3211521-3211561 - - OK 0 0 0 0 0 0 +XLOC_000034 - - XLOC_000034 - - chr1:3212213-3212292 - - OK 0 0 0 5.42247e+06 0 1.3091e+07 +XLOC_000035 - - XLOC_000035 - - chr1:3212367-3212439 - - OK 0 0 0 1.60978e+07 0 3.46859e+07 +XLOC_000036 - - XLOC_000036 - - chr1:3212717-3212801 - - OK 2.10791e+06 0 6.32372e+06 0 0 0 +XLOC_000037 - - XLOC_000037 - - chr1:3213095-3213192 - - OK 2.38694e+06 0 5.76259e+06 1.19347e+06 0 3.58042e+06 +XLOC_000038 - - XLOC_000038 - - chr1:3240606-3240633 - - OK 0 0 0 0 0 0 +XLOC_000039 - - XLOC_000039 - - chr1:3242479-3242512 - - OK 0 0 0 0 0 0 +XLOC_000040 - - XLOC_000040 - - chr1:3242633-3242923 - - OK 27029.9 0 81089.8 243269 0 494190 +XLOC_000041 - - XLOC_000041 - - chr1:3242924-3243005 - - OK 0 0 0 0 0 0 +XLOC_000042 - - XLOC_000042 - - chr1:3243018-3243079 - - OK 0 0 0 1.73712e+07 0 4.19378e+07 +XLOC_000043 - - XLOC_000043 - - chr1:3243108-3243154 - - OK 4.79961e+07 0 1.43988e+08 0 0 0 +XLOC_000044 - - XLOC_000044 - - chr1:3243347-3243401 - - OK 0 0 0 3.32455e+07 0 8.02618e+07 +XLOC_000045 - - XLOC_000045 - - chr1:3254079-3254106 - - OK 0 0 0 0 0 0 +XLOC_000046 - - XLOC_000046 - - chr1:3256974-3257011 - - OK 0 0 0 1.34946e+09 0 3.25789e+09 +XLOC_000047 - - XLOC_000047 - - chr1:3277155-3277182 - - OK 0 0 0 0 0 0 +XLOC_000048 - - XLOC_000048 - - chr1:3277190-3277218 - - OK 0 0 0 0 0 0 +XLOC_000049 - - XLOC_000049 - - chr1:3277913-3278390 - - OK 127495 8942.18 246048 27320.3 0 58867.2 +XLOC_000050 - - XLOC_000050 - - chr1:3280117-3280144 - - OK 0 0 0 0 0 0 +XLOC_000051 - - XLOC_000051 - - chr1:3280498-3280525 - - OK 0 0 0 0 0 0 +XLOC_000052 - - XLOC_000052 - - chr1:3280686-3280741 - - OK 0 0 0 1.49798e+07 0 4.49395e+07 +XLOC_000053 - - XLOC_000053 - - chr1:3282504-3282531 - - OK 0 0 0 0 0 0 +XLOC_000054 - - XLOC_000054 - - chr1:3282650-3282677 - - OK 0 0 0 0 0 0 +XLOC_000055 - - XLOC_000055 - - chr1:3282760-3282832 - - OK 0 0 0 0 0 0 +XLOC_000056 - - XLOC_000056 - - chr1:3284966-3284993 - - OK 0 0 0 0 0 0 +XLOC_000057 - - XLOC_000057 - - chr1:3290488-3290553 - - OK 0 0 0 6.39146e+06 0 1.91744e+07 +XLOC_000058 - - XLOC_000058 - - chr1:3290798-3290859 - - OK 8.68561e+06 0 2.60568e+07 0 0 0 +XLOC_000059 - - XLOC_000059 - - chr1:3290919-3291273 - - OK 7.79612e+06 0 1.75364e+07 1.49584e+06 0 4.5057e+06 +XLOC_000060 - - XLOC_000060 - - chr1:3299443-3299664 - - OK 449954 0 952175 89990.7 0 269972 +XLOC_000061 - - XLOC_000061 - - chr1:3299691-3299733 - - OK 0 0 0 0 0 0 +XLOC_000062 - - XLOC_000062 - - chr1:3300051-3300078 - - OK 0 0 0 0 0 0 +XLOC_000063 - - XLOC_000063 - - chr1:3307748-3307775 - - OK 0 0 0 0 0 0 +XLOC_000064 - - XLOC_000064 - - chr1:3318620-3318647 - - OK 0 0 0 0 0 0 +XLOC_000065 - - XLOC_000065 - - chr1:3318999-3319051 - - OK 0 0 0 0 0 0 +XLOC_000066 - - XLOC_000066 - - chr1:3330527-3330554 - - OK 0 0 0 0 0 0 +XLOC_000067 - - XLOC_000067 - - chr1:3351240-3351311 - - OK 4.27915e+06 0 1.28374e+07 0 0 0 +XLOC_000068 - - XLOC_000068 - - chr1:3355887-3356119 - - OK 281197 0 605895 0 0 0 +XLOC_000069 - - XLOC_000069 - - chr1:3356180-3356225 - - OK 5.72196e+07 0 1.71659e+08 0 0 0 +XLOC_000070 - - XLOC_000070 - - chr1:3363076-3363176 - - OK 2.1224e+06 0 5.12392e+06 0 0 0 +XLOC_000071 - - XLOC_000071 - - chr1:3363214-3363278 - - OK 0 0 0 0 0 0 +XLOC_000072 - - XLOC_000072 - - chr1:3363387-3363446 - - OK 3.08417e+07 0 6.64547e+07 0 0 0 +XLOC_000073 - - XLOC_000073 - - chr1:3363753-3363849 - - OK 0 0 0 0 0 0 +XLOC_000074 - - XLOC_000074 - - chr1:3364871-3364919 - - OK 3.50371e+07 0 1.05111e+08 0 0 0 +XLOC_000075 - - XLOC_000075 - - chr1:3367135-3367162 - - OK 0 0 0 0 0 0 +XLOC_000076 - - XLOC_000076 - - chr1:3367210-3367237 - - OK 0 0 0 0 0 0 +XLOC_000077 - - XLOC_000077 - - chr1:3367333-3367382 - - OK 0 0 0 0 0 0 +XLOC_000078 - - XLOC_000078 - - chr1:3369580-3369607 - - OK 0 0 0 0 0 0 +XLOC_000079 - - XLOC_000079 - - chr1:3375001-3375028 - - OK 0 0 0 0 0 0 +XLOC_000080 - - XLOC_000080 - - chr1:3377211-3377262 - - OK 0 0 0 0 0 0 +XLOC_000081 - - XLOC_000081 - - chr1:3379888-3379915 - - OK 0 0 0 0 0 0 +XLOC_000082 - - XLOC_000082 - - chr1:3386739-3386836 - - OK 0 0 0 0 0 0 +XLOC_000083 - - XLOC_000083 - - chr1:3391325-3391352 - - OK 0 0 0 0 0 0 +XLOC_000084 - - XLOC_000084 - - chr1:3435841-3435880 - - OK 0 0 0 0 0 0 +XLOC_000085 - - XLOC_000085 - - chr1:3447761-3447788 - - OK 0 0 0 0 0 0 +XLOC_000086 - - XLOC_000086 - - chr1:3450906-3450965 - - OK 0 0 0 0 0 0 +XLOC_000087 - - XLOC_000087 - - chr1:3451051-3451109 - - OK 0 0 0 0 0 0 --- a/test-data/cuffdiff_out7.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out7.txt Mon May 09 13:28:26 2011 -0400 @@ -1,1 +1,1 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status --- a/test-data/cuffdiff_out8.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out8.txt Mon May 09 13:28:26 2011 -0400 @@ -1,1 +1,1 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status --- a/test-data/cuffdiff_out9.txt Mon May 09 13:11:45 2011 -0400 +++ b/test-data/cuffdiff_out9.txt Mon May 09 13:28:26 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant --- a/tools/ngs_rna/cuffdiff_wrapper.py Mon May 09 13:11:45 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Mon May 09 13:28:26 2011 -0400 @@ -57,7 +57,6 @@ parser.add_option( '-m', '--inner-mean-dist', dest='inner_mean_dist', help='This is the expected (mean) inner distance between mate pairs. \ For, example, for paired end runs with fragments selected at 300bp, \ where each end is 50bp, you should set -r to be 200. The default is 45bp.') - parser.add_option( '-Q', '--min-mapqual', dest='min_mapqual', help='Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0.' ) parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus\' observed changes don\'t contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' ) parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' ) @@ -78,7 +77,7 @@ parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" ) # Bias correction options. - parser.add_option( '-r', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') + parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) @@ -145,8 +144,6 @@ cmd += ( " -p %i" % int ( options.num_threads ) ) if options.inner_mean_dist: cmd += ( " -m %i" % int ( options.inner_mean_dist ) ) - if options.min_mapqual: - cmd += ( " -Q %i" % int ( options.min_mapqual ) ) if options.min_alignment_count: cmd += ( " -c %i" % int ( options.min_alignment_count ) ) if options.FDR: @@ -158,7 +155,7 @@ if options.do_normalization: cmd += ( " -N" ) if options.do_bias_correction: - cmd += ( " -r %s" % seq_path ) + cmd += ( " -b %s" % seq_path ) # Add inputs. # For replicate analysis: group1_rep1,group1_rep2 groupN_rep1,groupN_rep2 --- a/tools/ngs_rna/cuffdiff_wrapper.xml Mon May 09 13:11:45 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Mon May 09 13:28:26 2011 -0400 @@ -7,7 +7,6 @@ cuffdiff_wrapper.py --FDR=$fdr --num-threads="4" - --min-mapqual=$min_mapqual --min-alignment-count=$min_alignment_count --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking @@ -36,7 +35,7 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -r + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: @@ -97,7 +96,6 @@ </conditional><param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/> - <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/><param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option> @@ -169,8 +167,8 @@ Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? --> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="10"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="56"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="30"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/><output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="16"/> @@ -238,7 +236,6 @@ -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 13:11:45 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 13:28:26 2011 -0400 @@ -209,7 +209,6 @@ -I INT The minimum intron length. Cufflinks will not report transcripts with introns longer than this, and will ignore SAM alignments with REF_SKIP CIGAR operations longer than this. The default is 300,000. -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene. -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript. -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. </help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Update cuffdiff wrapper and test data for v1.0.1
by Bitbucket 09 May '11

09 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/84942418e699/ changeset: r5523:84942418e699 user: jgoecks date: 2011-05-09 18:59:42 summary: Update cuffdiff wrapper and test data for v1.0.1 affected #: 14 files (12.0 KB) --- a/test-data/cuffdiff_out1.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out1.txt Mon May 09 12:59:42 2011 -0400 @@ -1,99 +1,99 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant -TCONS_00000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no -TCONS_00000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no -TCONS_00000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no -TCONS_00000004 - chr1:3189810-3190789 q1 q2 OK 0 645918 6.95322e-310 1.79769e+308 0 yes -TCONS_00000005 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no -TCONS_00000006 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 no -TCONS_00000007 - chr1:3191512-3192077 q1 q2 OK 0 704881 6.95322e-310 1.79769e+308 0 yes -TCONS_00000008 - chr1:3191512-3192077 q1 q2 OK 0 0 0 0 1 no -TCONS_00000009 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no -TCONS_00000010 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no -TCONS_00000011 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no -TCONS_00000012 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no -TCONS_00000013 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no -TCONS_00000014 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no -TCONS_00000015 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no -TCONS_00000016 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no -TCONS_00000017 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no -TCONS_00000018 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000019 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no -TCONS_00000020 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no -TCONS_00000021 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no -TCONS_00000022 - chr1:3201077-3201481 q1 q2 OK 0 155328 0 1.79769e+308 0 yes -TCONS_00000023 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no -TCONS_00000024 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no -TCONS_00000025 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no -TCONS_00000026 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no -TCONS_00000027 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no -TCONS_00000028 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no -TCONS_00000029 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no -TCONS_00000030 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no -TCONS_00000031 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no -TCONS_00000032 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 no -TCONS_00000033 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no -TCONS_00000034 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no -TCONS_00000035 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000036 - chr1:3290919-3291273 q1 q2 OK 0 0 0 0 1 no -TCONS_00000037 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -TCONS_00000038 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no -TCONS_00000039 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no -TCONS_00000040 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -TCONS_00000041 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no -TCONS_00000042 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no -TCONS_00000043 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no -TCONS_00000044 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no -TCONS_00000045 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no -TCONS_00000046 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no -TCONS_00000047 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no -TCONS_00000048 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no -TCONS_00000049 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no -TCONS_00000050 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no -TCONS_00000051 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no -TCONS_00000052 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no -TCONS_00000053 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no -TCONS_00000054 - chr1:3189810-3190789 q1 q2 OK 343500 303241 -0.124659 2.28891 0.0220846 no -TCONS_00000055 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes -TCONS_00000056 - chr1:3191512-3192077 q1 q2 OK 345096 376320 0.0866161 -1.17079 0.241685 no -TCONS_00000057 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no -TCONS_00000058 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no -TCONS_00000059 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no -TCONS_00000060 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no -TCONS_00000061 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no -TCONS_00000062 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no -TCONS_00000063 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 no -TCONS_00000064 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no -TCONS_00000065 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no -TCONS_00000066 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no -TCONS_00000067 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no -TCONS_00000068 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no -TCONS_00000069 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no -TCONS_00000070 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no -TCONS_00000071 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no -TCONS_00000072 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no -TCONS_00000073 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no -TCONS_00000074 - chr1:3277913-3278390 q1 q2 OK 165459 0 0 2.22507e-308 0 yes -TCONS_00000075 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no -TCONS_00000076 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no -TCONS_00000077 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no -TCONS_00000078 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no -TCONS_00000079 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no -TCONS_00000080 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no -TCONS_00000081 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no -TCONS_00000082 - chr1:3290919-3291273 q1 q2 OK 163613 0 0 2.22507e-308 0 yes -TCONS_00000083 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -TCONS_00000084 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no -TCONS_00000085 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no -TCONS_00000086 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no -TCONS_00000087 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no -TCONS_00000088 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no -TCONS_00000089 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -TCONS_00000090 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no -TCONS_00000091 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no -TCONS_00000092 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no -TCONS_00000093 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no -TCONS_00000094 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no -TCONS_00000095 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no -TCONS_00000096 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no -TCONS_00000097 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no -TCONS_00000098 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant +TCONS_00000001 XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.550547 no +TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.777411 no +TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 1.24051 no +TCONS_00000004 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 2.49256e+06 5.29759e+06 0.753941 -1.11223 0.266041 0.790061 no +TCONS_00000005 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 1.25641 no +TCONS_00000006 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 0 0 0 0 1 1.27273 no +TCONS_00000007 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 2.77423e+06 6.7156e+06 0.88406 -1.27269 0.203128 0.663553 no +TCONS_00000008 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 1.11098e+07 3.03942e+07 1.00642 -0.806752 0.419809 1.17547 no +TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.56023e+07 1.79769e+308 1.79769e+308 0.0416323 0.582852 no +TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 2.71123e+06 1.79769e+308 1.79769e+308 0.158655 0.598008 no +TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 1.28947 no +TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 3.93442e+06 1.79769e+308 1.79769e+308 0.0416319 0.679987 no +TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.818327 no +TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 1.30667 no +TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 1.32432 no +TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 1.34247 no +TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 1.36111 no +TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 1.38028 no +TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 1.4 no +TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 460348 460348 0 0 1 1.42029 no +TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 