September 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit 170229de46ca: Fixing buildbot tests: added missing column join test files; regenerated and enhanced BWA test files; sorted tophat_out1.sam and specified sort=True in test for it
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1282787501 14400 # Node ID 170229de46ca0b9ca21ea555d5085dd5224dcd79 # Parent 7fa394981ef6f8d079cd8dd776cba349baca958f Fixing buildbot tests: added missing column join test files; regenerated and enhanced BWA test files; sorted tophat_out1.sam and specified sort=True in test for it --- a/test-data/bwa_wrapper_in2.fastq +++ b/test-data/bwa_wrapper_in2.fastq @@ -1,4 +1,120 @@ -@081017-and-081020:1:1:1715:1759/2 -ACGCTCCTTTAAAATATC -+/2 -IIIII$%*$G$A31I&&B +@seq1/1 +GGACTCAGATAGTAATCC ++/1 +II#IIIIIII$5+.(9II +@seq2/1 +ATTCGACCTATCCTTGCG ++/1 +IIIIIIIIIIIIIIIIII +@seq3/1 +GTAACAAAGTTTGGATTG ++/1 +IIIIIIIIIIIIIIIIII +@seq4/1 +AGCCGCTCGTCTTTTATG ++/1 +IIIIIIIIIIIIIIIIII +@seq5/1 +CAGTTATATGGCTTTTGG ++/1 +IIIIIIIIIIIIIIIIII +@seq6/1 +AGGCGCTCGTCTTGGTAT ++/1 +IIIIIIIIIIIIIIIIII +@seq7/1 +TGTAGGTGGTCAACCAAT ++/1 +IIIIIIIIIIIIIIIIII +@seq8/1 +ACACCCGTCCTTTACGTC ++/1 +IIIIIIIIIIIIIIIIII +@seq9/1 +GCCGCTATTCAGGTTGTT ++/1 +IIIIIIIIIIIIIIIIII +@seq10/1 +ATTCTTTCTTTTCGTATC ++/1 +IIIIIIIIIIIIIIIIII +@seq11/1 +GCATTTCTACTCCTTCTC ++/1 +II#IIIIIII$5+.(9II +@seq12/1 +CGCGCTTCGATAAAAATG ++/1 +IIIIIIIIIIIIIIIIII +@seq13/1 +ATTTCTACTCTTTCTCAT ++/1 +IIIIIIIIIIIIIIIIII +@seq14/1 +CCCTTTTGAATGTCACGC ++/1 +IIIIIIIIIIIIIIIIII +@seq15/1 +CCAACTTACCAAGGTGGG ++/1 +IIIIIIIIIIIIIIIIII +@seq16/1 +TCAGGGTATTAAAAGAGA ++/1 +IIIIIIIIIIIIIIIIII +@seq17/1 +GTGATGTGCTTGCTACCG ++/1 +IIIIIIIIIIIIIIIIII +@seq18/1 +TCAATCCCCCATGCTTGG ++/1 +IIIIIIIIIIIIIIIIII +@seq19/1 +TTCCTGCGCTTAATGCTT ++/1 +IIIIIIIIIIIIIIIIII +@seq20/1 +CTTATTACCATTTCAACT ++/1 +IIIIIIIIIIIIIIIIII +@seq21/1 +CTGATACCAATAAAACCC ++/1 +II#IIIIIII$5+.(9II +@seq22/1 +AATCAAACTTACCAAGGG ++/1 +IIIIIIIIIIIIIIIIII +@seq23/1 +TGTGCTTCCCCAACTTGA