1.44118 no +TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 37206.6 186033 1.60944 -2.18263 0.0290634 2.84821 no +TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 1.46269 no +TCONS_00000024 XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.642305 no +TCONS_00000025 XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 1.60978e+07 1.79769e+308 1.79769e+308 0.0416319 1.35997 no +TCONS_00000026 XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 2.38694e+06 1.19347e+06 -0.693147 0.565952 0.571426 1.55555 no +TCONS_00000027 XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 27029.9 243269 2.19722 -1.95282 0.0508409 0.553601 no +TCONS_00000028 XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 1.73712e+07 1.79769e+308 1.79769e+308 0.0786496 0.700696 no +TCONS_00000029 XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 3.32455e+07 1.79769e+308 1.79769e+308 0.0786496 0.770766 no +TCONS_00000030 XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 1.34946e+09 1.79769e+308 1.79769e+308 0.0786496 0.481729 no +TCONS_00000031 XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 1.48485 no +TCONS_00000032 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 0 0 0 0 1 1.50769 no +TCONS_00000033 XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 1.49798e+07 1.79769e+308 1.79769e+308 0.158655 0.86379 no +TCONS_00000034 XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 6.39146e+06 1.79769e+308 1.79769e+308 0.158655 0.676009 no +TCONS_00000035 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 6.40392e+06 0 -1.79769e+308 -1.79769e+308 0.0814259 0.469396 no +TCONS_00000036 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 1.2964e+06 1.46758e+06 0.124018 -0.0764318 0.939076 2.42183 no +TCONS_00000037 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 1.53125 no +TCONS_00000038 XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 1.55556 no +TCONS_00000039 XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 1.58065 no +TCONS_00000040 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 1 no +TCONS_00000041 XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 1.01031 no +TCONS_00000042 XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 1.02083 no +TCONS_00000043 XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 1.03158 no +TCONS_00000044 XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 1.04255 no +TCONS_00000045 XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 1.05376 no +TCONS_00000046 XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 1.06522 no +TCONS_00000047 XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 1.07692 no +TCONS_00000048 XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 1.08889 no +TCONS_00000049 XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 1.10112 no +TCONS_00000050 XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 1.11364 no +TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 1.12644 no +TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 1.13953 no +TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 1.15294 no +TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 171639 239968 0.335111 -1.01532 0.309956 0.893401 no +TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 227564 240951 0.0571584 -0.115428 0.908106 2.40525 no +TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 175955 319423 0.596288 -1.18662 0.235378 0.720847 no +TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 1.91712e+06 1.91712e+06 0 0 1 1.16667 no +TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 1.18072 no +TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 1.19512 no +TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 1.20988 no +TCONS_00000061 XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 1.225 no +TCONS_00000062 XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 2.27907 no +TCONS_00000063 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 0 0 0 1 2.51282 no +TCONS_00000064 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 9.11292e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.513844 no +TCONS_00000065 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 8.43162e+06 0 -1.79769e+308 -1.79769e+308 0.0416319 0.815985 no +TCONS_00000066 XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 2.13043 no +TCONS_00000067 XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 2.10791e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.647842 no +TCONS_00000068 XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 2.45 no +TCONS_00000069 XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 2.39024 no +TCONS_00000070 XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 2.33333 no +TCONS_00000071 XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 4.79961e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.740391 no +TCONS_00000072 XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 2.22727 no +TCONS_00000073 XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 2.17778 no +TCONS_00000074 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 127495 27320.3 -1.54045 2.07809 0.037701 1.84735 no +TCONS_00000075 XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 2.08511 no +TCONS_00000076 XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 2.04167 no +TCONS_00000077 XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 2 no +TCONS_00000078 XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 1.96 no +TCONS_00000079 XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 1.92157 no +TCONS_00000080 XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 1.88462 no +TCONS_00000081 XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 8.68561e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.706737 no +TCONS_00000082 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 95795.4 28263.3 -1.22065 1.20083 0.229815 0.726513 no +TCONS_00000083 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 449954 89990.7 -1.60944 1.40539 0.159905 0.540368 no +TCONS_00000084 XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 1.84906 no +TCONS_00000085 XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 1.81481 no +TCONS_00000086 XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 1.78182 no +TCONS_00000087 XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 1.75 no +TCONS_00000088 XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 4.27915e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.555293 no +TCONS_00000089 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 281197 0 -1.79769e+308 -1.79769e+308 0.0416319 1.01998 no +TCONS_00000090 XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 5.72196e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.57586 no +TCONS_00000091 XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 2.1224e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.592897 no +TCONS_00000092 XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 3.08417e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.509995 no +TCONS_00000093 XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 3.50371e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.621929 no +TCONS_00000094 XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 1.7193 no +TCONS_00000095 XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 1.68966 no +TCONS_00000096 XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 1.66102 no +TCONS_00000097 XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 1.63333 no +TCONS_00000098 XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 1.60656 no --- a/test-data/cuffdiff_out10.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out10.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant --- a/test-data/cuffdiff_out11.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out11.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant --- a/test-data/cuffdiff_out2.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out2.txt Mon May 09 12:59:42 2011 -0400 @@ -1,88 +1,88 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant -XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 0 0 0 1 no -XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 0 0 0 1 no -XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 no -XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 no -XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 no -XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 no -XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 343500 949159 1.01639 -7.54436 4.55191e-14 yes -XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 328433 254485 -0.255089 96.5921 0 yes -XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 345096 1.0812e+06 1.142 -9.91597 0 yes -XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 0 0 0 0 1 no -XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 0 0 0 1 no -XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 0 0 0 1 no -XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 no -XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 no -XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 0 0 0 1 no -XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 0 0 0 1 no -XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 no -XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 no -XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 no -XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 no -XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 no -XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 no -XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 no -XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 no -XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 0 0 0 0 1 no -XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 no -XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 no -XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 no -XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 0 155328 6.95322e-310 1.79769e+308 0 yes -XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 0 0 0 0 1 no -XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 no -XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 0 0 0 0 1 no -XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 no -XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 0 0 0 1 no -XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 0 0 0 1 no -XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 0 0 0 0 1 no -XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 0 0 0 0 1 no -XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 no -XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 no -XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 0 0 0 0 1 no -XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 no -XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 0 0 0 1 no -XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 0 0 0 0 1 no -XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 0 0 0 1 no -XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 no -XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 0 0 0 1 no -XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 no -XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 no -XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 165459 0 6.95322e-310 2.22507e-308 0 yes -XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 no -XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 no -XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 0 0 0 1 no -XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 no -XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 no -XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 no -XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 no -XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 0 0 0 1 no -XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 0 0 0 0 1 no -XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 163613 0 6.95322e-310 2.22507e-308 0 yes -XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 0 0 0 0 1 no -XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 no -XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 no -XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 no -XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 no -XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 no -XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 no -XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 0 0 0 0 1 no -XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 0 0 0 0 1 no -XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 0 0 0 0 1 no -XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 0 0 0 0 1 no -XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 no -XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 0 0 0 0 1 no -XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 no -XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 0 0 0 0 1 no -XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 no -XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 no -XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 no -XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 no -XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 no -XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 no -XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 no -XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 no -XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 no -XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 no -XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 no -XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 no -XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 no +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant +XLOC_000001 XLOC_000001 - chr1:3204754-3204833 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.456168 no +XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.726474 no +XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 OK 0 0 0 0 1 1.8125 no +XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 OK 0 0 0 0 1 1.07407 no +XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 OK 0 0 0 0 1 1.12987 no +XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 OK 0 0 0 0 1 1.14474 no +XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 OK 2.6642e+06 5.53756e+06 0.731649 -1.14241 0.253284 0.734525 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 OK 227564 240951 0.0571584 -0.115428 0.908106 2.3941 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 OK 1.406e+07 3.74293e+07 0.979119 -0.979283 0.32744 0.918944 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 OK 1.91712e+06 1.91712e+06 0 0 1 1.22535 no +XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.56023e+07 1.79769e+308 1.79769e+308 0.0416323 0.452751 no +XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 2.71123e+06 1.79769e+308 1.79769e+308 0.158655 0.55212 no +XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 OK 0 0 0 0 1 1.26087 no +XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 OK 0 0 0 0 1 1.55357 no +XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 3.93442e+06 1.79769e+308 1.79769e+308 0.0416319 0.603662 no +XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 1.39654e+08 1.79769e+308 1.79769e+308 0.158655 0.811942 no +XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 OK 0 0 0 0 1 1.52632 no +XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 OK 0 0 0 0 1 1.5 no +XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 OK 0 0 0 0 1 1.47458 no +XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 OK 0 0 0 0 1 1.45 no +XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 OK 0 0 0 0 1 1.42623 no +XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 OK 0 0 0 0 1 1.40323 no +XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 OK 0 0 0 0 1 1.38095 no +XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 OK 0 0 0 0 1 1.35938 no +XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 OK 460348 460348 0 0 1 1.33846 no +XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 OK 0 0 0 0 1 1.31818 no +XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 OK 0 0 0 0 1 1.29851 no +XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 OK 0 0 0 0 1 1.27941 no +XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 OK 37206.6 186033 1.60944 -2.18263 0.0290634 2.52852 no +XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 9.11292e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.488751 no +XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 OK 0 0 0 0 1 1.24286 no +XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 8.43162e+06 0 -1.79769e+308 -1.79769e+308 0.0416319 0.724395 no +XLOC_000033 XLOC_000033 - chr1:3211521-3211561 q1 q2 OK 0 0 0 0 1 1.20833 no +XLOC_000034 XLOC_000034 - chr1:3212213-3212292 q1 q2 OK 0 5.42247e+06 1.79769e+308 1.79769e+308 0.0786496 0.526347 no +XLOC_000035 XLOC_000035 - chr1:3212367-3212439 q1 q2 OK 0 1.60978e+07 1.79769e+308 1.79769e+308 0.0416319 0.905494 no +XLOC_000036 XLOC_000036 - chr1:3212717-3212801 q1 q2 OK 2.10791e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.530885 no +XLOC_000037 XLOC_000037 - chr1:3213095-3213192 q1 q2 OK 2.38694e+06 1.19347e+06 -0.693147 0.565952 0.571426 1.55356 no +XLOC_000038 XLOC_000038 - chr1:3240606-3240633 q1 q2 OK 0 0 0 0 1 1.19178 no +XLOC_000039 XLOC_000039 - chr1:3242479-3242512 q1 q2 OK 0 0 0 0 1 1.17568 no +XLOC_000040 XLOC_000040 - chr1:3242633-3242923 q1 q2 OK 27029.9 243269 2.19722 -1.95282 0.0508409 0.491462 no +XLOC_000041 XLOC_000041 - chr1:3242924-3243005 q1 q2 OK 0 0 0 0 1 1.16 no +XLOC_000042 XLOC_000042 - chr1:3243018-3243079 q1 q2 OK 0 1.73712e+07 1.79769e+308 1.79769e+308 0.0786496 0.57021 no +XLOC_000043 XLOC_000043 - chr1:3243108-3243154 q1 q2 OK 4.79961e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.627409 no +XLOC_000044 XLOC_000044 - chr1:3243347-3243401 q1 q2 OK 0 3.32455e+07 1.79769e+308 1.79769e+308 0.0786496 0.622047 no +XLOC_000045 XLOC_000045 - chr1:3254079-3254106 q1 q2 OK 0 0 0 0 1 1.11538 no +XLOC_000046 XLOC_000046 - chr1:3256974-3257011 q1 q2 OK 0 1.34946e+09 1.79769e+308 1.79769e+308 0.0786496 0.427657 no +XLOC_000047 XLOC_000047 - chr1:3277155-3277182 q1 q2 OK 0 0 0 0 1 1.10127 no +XLOC_000048 XLOC_000048 - chr1:3277190-3277218 q1 q2 OK 0 0 0 0 1 1.0875 no +XLOC_000049 XLOC_000049 - chr1:3277913-3278390 q1 q2 OK 127495 27320.3 -1.54045 2.07809 0.037701 1.63999 no +XLOC_000050 XLOC_000050 - chr1:3280117-3280144 q1 q2 OK 0 0 0 0 1 1.06098 no +XLOC_000051 XLOC_000051 - chr1:3280498-3280525 q1 q2 OK 0 0 0 0 1 1.04819 no +XLOC_000052 XLOC_000052 - chr1:3280686-3280741 q1 q2 OK 0 1.49798e+07 1.79769e+308 1.79769e+308 0.158655 0.766834 no +XLOC_000053 XLOC_000053 - chr1:3282504-3282531 q1 q2 OK 0 0 0 0 1 1.03571 no +XLOC_000054 XLOC_000054 - chr1:3282650-3282677 q1 q2 OK 0 0 0 0 1 1.02353 no +XLOC_000055 XLOC_000055 - chr1:3282760-3282832 q1 q2 OK 0 0 0 0 1 1.01163 no +XLOC_000056 XLOC_000056 - chr1:3284966-3284993 q1 q2 OK 0 0 0 0 1 1 no +XLOC_000057 XLOC_000057 - chr1:3290488-3290553 q1 q2 OK 0 6.39146e+06 1.79769e+308 1.79769e+308 0.158655 0.69015 no +XLOC_000058 XLOC_000058 - chr1:3290798-3290859 q1 q2 OK 8.68561e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.657286 no +XLOC_000059 XLOC_000059 - chr1:3290919-3291273 q1 q2 OK 7.79612e+06 1.49584e+06 -1.65094 1.39409 0.16329 0.48987 no +XLOC_000060 XLOC_000060 - chr1:3299443-3299664 q1 q2 OK 449954 89990.7 -1.60944 1.40539 0.159905 0.496847 no +XLOC_000061 XLOC_000061 - chr1:3299691-3299733 q1 q2 OK 0 0 0 0 1 2.23077 no +XLOC_000062 XLOC_000062 - chr1:3300051-3300078 q1 q2 OK 0 0 0 0 1 2.175 no +XLOC_000063 XLOC_000063 - chr1:3307748-3307775 q1 q2 OK 0 0 0 0 1 2.12195 no +XLOC_000064 XLOC_000064 - chr1:3318620-3318647 q1 q2 OK 0 0 0 0 1 2.07143 no +XLOC_000065 XLOC_000065 - chr1:3318999-3319051 q1 q2 OK 0 0 0 0 1 1.97727 no +XLOC_000066 XLOC_000066 - chr1:3330527-3330554 q1 q2 OK 0 0 0 0 1 1.93333 no +XLOC_000067 XLOC_000067 - chr1:3351240-3351311 q1 q2 OK 4.27915e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.600131 no +XLOC_000068 XLOC_000068 - chr1:3355887-3356119 q1 q2 OK 281197 0 -1.79769e+308 -1.79769e+308 0.0416319 1.20732 no +XLOC_000069 XLOC_000069 - chr1:3356180-3356225 q1 q2 OK 5.72196e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.575125 no +XLOC_000070 XLOC_000070 - chr1:3363076-3363176 q1 q2 OK 2.1224e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 0.684252 no +XLOC_000071 XLOC_000071 - chr1:3363214-3363278 q1 q2 OK 0 0 0 0 1 1.58182 no +XLOC_000072 XLOC_000072 - chr1:3363387-3363446 q1 q2 OK 3.08417e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.517429 no +XLOC_000073 XLOC_000073 - chr1:3363753-3363849 q1 q2 OK 0 0 0 0 1 1.61111 no +XLOC_000074 XLOC_000074 - chr1:3364871-3364919 q1 q2 OK 3.50371e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.511222 no +XLOC_000075 XLOC_000075 - chr1:3367135-3367162 q1 q2 OK 0 0 0 0 1 1.64151 no +XLOC_000076 XLOC_000076 - chr1:3367210-3367237 q1 q2 OK 0 0 0 0 1 1.67308 no +XLOC_000077 XLOC_000077 - chr1:3367333-3367382 q1 q2 OK 0 0 0 0 1 1.70588 no +XLOC_000078 XLOC_000078 - chr1:3369580-3369607 q1 q2 OK 0 0 0 0 1 1.74 no +XLOC_000079 XLOC_000079 - chr1:3375001-3375028 q1 q2 OK 0 0 0 0 1 1.77551 no +XLOC_000080 XLOC_000080 - chr1:3377211-3377262 q1 q2 OK 0 0 0 0 1 1.85106 no +XLOC_000081 XLOC_000081 - chr1:3379888-3379915 q1 q2 OK 0 0 0 0 1 1.8913 no +XLOC_000082 XLOC_000082 - chr1:3386739-3386836 q1 q2 OK 0 0 0 0 1 2.02326 no +XLOC_000083 XLOC_000083 - chr1:3391325-3391352 q1 q2 OK 0 0 0 0 1 2.28947 no +XLOC_000084 XLOC_000084 - chr1:3435841-3435880 q1 q2 OK 0 0 0 0 1 2.35135 no +XLOC_000085 XLOC_000085 - chr1:3447761-3447788 q1 q2 OK 0 0 0 0 1 2.41667 no +XLOC_000086 XLOC_000086 - chr1:3450906-3450965 q1 q2 OK 0 0 0 0 1 2.48571 no +XLOC_000087 XLOC_000087 - chr1:3451051-3451109 q1 q2 OK 0 0 0 0 1 2.55882 no --- a/test-data/cuffdiff_out3.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out3.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant --- a/test-data/cuffdiff_out4.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out4.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 ln(fold_change) test_stat p_value q_value significant --- a/test-data/cuffdiff_out5.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out5.txt Mon May 09 12:59:42 2011 -0400 @@ -1,99 +1,99 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -TCONS_00000001 c Xkr4 - - chr1:3204754-3204833 0 0 0 0 0 0 -TCONS_00000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 -TCONS_00000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 -TCONS_00000004 - - - - chr1:3189810-3190789 0 0 0 645918 357201 934636 -TCONS_00000005 - - - - chr1:3189810-3190789 0 0 0 0 0 0 -TCONS_00000006 - - - - chr1:3189810-3190789 0 0 0 0 0 0 -TCONS_00000007 - - - - chr1:3191512-3192077 0 0 0 704881 400219 1.00954e+06 -TCONS_00000008 - - - - chr1:3191512-3192077 0 0 0 0 0 0 -TCONS_00000009 - - - - chr1:3192441-3192494 0 0 0 0 0 0 -TCONS_00000010 - - - - chr1:3192550-3192629 0 0 0 0 0 0 -TCONS_00000011 - - - - chr1:3192731-3192811 0 0 0 0 0 0 -TCONS_00000012 - - - - chr1:3192940-3193042 0 0 0 0 0 0 -TCONS_00000013 - - - - chr1:3194185-3194226 0 0 0 0 0 0 -TCONS_00000014 - - - - chr1:3194302-3194329 0 0 0 0 0 0 -TCONS_00000015 - - - - chr1:3195083-3195110 0 0 0 0 0 0 -TCONS_00000016 - - - - chr1:3195450-3195477 0 0 0 0 0 0 -TCONS_00000017 - - - - chr1:3197089-3197116 0 0 0 0 0 0 -TCONS_00000018 - - - - chr1:3197246-3197273 0 0 0 0 0 0 -TCONS_00000019 - - - - chr1:3197346-3197373 0 0 0 0 0 0 -TCONS_00000020 - - - - chr1:3200022-3200191 0 0 0 0 0 0 -TCONS_00000021 - - - - chr1:3200325-3200352 0 0 0 0 0 0 -TCONS_00000022 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 -TCONS_00000023 - - - - chr1:3201672-3201699 0 0 0 0 0 0 -TCONS_00000024 i Xkr4 - - chr1:3212213-3212292 0 0 0 0 0 0 -TCONS_00000025 i Xkr4 - - chr1:3212367-3212439 0 0 0 0 0 0 -TCONS_00000026 i Xkr4 - - chr1:3213095-3213192 0 0 0 0 0 0 -TCONS_00000027 i Xkr4 - - chr1:3242633-3242923 0 0 0 0 0 0 -TCONS_00000028 i Xkr4 - - chr1:3243018-3243079 0 0 0 0 0 0 -TCONS_00000029 i Xkr4 - - chr1:3243347-3243401 0 0 0 0 0 0 -TCONS_00000030 i Xkr4 - - chr1:3256974-3257011 0 0 0 0 0 0 -TCONS_00000031 i Xkr4 - - chr1:3277190-3277218 0 0 0 0 0 0 -TCONS_00000032 i Xkr4 - - chr1:3277913-3278390 0 0 0 0 0 0 -TCONS_00000033 i Xkr4 - - chr1:3280686-3280741 0 0 0 0 0 0 -TCONS_00000034 i Xkr4 - - chr1:3290488-3290553 0 0 0 0 0 0 -TCONS_00000035 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 -TCONS_00000036 i Xkr4 - - chr1:3290919-3291273 0 0 0 0 0 0 -TCONS_00000037 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 -TCONS_00000038 i Xkr4 - - chr1:3300051-3300078 0 0 0 0 0 0 -TCONS_00000039 i Xkr4 - - chr1:3318999-3319051 0 0 0 0 0 0 -TCONS_00000040 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 -TCONS_00000041 i Xkr4 - - chr1:3363214-3363278 0 0 0 0 0 0 -TCONS_00000042 i Xkr4 - - chr1:3363753-3363849 0 0 0 0 0 0 -TCONS_00000043 i Xkr4 - - chr1:3367135-3367162 0 0 0 0 0 0 -TCONS_00000044 i Xkr4 - - chr1:3367333-3367382 0 0 0 0 0 0 -TCONS_00000045 i Xkr4 - - chr1:3377211-3377262 0 0 0 0 0 0 -TCONS_00000046 i Xkr4 - - chr1:3391325-3391352 0 0 0 0 0 0 -TCONS_00000047 i Xkr4 - - chr1:3435841-3435880 0 0 0 0 0 0 -TCONS_00000048 i Xkr4 - - chr1:3447761-3447788 0 0 0 0 0 0 -TCONS_00000049 i Xkr4 - - chr1:3450906-3450965 0 0 0 0 0 0 -TCONS_00000050 i Xkr4 - - chr1:3451051-3451109 0 0 0 0 0 0 -TCONS_00000051 - - - - chr1:3174765-3174792 0 0 0 0 0 0 -TCONS_00000052 - - - - chr1:3187401-3187428 0 0 0 0 0 0 -TCONS_00000053 - - - - chr1:3188521-3188548 0 0 0 0 0 0 -TCONS_00000054 - - - - chr1:3189810-3190789 343500 342328 344672 303241 270227 336255 -TCONS_00000055 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 -TCONS_00000056 - - - - chr1:3191512-3192077 345096 343921 346271 376320 320653 431986 -TCONS_00000057 - - - - chr1:3192250-3192336 0 0 0 0 0 0 -TCONS_00000058 - - - - chr1:3192649-3192676 0 0 0 0 0 0 -TCONS_00000059 - - - - chr1:3194706-3194733 0 0 0 0 0 0 -TCONS_00000060 - - - - chr1:3197425-3197452 0 0 0 0 0 0 -TCONS_00000061 - - - - chr1:3200430-3200457 0 0 0 0 0 0 -TCONS_00000062 - - - - chr1:3201007-3201039 0 0 0 0 0 0 -TCONS_00000063 - - - - chr1:3201077-3201481 0 0 0 0 0 0 -TCONS_00000064 - - - - chr1:3201596-3201666 0 0 0 0 0 0 -TCONS_00000065 - - - - chr1:3201725-3201809 0 0 0 0 0 0 -TCONS_00000066 i Xkr4 - - chr1:3211521-3211561 0 0 0 0 0 0 -TCONS_00000067 i Xkr4 - - chr1:3212717-3212801 0 0 0 0 0 0 -TCONS_00000068 i Xkr4 - - chr1:3240606-3240633 0 0 0 0 0 0 -TCONS_00000069 i Xkr4 - - chr1:3242479-3242512 0 0 0 0 0 0 -TCONS_00000070 i Xkr4 - - chr1:3242924-3243005 0 0 0 0 0 0 -TCONS_00000071 i Xkr4 - - chr1:3243108-3243154 0 0 0 0 0 0 -TCONS_00000072 i Xkr4 - - chr1:3254079-3254106 0 0 0 0 0 0 -TCONS_00000073 i Xkr4 - - chr1:3277155-3277182 0 0 0 0 0 0 -TCONS_00000074 i Xkr4 - - chr1:3277913-3278390 165459 164646 166273 0 0 0 -TCONS_00000075 i Xkr4 - - chr1:3280117-3280144 0 0 0 0 0 0 -TCONS_00000076 i Xkr4 - - chr1:3280498-3280525 0 0 0 0 0 0 -TCONS_00000077 i Xkr4 - - chr1:3282504-3282531 0 0 0 0 0 0 -TCONS_00000078 i Xkr4 - - chr1:3282650-3282677 0 0 0 0 0 0 -TCONS_00000079 i Xkr4 - - chr1:3282760-3282832 0 0 0 0 0 0 -TCONS_00000080 i Xkr4 - - chr1:3284966-3284993 0 0 0 0 0 0 -TCONS_00000081 i Xkr4 - - chr1:3290798-3290859 0 0 0 0 0 0 -TCONS_00000082 i Xkr4 - - chr1:3290919-3291273 163613 162804 164422 0 0 0 -TCONS_00000083 i Xkr4 - - chr1:3299443-3299664 0 0 0 0 0 0 -TCONS_00000084 i Xkr4 - - chr1:3299691-3299733 0 0 0 0 0 0 -TCONS_00000085 i Xkr4 - - chr1:3307748-3307775 0 0 0 0 0 0 -TCONS_00000086 i Xkr4 - - chr1:3318620-3318647 0 0 0 0 0 0 -TCONS_00000087 i Xkr4 - - chr1:3330527-3330554 0 0 0 0 0 0 -TCONS_00000088 i Xkr4 - - chr1:3351240-3351311 0 0 0 0 0 0 -TCONS_00000089 i Xkr4 - - chr1:3355887-3356119 0 0 0 0 0 0 -TCONS_00000090 i Xkr4 - - chr1:3356180-3356225 0 0 0 0 0 0 -TCONS_00000091 i Xkr4 - - chr1:3363076-3363176 0 0 0 0 0 0 -TCONS_00000092 i Xkr4 - - chr1:3363387-3363446 0 0 0 0 0 0 -TCONS_00000093 i Xkr4 - - chr1:3364871-3364919 0 0 0 0 0 0 -TCONS_00000094 i Xkr4 - - chr1:3367210-3367237 0 0 0 0 0 0 -TCONS_00000095 i Xkr4 - - chr1:3369580-3369607 0 0 0 0 0 0 -TCONS_00000096 i Xkr4 - - chr1:3375001-3375028 0 0 0 0 0 0 -TCONS_00000097 i Xkr4 - - chr1:3379888-3379915 0 0 0 0 0 0 -TCONS_00000098 i Xkr4 - - chr1:3386739-3386836 0 0 0 0 0 0 +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +TCONS_00000001 c Xkr4 XLOC_000001 - - chr1:3204754-3204833 79 - OK 0 0 0 5.42247e+06 0 1.3091e+07 +TCONS_00000002 - - XLOC_000002 - - chr1:3111449-3111490 41 - OK 0 0 0 1.39654e+08 0 4.18963e+08 +TCONS_00000003 - - XLOC_000003 - - chr1:3111545-3111576 31 - OK 0 0 0 0 0 0 +TCONS_00000004 - - XLOC_000007 - - chr1:3189810-3190789 142 - OK 2.49256e+06 0 5.08341e+06 5.29759e+06 686576 9.90861e+06 +TCONS_00000005 - - XLOC_000007 - - chr1:3189810-3190789 31 - OK 0 0 0 0 0 0 +TCONS_00000006 - - XLOC_000007 - - chr1:3189810-3190789 27 - OK 0 0 0 0 0 0 +TCONS_00000007 - - XLOC_000009 - - chr1:3191512-3192077 131 - OK 2.77423e+06 0 5.7461e+06 6.7156e+06 774909 1.26563e+07 +TCONS_00000008 - - XLOC_000009 - - chr1:3191512-3192077 69 - OK 1.11098e+07 0 3.60229e+07 3.03942e+07 0 6.3641e+07 +TCONS_00000009 - - XLOC_000011 - - chr1:3192441-3192494 53 - OK 0 0 0 5.56023e+07 0 1.19806e+08 +TCONS_00000010 - - XLOC_000012 - - chr1:3192550-3192629 79 - OK 0 0 0 2.71123e+06 0 8.1337e+06 +TCONS_00000011 - - XLOC_000014 - - chr1:3192731-3192811 80 - OK 0 0 0 0 0 0 +TCONS_00000012 - - XLOC_000015 - - chr1:3192940-3193042 102 - OK 0 0 0 3.93442e+06 0 8.47748e+06 +TCONS_00000013 - - XLOC_000016 - - chr1:3194185-3194226 41 - OK 0 0 0 1.39654e+08 0 4.18963e+08 +TCONS_00000014 - - XLOC_000017 - - chr1:3194302-3194329 27 - OK 0 0 0 0 0 0 +TCONS_00000015 - - XLOC_000019 - - chr1:3195083-3195110 27 - OK 0 0 0 0 0 0 +TCONS_00000016 - - XLOC_000020 - - chr1:3195450-3195477 27 - OK 0 0 0 0 0 0 +TCONS_00000017 - - XLOC_000021 - - chr1:3197089-3197116 27 - OK 0 0 0 0 0 0 +TCONS_00000018 - - XLOC_000022 - - chr1:3197246-3197273 27 - OK 0 0 0 0 0 0 +TCONS_00000019 - - XLOC_000023 - - chr1:3197346-3197373 27 - OK 0 0 0 0 0 0 +TCONS_00000020 - - XLOC_000025 - - chr1:3200022-3200191 169 - OK 460348 0 991912 460348 0 991912 +TCONS_00000021 - - XLOC_000026 - - chr1:3200325-3200352 27 - OK 0 0 0 0 0 0 +TCONS_00000022 - - XLOC_000029 - - chr1:3201077-3201481 404 - OK 37206.6 0 80169.2 186033 15366.6 356700 +TCONS_00000023 - - XLOC_000031 - - chr1:3201672-3201699 27 - OK 0 0 0 0 0 0 +TCONS_00000024 i Xkr4 XLOC_000034 - - chr1:3212213-3212292 79 - OK 0 0 0 5.42247e+06 0 1.3091e+07 +TCONS_00000025 i Xkr4 XLOC_000035 - - chr1:3212367-3212439 72 - OK 0 0 0 1.60978e+07 0 3.46859e+07 +TCONS_00000026 i Xkr4 XLOC_000037 - - chr1:3213095-3213192 97 - OK 2.38694e+06 0 5.76259e+06 1.19347e+06 0 3.58042e+06 +TCONS_00000027 i Xkr4 XLOC_000040 - - chr1:3242633-3242923 290 - OK 27029.9 0 81089.8 243269 0 494190 +TCONS_00000028 i Xkr4 XLOC_000042 - - chr1:3243018-3243079 61 - OK 0 0 0 1.73712e+07 0 4.19378e+07 +TCONS_00000029 i Xkr4 XLOC_000044 - - chr1:3243347-3243401 54 - OK 0 0 0 3.32455e+07 0 8.02618e+07 +TCONS_00000030 i Xkr4 XLOC_000046 - - chr1:3256974-3257011 37 - OK 0 0 0 1.34946e+09 0 3.25789e+09 +TCONS_00000031 i Xkr4 XLOC_000048 - - chr1:3277190-3277218 28 - OK 0 0 0 0 0 0 +TCONS_00000032 i Xkr4 XLOC_000049 - - chr1:3277913-3278390 27 - OK 0 0 0 0 0 0 +TCONS_00000033 i Xkr4 XLOC_000052 - - chr1:3280686-3280741 55 - OK 0 0 0 1.49798e+07 0 4.49395e+07 +TCONS_00000034 i Xkr4 XLOC_000057 - - chr1:3290488-3290553 65 - OK 0 0 0 6.39146e+06 0 1.91744e+07 +TCONS_00000035 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 84 - OK 6.40392e+06 0 1.55816e+07 0 0 0 +TCONS_00000036 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 98 - OK 1.2964e+06 0 4.55711e+06 1.46758e+06 0 4.47705e+06 +TCONS_00000037 i Xkr4 XLOC_000060 - - chr1:3299443-3299664 55 - OK 0 0 0 0 0 0 +TCONS_00000038 i Xkr4 XLOC_000062 - - chr1:3300051-3300078 27 - OK 0 0 0 0 0 0 +TCONS_00000039 i Xkr4 XLOC_000065 - - chr1:3318999-3319051 52 - OK 0 0 0 0 0 0 +TCONS_00000040 i Xkr4 XLOC_000068 - - chr1:3355887-3356119 27 - OK 0 0 0 0 0 0 +TCONS_00000041 i Xkr4 XLOC_000071 - - chr1:3363214-3363278 64 - OK 0 0 0 0 0 0 +TCONS_00000042 i Xkr4 XLOC_000073 - - chr1:3363753-3363849 96 - OK 0 0 0 0 0 0 +TCONS_00000043 i Xkr4 XLOC_000075 - - chr1:3367135-3367162 27 - OK 0 0 0 0 0 0 +TCONS_00000044 i Xkr4 XLOC_000077 - - chr1:3367333-3367382 49 - OK 0 0 0 0 0 0 +TCONS_00000045 i Xkr4 XLOC_000080 - - chr1:3377211-3377262 51 - OK 0 0 0 0 0 0 +TCONS_00000046 i Xkr4 XLOC_000083 - - chr1:3391325-3391352 27 - OK 0 0 0 0 0 0 +TCONS_00000047 i Xkr4 XLOC_000084 - - chr1:3435841-3435880 39 - OK 0 0 0 0 0 0 +TCONS_00000048 i Xkr4 XLOC_000085 - - chr1:3447761-3447788 27 - OK 0 0 0 0 0 0 +TCONS_00000049 i Xkr4 XLOC_000086 - - chr1:3450906-3450965 59 - OK 0 0 0 0 0 0 +TCONS_00000050 i Xkr4 XLOC_000087 - - chr1:3451051-3451109 58 - OK 0 0 0 0 0 0 +TCONS_00000051 - - XLOC_000004 - - chr1:3174765-3174792 27 - OK 0 0 0 0 0 0 +TCONS_00000052 - - XLOC_000005 - - chr1:3187401-3187428 27 - OK 0 0 0 0 0 0 +TCONS_00000053 - - XLOC_000006 - - chr1:3188521-3188548 27 - OK 0 0 0 0 0 0 +TCONS_00000054 - - XLOC_000007 - - chr1:3189810-3190789 979 - OK 171639 69105.7 274173 239968 172568 307367 +TCONS_00000055 - - XLOC_000008 - - chr1:3190858-3191434 576 - OK 227564 66605.9 388523 240951 73918.5 407983 +TCONS_00000056 - - XLOC_000009 - - chr1:3191512-3192077 565 - OK 175955 38281.8 313628 319423 117942 520904 +TCONS_00000057 - - XLOC_000010 - - chr1:3192250-3192336 86 - OK 1.91712e+06 0 5.75136e+06 1.91712e+06 0 5.75136e+06 +TCONS_00000058 - - XLOC_000013 - - chr1:3192649-3192676 27 - OK 0 0 0 0 0 0 +TCONS_00000059 - - XLOC_000018 - - chr1:3194706-3194733 27 - OK 0 0 0 0 0 0 +TCONS_00000060 - - XLOC_000024 - - chr1:3197425-3197452 27 - OK 0 0 0 0 0 0 +TCONS_00000061 - - XLOC_000027 - - chr1:3200430-3200457 27 - OK 0 0 0 0 0 0 +TCONS_00000062 - - XLOC_000028 - - chr1:3201007-3201039 32 - OK 0 0 0 0 0 0 +TCONS_00000063 - - XLOC_000029 - - chr1:3201077-3201481 27 - OK 0 0 0 0 0 0 +TCONS_00000064 - - XLOC_000030 - - chr1:3201596-3201666 70 - OK 9.11292e+06 0 2.20005e+07 0 0 0 +TCONS_00000065 - - XLOC_000032 - - chr1:3201725-3201809 84 - OK 8.43162e+06 0 1.81676e+07 0 0 0 +TCONS_00000066 i Xkr4 XLOC_000033 - - chr1:3211521-3211561 40 - OK 0 0 0 0 0 0 +TCONS_00000067 i Xkr4 XLOC_000036 - - chr1:3212717-3212801 84 - OK 2.10791e+06 0 6.32372e+06 0 0 0 +TCONS_00000068 i Xkr4 XLOC_000038 - - chr1:3240606-3240633 27 - OK 0 0 0 0 0 0 +TCONS_00000069 i Xkr4 XLOC_000039 - - chr1:3242479-3242512 33 - OK 0 0 0 0 0 0 +TCONS_00000070 i Xkr4 XLOC_000041 - - chr1:3242924-3243005 81 - OK 0 0 0 0 0 0 +TCONS_00000071 i Xkr4 XLOC_000043 - - chr1:3243108-3243154 46 - OK 4.79961e+07 0 1.43988e+08 0 0 0 +TCONS_00000072 i Xkr4 XLOC_000045 - - chr1:3254079-3254106 27 - OK 0 0 0 0 0 0 +TCONS_00000073 i Xkr4 XLOC_000047 - - chr1:3277155-3277182 27 - OK 0 0 0 0 0 0 +TCONS_00000074 i Xkr4 XLOC_000049 - - chr1:3277913-3278390 477 - OK 127495 8942.18 246048 27320.3 0 58867.2 +TCONS_00000075 i Xkr4 XLOC_000050 - - chr1:3280117-3280144 27 - OK 0 0 0 0 0 0 +TCONS_00000076 i Xkr4 XLOC_000051 - - chr1:3280498-3280525 27 - OK 0 0 0 0 0 0 +TCONS_00000077 i Xkr4 XLOC_000053 - - chr1:3282504-3282531 27 - OK 0 0 0 0 0 0 +TCONS_00000078 i Xkr4 XLOC_000054 - - chr1:3282650-3282677 27 - OK 0 0 0 0 0 0 +TCONS_00000079 i Xkr4 XLOC_000055 - - chr1:3282760-3282832 72 - OK 0 0 0 0 0 0 +TCONS_00000080 i Xkr4 XLOC_000056 - - chr1:3284966-3284993 27 - OK 0 0 0 0 0 0 +TCONS_00000081 i Xkr4 XLOC_000058 - - chr1:3290798-3290859 61 - OK 8.68561e+06 0 2.60568e+07 0 0 0 +TCONS_00000082 i Xkr4 XLOC_000059 - - chr1:3290919-3291273 354 - OK 95795.4 0 201253 28263.3 0 76569.5 +TCONS_00000083 i Xkr4 XLOC_000060 - - chr1:3299443-3299664 197 - OK 449954 0 952175 89990.7 0 269972 +TCONS_00000084 i Xkr4 XLOC_000061 - - chr1:3299691-3299733 42 - OK 0 0 0 0 0 0 +TCONS_00000085 i Xkr4 XLOC_000063 - - chr1:3307748-3307775 27 - OK 0 0 0 0 0 0 +TCONS_00000086 i Xkr4 XLOC_000064 - - chr1:3318620-3318647 27 - OK 0 0 0 0 0 0 +TCONS_00000087 i Xkr4 XLOC_000066 - - chr1:3330527-3330554 27 - OK 0 0 0 0 0 0 +TCONS_00000088 i Xkr4 XLOC_000067 - - chr1:3351240-3351311 71 - OK 4.27915e+06 0 1.28374e+07 0 0 0 +TCONS_00000089 i Xkr4 XLOC_000068 - - chr1:3355887-3356119 212 - OK 281197 0 605895 0 0 0 +TCONS_00000090 i Xkr4 XLOC_000069 - - chr1:3356180-3356225 45 - OK 5.72196e+07 0 1.71659e+08 0 0 0 +TCONS_00000091 i Xkr4 XLOC_000070 - - chr1:3363076-3363176 100 - OK 2.1224e+06 0 5.12392e+06 0 0 0 +TCONS_00000092 i Xkr4 XLOC_000072 - - chr1:3363387-3363446 59 - OK 3.08417e+07 0 6.64547e+07 0 0 0 +TCONS_00000093 i Xkr4 XLOC_000074 - - chr1:3364871-3364919 48 - OK 3.50371e+07 0 1.05111e+08 0 0 0 +TCONS_00000094 i Xkr4 XLOC_000076 - - chr1:3367210-3367237 27 - OK 0 0 0 0 0 0 +TCONS_00000095 i Xkr4 XLOC_000078 - - chr1:3369580-3369607 27 - OK 0 0 0 0 0 0 +TCONS_00000096 i Xkr4 XLOC_000079 - - chr1:3375001-3375028 27 - OK 0 0 0 0 0 0 +TCONS_00000097 i Xkr4 XLOC_000081 - - chr1:3379888-3379915 27 - OK 0 0 0 0 0 0 +TCONS_00000098 i Xkr4 XLOC_000082 - - chr1:3386739-3386836 97 - OK 0 0 0 0 0 0 --- a/test-data/cuffdiff_out6.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out6.txt Mon May 09 12:59:42 2011 -0400 @@ -1,88 +1,88 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi -XLOC_000001 - - - - chr1:3204754-3204833 0 0 0 0 0 0 -XLOC_000002 - - - - chr1:3111449-3111490 0 0 0 0 0 0 -XLOC_000003 - - - - chr1:3111545-3111576 0 0 0 0 0 0 -XLOC_000004 - - - - chr1:3174765-3174792 0 0 0 0 0 0 -XLOC_000005 - - - - chr1:3187401-3187428 0 0 0 0 0 0 -XLOC_000006 - - - - chr1:3188521-3188548 0 0 0 0 0 0 -XLOC_000007 - - - - chr1:3189810-3190789 343500 342328 344672 947555 680603 1.21451e+06 -XLOC_000008 - - - - chr1:3190858-3191434 328433 327286 329579 254485 253476 255494 -XLOC_000009 - - - - chr1:3191512-3192077 345096 343921 346271 1.07827e+06 822433 1.33412e+06 -XLOC_000010 - - - - chr1:3192250-3192336 0 0 0 0 0 0 -XLOC_000011 - - - - chr1:3192441-3192494 0 0 0 0 0 0 -XLOC_000012 - - - - chr1:3192550-3192629 0 0 0 0 0 0 -XLOC_000013 - - - - chr1:3192649-3192676 0 0 0 0 0 0 -XLOC_000014 - - - - chr1:3192731-3192811 0 0 0 0 0 0 -XLOC_000015 - - - - chr1:3192940-3193042 0 0 0 0 0 0 -XLOC_000016 - - - - chr1:3194185-3194226 0 0 0 0 0 0 -XLOC_000017 - - - - chr1:3194302-3194329 0 0 0 0 0 0 -XLOC_000018 - - - - chr1:3194706-3194733 0 0 0 0 0 0 -XLOC_000019 - - - - chr1:3195083-3195110 0 0 0 0 0 0 -XLOC_000020 - - - - chr1:3195450-3195477 0 0 0 0 0 0 -XLOC_000021 - - - - chr1:3197089-3197116 0 0 0 0 0 0 -XLOC_000022 - - - - chr1:3197246-3197273 0 0 0 0 0 0 -XLOC_000023 - - - - chr1:3197346-3197373 0 0 0 0 0 0 -XLOC_000024 - - - - chr1:3197425-3197452 0 0 0 0 0 0 -XLOC_000025 - - - - chr1:3200022-3200191 0 0 0 0 0 0 -XLOC_000026 - - - - chr1:3200325-3200352 0 0 0 0 0 0 -XLOC_000027 - - - - chr1:3200430-3200457 0 0 0 0 0 0 -XLOC_000028 - - - - chr1:3201007-3201039 0 0 0 0 0 0 -XLOC_000029 - - - - chr1:3201077-3201481 0 0 0 155328 154540 156116 -XLOC_000030 - - - - chr1:3201596-3201666 0 0 0 0 0 0 -XLOC_000031 - - - - chr1:3201672-3201699 0 0 0 0 0 0 -XLOC_000032 - - - - chr1:3201725-3201809 0 0 0 0 0 0 -XLOC_000033 - - - - chr1:3211521-3211561 0 0 0 0 0 0 -XLOC_000034 - - - - chr1:3212213-3212292 0 0 0 0 0 0 -XLOC_000035 - - - - chr1:3212367-3212439 0 0 0 0 0 0 -XLOC_000036 - - - - chr1:3212717-3212801 0 0 0 0 0 0 -XLOC_000037 - - - - chr1:3213095-3213192 0 0 0 0 0 0 -XLOC_000038 - - - - chr1:3240606-3240633 0 0 0 0 0 0 -XLOC_000039 - - - - chr1:3242479-3242512 0 0 0 0 0 0 -XLOC_000040 - - - - chr1:3242633-3242923 0 0 0 0 0 0 -XLOC_000041 - - - - chr1:3242924-3243005 0 0 0 0 0 0 -XLOC_000042 - - - - chr1:3243018-3243079 0 0 0 0 0 0 -XLOC_000043 - - - - chr1:3243108-3243154 0 0 0 0 0 0 -XLOC_000044 - - - - chr1:3243347-3243401 0 0 0 0 0 0 -XLOC_000045 - - - - chr1:3254079-3254106 0 0 0 0 0 0 -XLOC_000046 - - - - chr1:3256974-3257011 0 0 0 0 0 0 -XLOC_000047 - - - - chr1:3277155-3277182 0 0 0 0 0 0 -XLOC_000048 - - - - chr1:3277190-3277218 0 0 0 0 0 0 -XLOC_000049 - - - - chr1:3277913-3278390 165459 164646 166273 0 0 0 -XLOC_000050 - - - - chr1:3280117-3280144 0 0 0 0 0 0 -XLOC_000051 - - - - chr1:3280498-3280525 0 0 0 0 0 0 -XLOC_000052 - - - - chr1:3280686-3280741 0 0 0 0 0 0 -XLOC_000053 - - - - chr1:3282504-3282531 0 0 0 0 0 0 -XLOC_000054 - - - - chr1:3282650-3282677 0 0 0 0 0 0 -XLOC_000055 - - - - chr1:3282760-3282832 0 0 0 0 0 0 -XLOC_000056 - - - - chr1:3284966-3284993 0 0 0 0 0 0 -XLOC_000057 - - - - chr1:3290488-3290553 0 0 0 0 0 0 -XLOC_000058 - - - - chr1:3290798-3290859 0 0 0 0 0 0 -XLOC_000059 - - - - chr1:3290919-3291273 163613 162804 164422 0 0 0 -XLOC_000060 - - - - chr1:3299443-3299664 0 0 0 0 0 0 -XLOC_000061 - - - - chr1:3299691-3299733 0 0 0 0 0 0 -XLOC_000062 - - - - chr1:3300051-3300078 0 0 0 0 0 0 -XLOC_000063 - - - - chr1:3307748-3307775 0 0 0 0 0 0 -XLOC_000064 - - - - chr1:3318620-3318647 0 0 0 0 0 0 -XLOC_000065 - - - - chr1:3318999-3319051 0 0 0 0 0 0 -XLOC_000066 - - - - chr1:3330527-3330554 0 0 0 0 0 0 -XLOC_000067 - - - - chr1:3351240-3351311 0 0 0 0 0 0 -XLOC_000068 - - - - chr1:3355887-3356119 0 0 0 0 0 0 -XLOC_000069 - - - - chr1:3356180-3356225 0 0 0 0 0 0 -XLOC_000070 - - - - chr1:3363076-3363176 0 0 0 0 0 0 -XLOC_000071 - - - - chr1:3363214-3363278 0 0 0 0 0 0 -XLOC_000072 - - - - chr1:3363387-3363446 0 0 0 0 0 0 -XLOC_000073 - - - - chr1:3363753-3363849 0 0 0 0 0 0 -XLOC_000074 - - - - chr1:3364871-3364919 0 0 0 0 0 0 -XLOC_000075 - - - - chr1:3367135-3367162 0 0 0 0 0 0 -XLOC_000076 - - - - chr1:3367210-3367237 0 0 0 0 0 0 -XLOC_000077 - - - - chr1:3367333-3367382 0 0 0 0 0 0 -XLOC_000078 - - - - chr1:3369580-3369607 0 0 0 0 0 0 -XLOC_000079 - - - - chr1:3375001-3375028 0 0 0 0 0 0 -XLOC_000080 - - - - chr1:3377211-3377262 0 0 0 0 0 0 -XLOC_000081 - - - - chr1:3379888-3379915 0 0 0 0 0 0 -XLOC_000082 - - - - chr1:3386739-3386836 0 0 0 0 0 0 -XLOC_000083 - - - - chr1:3391325-3391352 0 0 0 0 0 0 -XLOC_000084 - - - - chr1:3435841-3435880 0 0 0 0 0 0 -XLOC_000085 - - - - chr1:3447761-3447788 0 0 0 0 0 0 -XLOC_000086 - - - - chr1:3450906-3450965 0 0 0 0 0 0 -XLOC_000087 - - - - chr1:3451051-3451109 0 0 0 0 0 0 +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi +XLOC_000001 - - XLOC_000001 - - chr1:3204754-3204833 - - OK 0 0 0 5.42247e+06 0 1.3091e+07 +XLOC_000002 - - XLOC_000002 - - chr1:3111449-3111490 - - OK 0 0 0 1.39654e+08 0 4.18963e+08 +XLOC_000003 - - XLOC_000003 - - chr1:3111545-3111576 - - OK 0 0 0 0 0 0 +XLOC_000004 - - XLOC_000004 - - chr1:3174765-3174792 - - OK 0 0 0 0 0 0 +XLOC_000005 - - XLOC_000005 - - chr1:3187401-3187428 - - OK 0 0 0 0 0 0 +XLOC_000006 - - XLOC_000006 - - chr1:3188521-3188548 - - OK 0 0 0 0 0 0 +XLOC_000007 - - XLOC_000007 - - chr1:3189810-3190789 - - OK 2.6642e+06 71325.8 5.25708e+06 5.53756e+06 926051 1.01491e+07 +XLOC_000008 - - XLOC_000008 - - chr1:3190858-3191434 - - OK 227564 66605.9 388523 240951 73918.5 407983 +XLOC_000009 - - XLOC_000009 - - chr1:3191512-3192077 - - OK 1.406e+07 0 3.91501e+07 3.74293e+07 3.65533e+06 7.12032e+07 +XLOC_000010 - - XLOC_000010 - - chr1:3192250-3192336 - - OK 1.91712e+06 0 5.75136e+06 1.91712e+06 0 5.75136e+06 +XLOC_000011 - - XLOC_000011 - - chr1:3192441-3192494 - - OK 0 0 0 5.56023e+07 0 1.19806e+08 +XLOC_000012 - - XLOC_000012 - - chr1:3192550-3192629 - - OK 0 0 0 2.71123e+06 0 8.1337e+06 +XLOC_000013 - - XLOC_000013 - - chr1:3192649-3192676 - - OK 0 0 0 0 0 0 +XLOC_000014 - - XLOC_000014 - - chr1:3192731-3192811 - - OK 0 0 0 0 0 0 +XLOC_000015 - - XLOC_000015 - - chr1:3192940-3193042 - - OK 0 0 0 3.93442e+06 0 8.47748e+06 +XLOC_000016 - - XLOC_000016 - - chr1:3194185-3194226 - - OK 0 0 0 1.39654e+08 0 4.18963e+08 +XLOC_000017 - - XLOC_000017 - - chr1:3194302-3194329 - - OK 0 0 0 0 0 0 +XLOC_000018 - - XLOC_000018 - - chr1:3194706-3194733 - - OK 0 0 0 0 0 0 +XLOC_000019 - - XLOC_000019 - - chr1:3195083-3195110 - - OK 0 0 0 0 0 0 +XLOC_000020 - - XLOC_000020 - - chr1:3195450-3195477 - - OK 0 0 0 0 0 0 +XLOC_000021 - - XLOC_000021 - - chr1:3197089-3197116 - - OK 0 0 0 0 0 0 +XLOC_000022 - - XLOC_000022 - - chr1:3197246-3197273 - - OK 0 0 0 0 0 0 +XLOC_000023 - - XLOC_000023 - - chr1:3197346-3197373 - - OK 0 0 0 0 0 0 +XLOC_000024 - - XLOC_000024 - - chr1:3197425-3197452 - - OK 0 0 0 0 0 0 +XLOC_000025 - - XLOC_000025 - - chr1:3200022-3200191 - - OK 460348 0 991912 460348 0 991912 +XLOC_000026 - - XLOC_000026 - - chr1:3200325-3200352 - - OK 0 0 0 0 0 0 +XLOC_000027 - - XLOC_000027 - - chr1:3200430-3200457 - - OK 0 0 0 0 0 0 +XLOC_000028 - - XLOC_000028 - - chr1:3201007-3201039 - - OK 0 0 0 0 0 0 +XLOC_000029 - - XLOC_000029 - - chr1:3201077-3201481 - - OK 37206.6 0 80169.2 186033 15366.6 356700 +XLOC_000030 - - XLOC_000030 - - chr1:3201596-3201666 - - OK 9.11292e+06 0 2.20005e+07 0 0 0 +XLOC_000031 - - XLOC_000031 - - chr1:3201672-3201699 - - OK 0 0 0 0 0 0 +XLOC_000032 - - XLOC_000032 - - chr1:3201725-3201809 - - OK 8.43162e+06 0 1.81676e+07 0 0 0 +XLOC_000033 - - XLOC_000033 - - chr1:3211521-3211561 - - OK 0 0 0 0 0 0 +XLOC_000034 - - XLOC_000034 - - chr1:3212213-3212292 - - OK 0 0 0 5.42247e+06 0 1.3091e+07 +XLOC_000035 - - XLOC_000035 - - chr1:3212367-3212439 - - OK 0 0 0 1.60978e+07 0 3.46859e+07 +XLOC_000036 - - XLOC_000036 - - chr1:3212717-3212801 - - OK 2.10791e+06 0 6.32372e+06 0 0 0 +XLOC_000037 - - XLOC_000037 - - chr1:3213095-3213192 - - OK 2.38694e+06 0 5.76259e+06 1.19347e+06 0 3.58042e+06 +XLOC_000038 - - XLOC_000038 - - chr1:3240606-3240633 - - OK 0 0 0 0 0 0 +XLOC_000039 - - XLOC_000039 - - chr1:3242479-3242512 - - OK 0 0 0 0 0 0 +XLOC_000040 - - XLOC_000040 - - chr1:3242633-3242923 - - OK 27029.9 0 81089.8 243269 0 494190 +XLOC_000041 - - XLOC_000041 - - chr1:3242924-3243005 - - OK 0 0 0 0 0 0 +XLOC_000042 - - XLOC_000042 - - chr1:3243018-3243079 - - OK 0 0 0 1.73712e+07 0 4.19378e+07 +XLOC_000043 - - XLOC_000043 - - chr1:3243108-3243154 - - OK 4.79961e+07 0 1.43988e+08 0 0 0 +XLOC_000044 - - XLOC_000044 - - chr1:3243347-3243401 - - OK 0 0 0 3.32455e+07 0 8.02618e+07 +XLOC_000045 - - XLOC_000045 - - chr1:3254079-3254106 - - OK 0 0 0 0 0 0 +XLOC_000046 - - XLOC_000046 - - chr1:3256974-3257011 - - OK 0 0 0 1.34946e+09 0 3.25789e+09 +XLOC_000047 - - XLOC_000047 - - chr1:3277155-3277182 - - OK 0 0 0 0 0 0 +XLOC_000048 - - XLOC_000048 - - chr1:3277190-3277218 - - OK 0 0 0 0 0 0 +XLOC_000049 - - XLOC_000049 - - chr1:3277913-3278390 - - OK 127495 8942.18 246048 27320.3 0 58867.2 +XLOC_000050 - - XLOC_000050 - - chr1:3280117-3280144 - - OK 0 0 0 0 0 0 +XLOC_000051 - - XLOC_000051 - - chr1:3280498-3280525 - - OK 0 0 0 0 0 0 +XLOC_000052 - - XLOC_000052 - - chr1:3280686-3280741 - - OK 0 0 0 1.49798e+07 0 4.49395e+07 +XLOC_000053 - - XLOC_000053 - - chr1:3282504-3282531 - - OK 0 0 0 0 0 0 +XLOC_000054 - - XLOC_000054 - - chr1:3282650-3282677 - - OK 0 0 0 0 0 0 +XLOC_000055 - - XLOC_000055 - - chr1:3282760-3282832 - - OK 0 0 0 0 0 0 +XLOC_000056 - - XLOC_000056 - - chr1:3284966-3284993 - - OK 0 0 0 0 0 0 +XLOC_000057 - - XLOC_000057 - - chr1:3290488-3290553 - - OK 0 0 0 6.39146e+06 0 1.91744e+07 +XLOC_000058 - - XLOC_000058 - - chr1:3290798-3290859 - - OK 8.68561e+06 0 2.60568e+07 0 0 0 +XLOC_000059 - - XLOC_000059 - - chr1:3290919-3291273 - - OK 7.79612e+06 0 1.75364e+07 1.49584e+06 0 4.5057e+06 +XLOC_000060 - - XLOC_000060 - - chr1:3299443-3299664 - - OK 449954 0 952175 89990.7 0 269972 +XLOC_000061 - - XLOC_000061 - - chr1:3299691-3299733 - - OK 0 0 0 0 0 0 +XLOC_000062 - - XLOC_000062 - - chr1:3300051-3300078 - - OK 0 0 0 0 0 0 +XLOC_000063 - - XLOC_000063 - - chr1:3307748-3307775 - - OK 0 0 0 0 0 0 +XLOC_000064 - - XLOC_000064 - - chr1:3318620-3318647 - - OK 0 0 0 0 0 0 +XLOC_000065 - - XLOC_000065 - - chr1:3318999-3319051 - - OK 0 0 0 0 0 0 +XLOC_000066 - - XLOC_000066 - - chr1:3330527-3330554 - - OK 0 0 0 0 0 0 +XLOC_000067 - - XLOC_000067 - - chr1:3351240-3351311 - - OK 4.27915e+06 0 1.28374e+07 0 0 0 +XLOC_000068 - - XLOC_000068 - - chr1:3355887-3356119 - - OK 281197 0 605895 0 0 0 +XLOC_000069 - - XLOC_000069 - - chr1:3356180-3356225 - - OK 5.72196e+07 0 1.71659e+08 0 0 0 +XLOC_000070 - - XLOC_000070 - - chr1:3363076-3363176 - - OK 2.1224e+06 0 5.12392e+06 0 0 0 +XLOC_000071 - - XLOC_000071 - - chr1:3363214-3363278 - - OK 0 0 0 0 0 0 +XLOC_000072 - - XLOC_000072 - - chr1:3363387-3363446 - - OK 3.08417e+07 0 6.64547e+07 0 0 0 +XLOC_000073 - - XLOC_000073 - - chr1:3363753-3363849 - - OK 0 0 0 0 0 0 +XLOC_000074 - - XLOC_000074 - - chr1:3364871-3364919 - - OK 3.50371e+07 0 1.05111e+08 0 0 0 +XLOC_000075 - - XLOC_000075 - - chr1:3367135-3367162 - - OK 0 0 0 0 0 0 +XLOC_000076 - - XLOC_000076 - - chr1:3367210-3367237 - - OK 0 0 0 0 0 0 +XLOC_000077 - - XLOC_000077 - - chr1:3367333-3367382 - - OK 0 0 0 0 0 0 +XLOC_000078 - - XLOC_000078 - - chr1:3369580-3369607 - - OK 0 0 0 0 0 0 +XLOC_000079 - - XLOC_000079 - - chr1:3375001-3375028 - - OK 0 0 0 0 0 0 +XLOC_000080 - - XLOC_000080 - - chr1:3377211-3377262 - - OK 0 0 0 0 0 0 +XLOC_000081 - - XLOC_000081 - - chr1:3379888-3379915 - - OK 0 0 0 0 0 0 +XLOC_000082 - - XLOC_000082 - - chr1:3386739-3386836 - - OK 0 0 0 0 0 0 +XLOC_000083 - - XLOC_000083 - - chr1:3391325-3391352 - - OK 0 0 0 0 0 0 +XLOC_000084 - - XLOC_000084 - - chr1:3435841-3435880 - - OK 0 0 0 0 0 0 +XLOC_000085 - - XLOC_000085 - - chr1:3447761-3447788 - - OK 0 0 0 0 0 0 +XLOC_000086 - - XLOC_000086 - - chr1:3450906-3450965 - - OK 0 0 0 0 0 0 +XLOC_000087 - - XLOC_000087 - - chr1:3451051-3451109 - - OK 0 0 0 0 0 0 --- a/test-data/cuffdiff_out7.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out7.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status --- a/test-data/cuffdiff_out8.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out8.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -tracking_id class_code nearest_ref_id gene_short_name tss_id locus +tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status --- a/test-data/cuffdiff_out9.txt Mon May 09 11:13:42 2011 -0400 +++ b/test-data/cuffdiff_out9.txt Mon May 09 12:59:42 2011 -0400 @@ -1,1 +1,1 @@ -test_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value significant +test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant --- a/tools/ngs_rna/cuffdiff_wrapper.py Mon May 09 11:13:42 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.py Mon May 09 12:59:42 2011 -0400 @@ -57,7 +57,6 @@ parser.add_option( '-m', '--inner-mean-dist', dest='inner_mean_dist', help='This is the expected (mean) inner distance between mate pairs. \ For, example, for paired end runs with fragments selected at 300bp, \ where each end is 50bp, you should set -r to be 200. The default is 45bp.') - parser.add_option( '-Q', '--min-mapqual', dest='min_mapqual', help='Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0.' ) parser.add_option( '-c', '--min-alignment-count', dest='min_alignment_count', help='The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus\' observed changes don\'t contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads).' ) parser.add_option( '--FDR', dest='FDR', help='The allowed false discovery rate. The default is 0.05.' ) @@ -78,7 +77,7 @@ parser.add_option( "-N", "--quartile-normalization", dest="do_normalization", action="store_true" ) # Bias correction options. - parser.add_option( '-r', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') + parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) @@ -145,8 +144,6 @@ cmd += ( " -p %i" % int ( options.num_threads ) ) if options.inner_mean_dist: cmd += ( " -m %i" % int ( options.inner_mean_dist ) ) - if options.min_mapqual: - cmd += ( " -Q %i" % int ( options.min_mapqual ) ) if options.min_alignment_count: cmd += ( " -c %i" % int ( options.min_alignment_count ) ) if options.FDR: @@ -158,7 +155,7 @@ if options.do_normalization: cmd += ( " -N" ) if options.do_bias_correction: - cmd += ( " -r %s" % seq_path ) + cmd += ( " -b %s" % seq_path ) # Add inputs. # For replicate analysis: group1_rep1,group1_rep2 groupN_rep1,groupN_rep2 --- a/tools/ngs_rna/cuffdiff_wrapper.xml Mon May 09 11:13:42 2011 -0400 +++ b/tools/ngs_rna/cuffdiff_wrapper.xml Mon May 09 12:59:42 2011 -0400 @@ -7,7 +7,6 @@ cuffdiff_wrapper.py --FDR=$fdr --num-threads="4" - --min-mapqual=$min_mapqual --min-alignment-count=$min_alignment_count --isoforms_fpkm_tracking_output=$isoforms_fpkm_tracking @@ -36,7 +35,7 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -r + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: @@ -97,7 +96,6 @@ </conditional><param name="fdr" type="float" value="0.05" label="False Discovery Rate" help="The allowed false discovery rate."/> - <param name="min_mapqual" type="integer" value="0" label="Min SAM Mapping Quality" help="Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number."/><param name="min_alignment_count" type="integer" value="1000" label="Min Alignment Count" help="The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples."/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option> @@ -169,8 +167,8 @@ Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? --> - <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="14"/> - <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="10"/> + <output name="isoforms_exp" file="cuffdiff_out1.txt" lines_diff="56"/> + <output name="genes_exp" file="cuffdiff_out2.txt" lines_diff="30"/><output name="tss_groups_exp" file="cuffdiff_out3.txt"/><output name="cds_exp_fpkm_tracking" file="cuffdiff_out4.txt"/><output name="isoforms_fpkm_tracking" file="cuffdiff_out5.txt" lines_diff="16"/> @@ -238,7 +236,6 @@ -m INT This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. The default is 45bp. -s INT The standard deviation for the distribution on inner distances between mate pairs. The default is 20bp. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -c INT The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not significant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 1,000 fragment alignments (up to 2,000 paired reads). --FDR FLOAT The allowed false discovery rate. The default is 0.05. --num-importance-samples INT Sets the number of importance samples generated for each locus during abundance estimation. Default: 1000 --- a/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 11:13:42 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Mon May 09 12:59:42 2011 -0400 @@ -209,7 +209,6 @@ -I INT The minimum intron length. Cufflinks will not report transcripts with introns longer than this, and will ignore SAM alignments with REF_SKIP CIGAR operations longer than this. The default is 300,000. -F After calculating isoform abundance for a gene, Cufflinks filters out transcripts that it believes are very low abundance, because isoforms expressed at extremely low levels often cannot reliably be assembled, and may even be artifacts of incompletely spliced precursors of processed transcripts. This parameter is also used to filter out introns that have far fewer spliced alignments supporting them. The default is 0.05, or 5% of the most abundant isoform (the major isoform) of the gene. -j Some RNA-Seq protocols produce a significant amount of reads that originate from incompletely spliced transcripts, and these reads can confound the assembly of fully spliced mRNAs. Cufflinks uses this parameter to filter out alignments that lie within the intronic intervals implied by the spliced alignments. The minimum depth of coverage in the intronic region covered by the alignment is divided by the number of spliced reads, and if the result is lower than this parameter value, the intronic alignments are ignored. The default is 5%. - -Q Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0. -G Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript. -N With this option, Cufflinks excludes the contribution of the top 25 percent most highly expressed genes from the number of mapped fragments used in the FPKM denominator. This can improve robustness of differential expression calls for less abundant genes and transcripts. </help> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 09 May '11

09 May '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/92d725e1a392/ changeset: r5521:92d725e1a392 user: kellyv date: 2011-05-09 17:11:23 summary: Adding picard loc file to buildbot setup affected #: 1 file (39 bytes) --- a/buildbot_setup.sh Fri Apr 22 15:10:04 2011 -0400 +++ b/buildbot_setup.sh Mon May 09 11:11:23 2011 -0400 @@ -53,6 +53,7 @@ /galaxy/data/location/perm_base_index.loc /galaxy/data/location/perm_color_index.loc /galaxy/data/location/phastOdds.loc +/galaxy/data/location/picard_index.loc /galaxy/data/location/quality_scores.loc /galaxy/data/location/regions.loc /galaxy/data/location/sam_fa_indices.loc http://bitbucket.org/galaxy/galaxy-central/changeset/5a446b4344f9/ changeset: r5522:5a446b4344f9 user: kellyv date: 2011-05-09 17:13:42 summary: merge affected #: 105 files (1.0 MB) Diff too large to display. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: fubar: Grrrr. Must have index - trying hg19 to see if that pleases the buildbot on picard asmetrics
by Bitbucket 09 May '11

09 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/6690fe6f5e1c/ changeset: r5520:6690fe6f5e1c user: fubar date: 2011-05-09 17:07:01 summary: Grrrr. Must have index - trying hg19 to see if that pleases the buildbot on picard asmetrics affected #: 3 files (1.3 KB) --- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May 09 10:57:14 2011 -0400 +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May 09 11:07:01 2011 -0400 @@ -1,35 +1,34 @@ <style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?xml version="1.0" encoding="utf-8" ?> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy rgPicardASMetrics.py tool output - see http://g2.trac.bx.psu.edu/" /> +<meta name="generator" content="Galaxy CollectAlignmentSummaryMetrics tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardASMetrics.py run at 09/05/2011 10:53:44</h3><b>Your job produced the following output files.</b><hr/> -<table> -<tr><td><a href="AsMetricsIndexed.log">AsMetricsIndexed.log</a></td></tr> +Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:57</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr></table><p/> -<b>No Picard output found - please consult the Picard log above for an explanation</b><b>Picard log</b><hr/> -<pre>[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_4.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/5/dataset_5_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/share/shared/data/genomes/hg18/hg18.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=9109504 -Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (3, 45) - at net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:93) - at net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:135) - at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:78) +<b>Picard log</b><hr/> +<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat returned status 1 and stderr: +[Mon May 09 11:03:51 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_4.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/5/dataset_5_files/hg19.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Mon May 09 11:03:57 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +Runtime.totalMemory()=912588800 +Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 0 < 1 + at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:78) + at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:115) at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:157) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117) at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignmentSummaryMetrics.java:106) + + </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> -generated all outputs reported here, using this command line:<br/> -<pre>java -Xmx2g -jar /share/shared/galaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar REFERENCE_SEQUENCE=/share/shared/data/genomes/hg18/hg18.fasta ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_4.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/5/dataset_5_files/rgPicardASMetrics.out VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp</pre> -</div></body></html> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> --- a/test-data/picard_output_alignment_summary_metrics.html Mon May 09 10:57:14 2011 -0400 +++ b/test-data/picard_output_alignment_summary_metrics.html Mon May 09 11:07:01 2011 -0400 @@ -1,56 +1,62 @@ <style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?xml version="1.0" encoding="utf-8" ?> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy rgPicardASMetrics.py tool output - see http://g2.trac.bx.psu.edu/" /> +<meta name="generator" content="Galaxy CollectAlignmentSummaryMetrics tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardASMetrics.py run at 09/05/2011 10:53:32</h3><b>Your job produced the following output files.</b><hr/> -<table> -<tr><td><a href="rgPicardASMetrics.out">rgPicardASMetrics.out</a></td></tr> -<tr><td><a href="AsMetrics.log">AsMetrics.log</a></td></tr> +Galaxy tool wrapper picard_wrapper at 09/05/2011 11:03:41</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectAlignmentSummaryMetrics.log">CollectAlignmentSummaryMetrics.log</a></td></tr> +<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr></table><p/> -<b>Picard on line resources</b><ul> +<b>Picard on line resources:</b><ul><li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li><li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> -<b>Picard output (transposed for readability)</b><hr/> +<b>Picard output (transposed to make it easier to see)</b><hr/><table cellpadding="3" > -<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Mon May 09 10:53:32 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d1"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr> -<tr class="d0"><td>TOTAL_READS</td><td>4</td></tr> -<tr class="d1"><td>PF_READS</td><td>4</td></tr> -<tr class="d0"><td>PCT_PF_READS</td><td>1</td></tr> -<tr class="d1"><td>PF_NOISE_READS</td><td>0</td></tr> -<tr class="d0"><td>PF_READS_ALIGNED</td><td>4</td></tr> -<tr class="d1"><td>PCT_PF_READS_ALIGNED</td><td>1</td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4</td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404</td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28</td></tr> -<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78</td></tr> -<tr class="d0"><td>PF_HQ_ERROR_RATE</td><td>0.777228</td></tr> -<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101</td></tr> -<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3</td></tr> -<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75</td></tr> -<tr class="d0"><td>BAD_CYCLES</td><td>63</td></tr> -<tr class="d1"><td>STRAND_BALANCE</td><td>0.25</td></tr> -<tr class="d0"><td>PCT_CHIMERAS</td><td>0</td></tr> -<tr class="d1"><td>PCT_ADAPTER +<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Mon May 09 11:03:41 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr> +<tr class="d1"><td>TOTAL_READS</td><td>4</td></tr> +<tr class="d0"><td>PF_READS</td><td>4</td></tr> +<tr class="d1"><td>PCT_PF_READS</td><td>1</td></tr> +<tr class="d0"><td>PF_NOISE_READS</td><td>0</td></tr> +<tr class="d1"><td>PF_READS_ALIGNED</td><td>4</td></tr> +<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1</td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_READS</td><td>4</td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_BASES</td><td>404</td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28</td></tr> +<tr class="d0"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78</td></tr> +<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228</td></tr> +<tr class="d0"><td>MEAN_READ_LENGTH</td><td>101</td></tr> +<tr class="d1"><td>READS_ALIGNED_IN_PAIRS</td><td>3</td></tr> +<tr class="d0"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75</td></tr> +<tr class="d1"><td>BAD_CYCLES</td><td>63</td></tr> +<tr class="d0"><td>STRAND_BALANCE</td><td>0.25</td></tr> +<tr class="d1"><td>PCT_CHIMERAS</td><td>0</td></tr> +<tr class="d0"><td>PCT_ADAPTER </td><td>0 </td></tr></table><b>Picard log</b><hr/> -<pre>[Mon May 09 10:53:32 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -WARNING 2011-05-09 10:53:32 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. -[Mon May 09 10:53:32 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsDXFFCP.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsDXFFCP.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and stderr: +[Mon May 09 11:03:40 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/CollectAlignmentSummaryMetricsDXFFCP.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsDXFFCP.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=false NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Mon May 09 11:03:40 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary done. Runtime.totalMemory()=9109504 + + +## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_2.dat returned status 0 and stderr: +[Mon May 09 11:03:41 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBrCiH5/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsDXFFCP.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +WARNING 2011-05-09 11:03:41 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. +[Mon May 09 11:03:41 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +Runtime.totalMemory()=9109504 + + </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> -generated all outputs reported here, using this command line:<br/> -<pre>java -Xmx2g -jar /share/shared/galaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp</pre> -</div></body></html> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> --- a/tools/picard/rgPicardASMetrics.xml Mon May 09 10:57:14 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Mon May 09 11:07:01 2011 -0400 @@ -70,7 +70,8 @@ <param name="adaptors" value="" /><param name="maxinsert" value="100000" /><param name="refGenomeSource" value="indexed" /> - <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg18" /> + <param name="index" value="hg19" /> + <param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg19" /><output name="html_file" file="picard_output_AsMetrics_indexed_hg18_sorted_pair.html" ftype="html" lines_diff="50"/></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: another change to try get around the buildbot for picard asmetrics
by Bitbucket 09 May '11

09 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ba0df93a1d0b/ changeset: r5519:ba0df93a1d0b user: fubar date: 2011-05-09 16:57:14 summary: another change to try get around the buildbot for picard asmetrics affected #: 3 files (1.4 KB) --- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May 09 09:57:21 2011 -0400 +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Mon May 09 10:57:14 2011 -0400 @@ -1,31 +1,35 @@ <style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?xml version="1.0" encoding="utf-8" ?> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<meta name="generator" content="Galaxy rgPicardASMetrics.py tool output - see http://g2.trac.bx.psu.edu/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -Galaxy tool wrapper run picard_wrapper at 06/05/2011 22:54:31</b><br/><b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/hg18.fasta_fake.fasta TMP_DIR=/tmp INPUT=/tmp/6728809.1.all.q/tmps-Xqx9/database/files/000/dataset_91.dat returned status 1 and stderr: -[Fri May 06 22:54:22 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/tmp/6728809.1.all.q/tmps-Xqx9/database/files/000/dataset_91.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/hg18.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Fri May 06 22:54:30 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=910163968 -Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 0 < 1 - at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:78) - at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:115) +<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardASMetrics.py run at 09/05/2011 10:53:44</h3><b>Your job produced the following output files.</b><hr/> +<table> +<tr><td><a href="AsMetricsIndexed.log">AsMetricsIndexed.log</a></td></tr> +</table><p/> +<b>No Picard output found - please consult the Picard log above for an explanation</b><b>Picard log</b><hr/> +<pre>[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_4.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/5/dataset_5_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/share/shared/data/genomes/hg18/hg18.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Mon May 09 10:53:44 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +Runtime.totalMemory()=9109504 +Exception in thread "main" net.sf.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (3, 45) + at net.sf.samtools.util.SequenceUtil.assertSequenceListsEqual(SequenceUtil.java:93) + at net.sf.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(SequenceUtil.java:135) + at net.sf.picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:78) at net.sf.picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:54) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:157) at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:117) at net.sf.picard.analysis.CollectAlignmentSummaryMetrics.main(CollectAlignmentSummaryMetrics.java:106) +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here, using this command line:<br/> +<pre>java -Xmx2g -jar /share/shared/galaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar REFERENCE_SEQUENCE=/share/shared/data/genomes/hg18/hg18.fasta ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_4.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/5/dataset_5_files/rgPicardASMetrics.out VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp</pre> +</div></body></html> - -</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> -generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> - --- a/test-data/picard_output_alignment_summary_metrics.html Mon May 09 09:57:21 2011 -0400 +++ b/test-data/picard_output_alignment_summary_metrics.html Mon May 09 10:57:14 2011 -0400 @@ -1,61 +1,56 @@ <style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?xml version="1.0" encoding="utf-8" ?> + tr.d0 td {background-color: oldlace; color: black;} + tr.d1 td {background-color: aliceblue; color: black;} + </style><?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /> +<meta name="generator" content="Galaxy rgPicardASMetrics.py tool output - see http://g2.trac.bx.psu.edu/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -Galaxy tool wrapper run picard_wrapper at 08/05/2011 21:08:01</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> -<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr> +<h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardASMetrics.py run at 09/05/2011 10:53:32</h3><b>Your job produced the following output files.</b><hr/> +<table> +<tr><td><a href="rgPicardASMetrics.out">rgPicardASMetrics.out</a></td></tr> +<tr><td><a href="AsMetrics.log">AsMetrics.log</a></td></tr></table><p/> -<b>Picard on line resources:</b><ul> +<b>Picard on line resources</b><ul><li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li><li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/> -<b>Picard output (transposed to make it easier to see)</b><hr/> +<b>Picard output (transposed for readability)</b><hr/><table cellpadding="3" > -<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpNfOoN9/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sun May 08 21:08:00 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr> -<tr class="d1"><td>TOTAL_READS</td><td>4</td></tr> -<tr class="d0"><td>PF_READS</td><td>4</td></tr> -<tr class="d1"><td>PCT_PF_READS</td><td>1</td></tr> -<tr class="d0"><td>PF_NOISE_READS</td><td>0</td></tr> -<tr class="d1"><td>PF_READS_ALIGNED</td><td>4</td></tr> -<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1</td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_READS</td><td>4</td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_BASES</td><td>404</td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28</td></tr> -<tr class="d0"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78</td></tr> -<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228</td></tr> -<tr class="d0"><td>MEAN_READ_LENGTH</td><td>101</td></tr> -<tr class="d1"><td>READS_ALIGNED_IN_PAIRS</td><td>3</td></tr> -<tr class="d0"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75</td></tr> -<tr class="d1"><td>BAD_CYCLES</td><td>63</td></tr> -<tr class="d0"><td>STRAND_BALANCE</td><td>0.25</td></tr> -<tr class="d1"><td>PCT_CHIMERAS</td><td>0</td></tr> -<tr class="d0"><td>PCT_ADAPTER +<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Mon May 09 10:53:32 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d1"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr> +<tr class="d0"><td>TOTAL_READS</td><td>4</td></tr> +<tr class="d1"><td>PF_READS</td><td>4</td></tr> +<tr class="d0"><td>PCT_PF_READS</td><td>1</td></tr> +<tr class="d1"><td>PF_NOISE_READS</td><td>0</td></tr> +<tr class="d0"><td>PF_READS_ALIGNED</td><td>4</td></tr> +<tr class="d1"><td>PCT_PF_READS_ALIGNED</td><td>1</td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4</td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404</td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28</td></tr> +<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78</td></tr> +<tr class="d0"><td>PF_HQ_ERROR_RATE</td><td>0.777228</td></tr> +<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101</td></tr> +<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3</td></tr> +<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75</td></tr> +<tr class="d0"><td>BAD_CYCLES</td><td>63</td></tr> +<tr class="d1"><td>STRAND_BALANCE</td><td>0.25</td></tr> +<tr class="d0"><td>PCT_CHIMERAS</td><td>0</td></tr> +<tr class="d1"><td>PCT_ADAPTER </td><td>0 </td></tr></table><b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and stderr: -[Sun May 08 21:08:00 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=false NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Sun May 08 21:08:00 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary done. +<pre>[Mon May 09 10:53:32 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +WARNING 2011-05-09 10:53:32 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. +[Mon May 09 10:53:32 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. Runtime.totalMemory()=9109504 +</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> +generated all outputs reported here, using this command line:<br/> +<pre>java -Xmx2g -jar /share/shared/galaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar REFERENCE_SEQUENCE=/export/tmp/tmpp-lP_s/database/files/000/dataset_1.dat.fasta ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 INPUT=/export/tmp/tmpp-lP_s/database/files/000/dataset_2.dat OUTPUT=/share/shared/galaxy/database/job_working_directory/3/dataset_3_files/rgPicardASMetrics.out VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp</pre> +</div></body></html> - -## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpNfOoN9/database/files/000/dataset_2.dat returned status 0 and stderr: -[Sun May 08 21:08:00 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpNfOoN9/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -WARNING 2011-05-08 21:08:00 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. -[Sun May 08 21:08:01 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. -Runtime.totalMemory()=9109504 - - -</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> -generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> - --- a/tools/picard/rgPicardASMetrics.xml Mon May 09 09:57:21 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Mon May 09 10:57:14 2011 -0400 @@ -70,7 +70,6 @@ <param name="adaptors" value="" /><param name="maxinsert" value="100000" /><param name="refGenomeSource" value="indexed" /> - <param name="index" value="hg18" /><param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg18" /><output name="html_file" file="picard_output_AsMetrics_indexed_hg18_sorted_pair.html" ftype="html" lines_diff="50"/></test> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Update Cuffcompare test-data for v1.0.1
by Bitbucket 09 May '11

09 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/b1d08298cb4c/ changeset: r5518:b1d08298cb4c user: jgoecks date: 2011-05-09 15:57:21 summary: Update Cuffcompare test-data for v1.0.1 affected #: 6 files (5.0 KB) --- a/test-data/cuffcompare_out1.tmap Sun May 08 22:16:18 2011 -0400 +++ b/test-data/cuffcompare_out1.tmap Mon May 09 09:57:21 2011 -0400 @@ -1,51 +1,51 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id -- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 -- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 -- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 -- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 -- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 -- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 -Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 -Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 -Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 -Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 -Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 -Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 -Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 -Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 -- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 -- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 -- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 -- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 -- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 -- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 -- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 -- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 -- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 -- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 -- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 -- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 -- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 -- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 -- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 -- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 - +- - u CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 - +- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - +- - u CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 - +- - u CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 - +- - u CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 - +- - u CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 - +- - u CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 - +- - u CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 - +- - u CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 - +- - u CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 - +- - u CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 - +- - u CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 - +- - u CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 - +- - u CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 - +- - u CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 - +- - u CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 - +- - u CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 - +- - u CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 - +- - u CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 - +- - u CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 - +- - u CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 - +- - u CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 - --- a/test-data/cuffcompare_out2.refmap Sun May 08 22:16:18 2011 -0400 +++ b/test-data/cuffcompare_out2.refmap Mon May 09 09:57:21 2011 -0400 @@ -1,2 +1,1 @@ ref_gene_id ref_id class_code cuff_id_list -Xkr4 Xkr4 c CUFF.13|CUFF.13.1 --- a/test-data/cuffcompare_out3.tmap Sun May 08 22:16:18 2011 -0400 +++ b/test-data/cuffcompare_out3.tmap Mon May 09 09:57:21 2011 -0400 @@ -1,51 +1,51 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id -- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 -- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 -- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 -- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 -- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 -- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 -- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 -- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 -- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 -- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 -- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 -- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 -- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 -- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 -- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 -- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 -Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 -Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 -Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 -Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 -Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 -Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 -Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 -Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 -Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 -Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 -Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 -Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 -Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 -Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 +ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len +- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - +- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - +- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - +- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - +- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - +- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - +- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - +- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - +- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - +- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - +- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - +- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - +- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - +- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - +- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - +- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - +- - u CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 - +- - u CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 - +- - u CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 - +- - u CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 - +- - u CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 - +- - u CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 - +- - u CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 - +- - u CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 - +- - u CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 - +- - u CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 - +- - u CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 - +- - u CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 - +- - u CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 - +- - u CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 - +- - u CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 - +- - u CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 - +- - u CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 - +- - u CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 - +- - u CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 - +- - u CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 - +- - u CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 - +- - u CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 - +- - u CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 - +- - u CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 - +- - u CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 - +- - u CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 - +- - u CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 - +- - u CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 - +- - u CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 - +- - u CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 - +- - u CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 - +- - u CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 - +- - u CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 - +- - u CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 - --- a/test-data/cuffcompare_out5.gtf Sun May 08 22:16:18 2011 -0400 +++ b/test-data/cuffcompare_out5.gtf Mon May 09 09:57:21 2011 -0400 @@ -1,98 +1,90 @@ -chr1 Cufflinks exon 3204755 3204833 . - . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; -chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; -chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; -chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; -chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; -chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; -chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; -chr1 Cufflinks exon 3189900 3190041 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000004"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; -chr1 Cufflinks exon 3190273 3190303 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000005"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; -chr1 Cufflinks exon 3190455 3190481 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000006"; exon_number "1"; oId "CUFF.33.1"; class_code "u"; -chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; -chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; -chr1 Cufflinks exon 3191539 3191669 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000007"; exon_number "1"; oId "CUFF.35.1"; class_code "u"; -chr1 Cufflinks exon 3191877 3191945 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000008"; exon_number "1"; oId "CUFF.37.1"; class_code "u"; -chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; -chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; -chr1 Cufflinks exon 3192551 3192629 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; -chr1 Cufflinks exon 3192650 3192676 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; -chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; -chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; -chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; -chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; -chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; -chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; -chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; -chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; -chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; -chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; -chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; -chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "."; -chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; -chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000061"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; -chr1 Cufflinks exon 3201008 3201039 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; -chr1 Cufflinks exon 3201078 3201481 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; -chr1 Cufflinks exon 3201161 3201187 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; -chr1 Cufflinks exon 3201597 3201666 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000064"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; -chr1 Cufflinks exon 3201673 3201699 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; -chr1 Cufflinks exon 3201726 3201809 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; -chr1 Cufflinks exon 3211522 3211561 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3212214 3212292 . . . gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3212368 3212439 . . . gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3212718 3212801 . . . gene_id "XLOC_000036"; transcript_id "TCONS_00000067"; exon_number "1"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3213096 3213192 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3240607 3240633 . . . gene_id "XLOC_000038"; transcript_id "TCONS_00000068"; exon_number "1"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3242480 3242512 . . . gene_id "XLOC_000039"; transcript_id "TCONS_00000069"; exon_number "1"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3242634 3242923 . . . gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3242925 3243005 . . . gene_id "XLOC_000041"; transcript_id "TCONS_00000070"; exon_number "1"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3243019 3243079 . . . gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3243109 3243154 . . . gene_id "XLOC_000043"; transcript_id "TCONS_00000071"; exon_number "1"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3243348 3243401 . . . gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3254080 3254106 . . . gene_id "XLOC_000045"; transcript_id "TCONS_00000072"; exon_number "1"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3256975 3257011 . . . gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3277156 3277182 . . . gene_id "XLOC_000047"; transcript_id "TCONS_00000073"; exon_number "1"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3277191 3277218 . . . gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3277914 3278390 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000074"; exon_number "1"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3278237 3278263 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000032"; exon_number "1"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3280118 3280144 . . . gene_id "XLOC_000050"; transcript_id "TCONS_00000075"; exon_number "1"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3280499 3280525 . . . gene_id "XLOC_000051"; transcript_id "TCONS_00000076"; exon_number "1"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3280687 3280741 . . . gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3282505 3282531 . . . gene_id "XLOC_000053"; transcript_id "TCONS_00000077"; exon_number "1"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3282651 3282677 . . . gene_id "XLOC_000054"; transcript_id "TCONS_00000078"; exon_number "1"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3282761 3282832 . . . gene_id "XLOC_000055"; transcript_id "TCONS_00000079"; exon_number "1"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3284967 3284993 . . . gene_id "XLOC_000056"; transcript_id "TCONS_00000080"; exon_number "1"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3290489 3290553 . . . gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3290799 3290859 . . . gene_id "XLOC_000058"; transcript_id "TCONS_00000081"; exon_number "1"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3290920 3291273 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000082"; exon_number "1"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3290940 3291023 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000035"; exon_number "1"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3291089 3291186 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000036"; exon_number "1"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3299444 3299640 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000083"; exon_number "1"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3299610 3299664 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3299692 3299733 . . . gene_id "XLOC_000061"; transcript_id "TCONS_00000084"; exon_number "1"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3300052 3300078 . . . gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3307749 3307775 . . . gene_id "XLOC_000063"; transcript_id "TCONS_00000085"; exon_number "1"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3318621 3318647 . . . gene_id "XLOC_000064"; transcript_id "TCONS_00000086"; exon_number "1"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3319000 3319051 . . . gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3330528 3330554 . . . gene_id "XLOC_000066"; transcript_id "TCONS_00000087"; exon_number "1"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3351241 3351311 . . . gene_id "XLOC_000067"; transcript_id "TCONS_00000088"; exon_number "1"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3355888 3355914 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3355908 3356119 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000089"; exon_number "1"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3356181 3356225 . . . gene_id "XLOC_000069"; transcript_id "TCONS_00000090"; exon_number "1"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3363077 3363176 . . . gene_id "XLOC_000070"; transcript_id "TCONS_00000091"; exon_number "1"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3363215 3363278 . . . gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3363388 3363446 . . . gene_id "XLOC_000072"; transcript_id "TCONS_00000092"; exon_number "1"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3363754 3363849 . . . gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3364872 3364919 . . . gene_id "XLOC_000074"; transcript_id "TCONS_00000093"; exon_number "1"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3367136 3367162 . . . gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3367211 3367237 . . . gene_id "XLOC_000076"; transcript_id "TCONS_00000094"; exon_number "1"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3367334 3367382 . . . gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3369581 3369607 . . . gene_id "XLOC_000078"; transcript_id "TCONS_00000095"; exon_number "1"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3375002 3375028 . . . gene_id "XLOC_000079"; transcript_id "TCONS_00000096"; exon_number "1"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3377212 3377262 . . . gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3379889 3379915 . . . gene_id "XLOC_000081"; transcript_id "TCONS_00000097"; exon_number "1"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3386740 3386836 . . . gene_id "XLOC_000082"; transcript_id "TCONS_00000098"; exon_number "1"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3391326 3391352 . . . gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3435842 3435880 . . . gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3447762 3447788 . . . gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3450907 3450965 . . . gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; -chr1 Cufflinks exon 3451052 3451109 . . . gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; +chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; +chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; +chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000003"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; +chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000004"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; +chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000005"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; +chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000006"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; +chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; +chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; +chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; +chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000008"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; +chr1 Cufflinks exon 3192551 3192629 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; +chr1 Cufflinks exon 3192650 3192676 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; +chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; +chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; +chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; +chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; +chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; +chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; +chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; +chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; +chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; +chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; +chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; +chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; +chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; +chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; +chr1 Cufflinks exon 3201008 3201039 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; +chr1 Cufflinks exon 3201078 3201481 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; +chr1 Cufflinks exon 3201597 3201666 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; +chr1 Cufflinks exon 3201673 3201699 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; +chr1 Cufflinks exon 3201726 3201809 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; +chr1 Cufflinks exon 3204755 3204833 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; +chr1 Cufflinks exon 3211522 3211561 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; oId "CUFF.33.1"; class_code "u"; +chr1 Cufflinks exon 3212214 3212292 . . . gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; +chr1 Cufflinks exon 3212368 3212439 . . . gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; +chr1 Cufflinks exon 3212718 3212801 . . . gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; oId "CUFF.35.1"; class_code "u"; +chr1 Cufflinks exon 3213096 3213192 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; +chr1 Cufflinks exon 3213119 3213242 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; oId "CUFF.37.1"; class_code "u"; +chr1 Cufflinks exon 3240607 3240633 . . . gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; +chr1 Cufflinks exon 3242480 3242512 . . . gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; +chr1 Cufflinks exon 3242634 3242923 . . . gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; oId "CUFF.25.1"; class_code "u"; +chr1 Cufflinks exon 3242925 3243005 . . . gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; +chr1 Cufflinks exon 3243019 3243079 . . . gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; +chr1 Cufflinks exon 3243109 3243154 . . . gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; +chr1 Cufflinks exon 3243348 3243401 . . . gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; oId "CUFF.23.1"; class_code "u"; +chr1 Cufflinks exon 3254080 3254106 . . . gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; +chr1 Cufflinks exon 3256975 3257011 . . . gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; oId "CUFF.27.1"; class_code "u"; +chr1 Cufflinks exon 3277156 3277182 . . . gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; +chr1 Cufflinks exon 3277191 3277218 . . . gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; oId "CUFF.61.1"; class_code "u"; +chr1 Cufflinks exon 3277914 3278390 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; +chr1 Cufflinks exon 3280118 3280144 . . . gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; +chr1 Cufflinks exon 3280499 3280525 . . . gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; +chr1 Cufflinks exon 3280687 3280741 . . . gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; oId "CUFF.65.1"; class_code "u"; +chr1 Cufflinks exon 3282505 3282531 . . . gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; +chr1 Cufflinks exon 3282651 3282677 . . . gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; +chr1 Cufflinks exon 3282761 3282832 . . . gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; oId "CUFF.61.1"; class_code "u"; +chr1 Cufflinks exon 3284967 3284993 . . . gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; oId "CUFF.63.1"; class_code "u"; +chr1 Cufflinks exon 3290489 3290553 . . . gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; oId "CUFF.67.1"; class_code "u"; +chr1 Cufflinks exon 3290799 3290859 . . . gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; oId "CUFF.65.1"; class_code "u"; +chr1 Cufflinks exon 3290920 3291273 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; oId "CUFF.69.1"; class_code "u"; +chr1 Cufflinks exon 3299444 3299640 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; oId "CUFF.67.1"; class_code "u"; +chr1 Cufflinks exon 3299610 3299664 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; oId "CUFF.73.1"; class_code "u"; +chr1 Cufflinks exon 3299692 3299733 . . . gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; oId "CUFF.71.1"; class_code "u"; +chr1 Cufflinks exon 3300052 3300078 . . . gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; oId "CUFF.75.1"; class_code "u"; +chr1 Cufflinks exon 3307749 3307775 . . . gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; oId "CUFF.73.1"; class_code "u"; +chr1 Cufflinks exon 3318621 3318647 . . . gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; oId "CUFF.75.1"; class_code "u"; +chr1 Cufflinks exon 3319000 3319051 . . . gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; oId "CUFF.77.1"; class_code "u"; +chr1 Cufflinks exon 3330528 3330554 . . . gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; oId "CUFF.77.1"; class_code "u"; +chr1 Cufflinks exon 3351241 3351311 . . . gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; oId "CUFF.79.1"; class_code "u"; +chr1 Cufflinks exon 3355888 3355914 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; oId "CUFF.79.1"; class_code "u"; +chr1 Cufflinks exon 3355908 3356119 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; oId "CUFF.81.1"; class_code "u"; +chr1 Cufflinks exon 3356181 3356225 . . . gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; oId "CUFF.83.1"; class_code "u"; +chr1 Cufflinks exon 3363077 3363176 . . . gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; oId "CUFF.85.1"; class_code "u"; +chr1 Cufflinks exon 3363215 3363278 . . . gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; oId "CUFF.81.1"; class_code "u"; +chr1 Cufflinks exon 3363388 3363446 . . . gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; oId "CUFF.87.1"; class_code "u"; +chr1 Cufflinks exon 3363754 3363849 . . . gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; oId "CUFF.83.1"; class_code "u"; +chr1 Cufflinks exon 3364872 3364919 . . . gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; oId "CUFF.89.1"; class_code "u"; +chr1 Cufflinks exon 3367136 3367162 . . . gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; oId "CUFF.85.1"; class_code "u"; +chr1 Cufflinks exon 3367211 3367237 . . . gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; oId "CUFF.91.1"; class_code "u"; +chr1 Cufflinks exon 3367334 3367382 . . . gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; oId "CUFF.87.1"; class_code "u"; +chr1 Cufflinks exon 3369581 3369607 . . . gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; oId "CUFF.93.1"; class_code "u"; +chr1 Cufflinks exon 3375002 3375028 . . . gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; oId "CUFF.95.1"; class_code "u"; +chr1 Cufflinks exon 3377212 3377262 . . . gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; oId "CUFF.89.1"; class_code "u"; +chr1 Cufflinks exon 3379889 3379915 . . . gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; oId "CUFF.97.1"; class_code "u"; +chr1 Cufflinks exon 3386740 3386836 . . . gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; oId "CUFF.99.1"; class_code "u"; +chr1 Cufflinks exon 3391326 3391352 . . . gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; oId "CUFF.91.1"; class_code "u"; +chr1 Cufflinks exon 3435842 3435880 . . . gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; oId "CUFF.93.1"; class_code "u"; +chr1 Cufflinks exon 3447762 3447788 . . . gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; oId "CUFF.95.1"; class_code "u"; +chr1 Cufflinks exon 3450907 3450965 . . . gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; oId "CUFF.97.1"; class_code "u"; +chr1 Cufflinks exon 3451052 3451109 . . . gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; oId "CUFF.99.1"; class_code "u"; --- a/test-data/cuffcompare_out6.tracking Sun May 08 22:16:18 2011 -0400 +++ b/test-data/cuffcompare_out6.tracking Mon May 09 09:57:21 2011 -0400 @@ -1,98 +1,100 @@ -TCONS_00000001 XLOC_000001 Xkr4|Xkr4 c q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000003 XLOC_000003 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - -TCONS_00000004 XLOC_000007 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - -TCONS_00000005 XLOC_000007 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - -TCONS_00000006 XLOC_000007 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - -TCONS_00000007 XLOC_000009 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - -TCONS_00000008 XLOC_000009 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - -TCONS_00000009 XLOC_000011 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - -TCONS_00000010 XLOC_000012 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000011 XLOC_000014 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - -TCONS_00000012 XLOC_000015 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - -TCONS_00000013 XLOC_000016 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000014 XLOC_000017 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000015 XLOC_000019 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000016 XLOC_000020 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000017 XLOC_000021 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000018 XLOC_000022 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000019 XLOC_000023 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000020 XLOC_000025 - . q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|169 q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|88 -TCONS_00000021 XLOC_000026 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000022 XLOC_000029 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|- - -TCONS_00000023 XLOC_000031 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000024 XLOC_000034 Xkr4|Xkr4 i q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000025 XLOC_000035 Xkr4|Xkr4 i q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - -TCONS_00000026 XLOC_000037 Xkr4|Xkr4 i q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|97 q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|124 -TCONS_00000027 XLOC_000040 Xkr4|Xkr4 i q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - -TCONS_00000028 XLOC_000042 Xkr4|Xkr4 i q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - -TCONS_00000029 XLOC_000044 Xkr4|Xkr4 i q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - -TCONS_00000030 XLOC_000046 Xkr4|Xkr4 i q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - -TCONS_00000031 XLOC_000048 Xkr4|Xkr4 i q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - -TCONS_00000032 XLOC_000049 Xkr4|Xkr4 i q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000033 XLOC_000052 Xkr4|Xkr4 i q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000034 XLOC_000057 Xkr4|Xkr4 i q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - -TCONS_00000035 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - -TCONS_00000036 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - -TCONS_00000037 XLOC_000060 Xkr4|Xkr4 i q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000038 XLOC_000062 Xkr4|Xkr4 i q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000039 XLOC_000065 Xkr4|Xkr4 i q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - -TCONS_00000040 XLOC_000068 Xkr4|Xkr4 i q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000041 XLOC_000071 Xkr4|Xkr4 i q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - -TCONS_00000042 XLOC_000073 Xkr4|Xkr4 i q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - -TCONS_00000043 XLOC_000075 Xkr4|Xkr4 i q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000044 XLOC_000077 Xkr4|Xkr4 i q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - -TCONS_00000045 XLOC_000080 Xkr4|Xkr4 i q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - -TCONS_00000046 XLOC_000083 Xkr4|Xkr4 i q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000047 XLOC_000084 Xkr4|Xkr4 i q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - -TCONS_00000048 XLOC_000085 Xkr4|Xkr4 i q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - -TCONS_00000049 XLOC_000086 Xkr4|Xkr4 i q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - -TCONS_00000050 XLOC_000087 Xkr4|Xkr4 i q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - -TCONS_00000051 XLOC_000004 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000052 XLOC_000005 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000053 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- -TCONS_00000054 XLOC_000007 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- -TCONS_00000055 XLOC_000008 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- -TCONS_00000056 XLOC_000009 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- -TCONS_00000057 XLOC_000010 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- -TCONS_00000058 XLOC_000013 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000059 XLOC_000018 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000060 XLOC_000024 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000061 XLOC_000027 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000062 XLOC_000028 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- -TCONS_00000063 XLOC_000029 - u - q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000064 XLOC_000030 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- -TCONS_00000065 XLOC_000032 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- -TCONS_00000066 XLOC_000033 Xkr4|Xkr4 i - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- -TCONS_00000067 XLOC_000036 Xkr4|Xkr4 i - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- -TCONS_00000068 XLOC_000038 Xkr4|Xkr4 i - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000069 XLOC_000039 Xkr4|Xkr4 i - q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|- -TCONS_00000070 XLOC_000041 Xkr4|Xkr4 i - q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|- -TCONS_00000071 XLOC_000043 Xkr4|Xkr4 i - q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|- -TCONS_00000072 XLOC_000045 Xkr4|Xkr4 i - q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000073 XLOC_000047 Xkr4|Xkr4 i - q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000074 XLOC_000049 Xkr4|Xkr4 i - q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|- -TCONS_00000075 XLOC_000050 Xkr4|Xkr4 i - q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000076 XLOC_000051 Xkr4|Xkr4 i - q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000077 XLOC_000053 Xkr4|Xkr4 i - q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000078 XLOC_000054 Xkr4|Xkr4 i - q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000079 XLOC_000055 Xkr4|Xkr4 i - q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|- -TCONS_00000080 XLOC_000056 Xkr4|Xkr4 i - q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000081 XLOC_000058 Xkr4|Xkr4 i - q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|- -TCONS_00000082 XLOC_000059 Xkr4|Xkr4 i - q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|- -TCONS_00000083 XLOC_000060 Xkr4|Xkr4 i - q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|- -TCONS_00000084 XLOC_000061 Xkr4|Xkr4 i - q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|- -TCONS_00000085 XLOC_000063 Xkr4|Xkr4 i - q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000086 XLOC_000064 Xkr4|Xkr4 i - q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000087 XLOC_000066 Xkr4|Xkr4 i - q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|- -TCONS_00000088 XLOC_000067 Xkr4|Xkr4 i - q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|- -TCONS_00000089 XLOC_000068 Xkr4|Xkr4 i - q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|- -TCONS_00000090 XLOC_000069 Xkr4|Xkr4 i - q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|- -TCONS_00000091 XLOC_000070 Xkr4|Xkr4 i - q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|- -TCONS_00000092 XLOC_000072 Xkr4|Xkr4 i - q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|- -TCONS_00000093 XLOC_000074 Xkr4|Xkr4 i - q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|- -TCONS_00000094 XLOC_000076 Xkr4|Xkr4 i - q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000095 XLOC_000078 Xkr4|Xkr4 i - q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000096 XLOC_000079 Xkr4|Xkr4 i - q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000097 XLOC_000081 Xkr4|Xkr4 i - q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000098 XLOC_000082 Xkr4|Xkr4 i - q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|- +TCONS_00000001 XLOC_000001 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - +TCONS_00000002 XLOC_000002 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - +TCONS_00000003 XLOC_000006 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - +TCONS_00000004 XLOC_000006 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - +TCONS_00000005 XLOC_000006 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - +TCONS_00000006 XLOC_000008 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - +TCONS_00000007 XLOC_000008 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - +TCONS_00000008 XLOC_000010 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - +TCONS_00000009 XLOC_000011 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - +TCONS_00000010 XLOC_000013 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - +TCONS_00000011 XLOC_000014 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - +TCONS_00000012 XLOC_000015 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - +TCONS_00000013 XLOC_000016 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000014 XLOC_000018 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000015 XLOC_000019 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000016 XLOC_000020 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000017 XLOC_000021 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000018 XLOC_000022 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000019 XLOC_000024 - u q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|- - +TCONS_00000020 XLOC_000025 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000021 XLOC_000028 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|- - +TCONS_00000022 XLOC_000030 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000023 XLOC_000032 - u q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - +TCONS_00000024 XLOC_000034 - u q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - +TCONS_00000025 XLOC_000035 - u q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - +TCONS_00000026 XLOC_000037 - u q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|- - +TCONS_00000027 XLOC_000040 - u q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - +TCONS_00000028 XLOC_000042 - u q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - +TCONS_00000029 XLOC_000044 - u q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - +TCONS_00000030 XLOC_000046 - u q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - +TCONS_00000031 XLOC_000048 - u q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - +TCONS_00000032 XLOC_000049 - u q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - +TCONS_00000033 XLOC_000052 - u q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - +TCONS_00000034 XLOC_000057 - u q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - +TCONS_00000035 XLOC_000059 - u q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - +TCONS_00000036 XLOC_000059 - u q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - +TCONS_00000037 XLOC_000060 - u q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - +TCONS_00000038 XLOC_000062 - u q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000039 XLOC_000065 - u q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - +TCONS_00000040 XLOC_000068 - u q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000041 XLOC_000071 - u q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - +TCONS_00000042 XLOC_000073 - u q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - +TCONS_00000043 XLOC_000075 - u q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000044 XLOC_000077 - u q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - +TCONS_00000045 XLOC_000080 - u q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - +TCONS_00000046 XLOC_000083 - u q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - +TCONS_00000047 XLOC_000084 - u q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - +TCONS_00000048 XLOC_000085 - u q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - +TCONS_00000049 XLOC_000086 - u q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - +TCONS_00000050 XLOC_000087 - u q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - +TCONS_00000051 XLOC_000003 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000052 XLOC_000004 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000053 XLOC_000005 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- +TCONS_00000054 XLOC_000006 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- +TCONS_00000055 XLOC_000007 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- +TCONS_00000056 XLOC_000008 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- +TCONS_00000057 XLOC_000009 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- +TCONS_00000058 XLOC_000012 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000059 XLOC_000017 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000060 XLOC_000023 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000061 XLOC_000024 - u - q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|- +TCONS_00000062 XLOC_000026 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000063 XLOC_000027 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- +TCONS_00000064 XLOC_000028 - u - q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000065 XLOC_000029 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- +TCONS_00000066 XLOC_000031 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- +TCONS_00000067 XLOC_000033 - u - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- +TCONS_00000068 XLOC_000036 - u - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- +TCONS_00000069 XLOC_000037 - u - q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|- +TCONS_00000070 XLOC_000038 - u - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000071 XLOC_000039 - u - q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|- +TCONS_00000072 XLOC_000041 - u - q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|- +TCONS_00000073 XLOC_000043 - u - q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|- +TCONS_00000074 XLOC_000045 - u - q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000075 XLOC_000047 - u - q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000076 XLOC_000049 - u - q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|- +TCONS_00000077 XLOC_000050 - u - q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000078 XLOC_000051 - u - q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000079 XLOC_000053 - u - q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000080 XLOC_000054 - u - q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000081 XLOC_000055 - u - q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|- +TCONS_00000082 XLOC_000056 - u - q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000083 XLOC_000058 - u - q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|- +TCONS_00000084 XLOC_000059 - u - q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|- +TCONS_00000085 XLOC_000060 - u - q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|- +TCONS_00000086 XLOC_000061 - u - q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|- +TCONS_00000087 XLOC_000063 - u - q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000088 XLOC_000064 - u - q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|- +TCONS_00000089 XLOC_000066 - u - q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|- +TCONS_00000090 XLOC_000067 - u - q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|- +TCONS_00000091 XLOC_000068 - u - q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|- +TCONS_00000092 XLOC_000069 - u - q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|- +TCONS_00000093 XLOC_000070 - u - q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|- +TCONS_00000094 XLOC_000072 - u - q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|- +TCONS_00000095 XLOC_000074 - u - q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|- +TCONS_00000096 XLOC_000076 - u - q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000097 XLOC_000078 - u - q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000098 XLOC_000079 - u - q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000099 XLOC_000081 - u - q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|- +TCONS_00000100 XLOC_000082 - u - q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|- --- a/test-data/cuffcompare_out7.txt Sun May 08 22:16:18 2011 -0400 +++ b/test-data/cuffcompare_out7.txt Mon May 09 09:57:21 2011 -0400 @@ -1,41 +1,15 @@ -# Cuffcompare v0.9.3 | Command line was: +# Cuffcompare v1.0.1 | Command line was: #cuffcompare -r cuffcompare_in3.gtf -R cuffcompare_in1.gtf cuffcompare_in2.gtf # #> Genomic sequence: chr1 # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 1 in 1 loci (1 multi-exon) -# Corresponding super-loci: 1 -#--------------------| Sn | Sp | fSn | fSp - Base level: 2.2 2.3 - - - Exon level: 0.0 0.0 0.0 0.0 - Intron level: 0.0 nan 0.0 nan -Intron chain level: 0.0 nan 0.0 nan - Transcript level: 0.0 0.0 0.0 0.0 - Locus level: 0.0 0.0 0.0 0.0 - Missed exons: 2/3 ( 66.7%) - Wrong exons: 49/50 ( 98.0%) - Missed introns: 2/2 (100.0%) - Missed loci: 0/1 ( 0.0%) - Wrong loci: 49/50 ( 98.0%) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) #= Summary for dataset: cuffcompare_in1.gtf : # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 1 in 1 loci (1 multi-exon) -# Corresponding super-loci: 1 -#--------------------| Sn | Sp | fSn | fSp - Base level: 2.2 2.3 - - - Exon level: 0.0 0.0 0.0 0.0 - Intron level: 0.0 nan 0.0 nan -Intron chain level: 0.0 nan 0.0 nan - Transcript level: 0.0 0.0 0.0 0.0 - Locus level: 0.0 0.0 0.0 0.0 - Missed exons: 2/3 ( 66.7%) - Wrong exons: 49/50 ( 98.0%) - Missed introns: 2/2 (100.0%) - Missed loci: 0/1 ( 0.0%) - Wrong loci: 49/50 ( 98.0%) +# Reference mRNAs : 0 in 0 loci (0 multi-exon) #> Genomic sequence: chr1 # Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) # (0 multi-transcript loci, ~1.0 transcripts per locus) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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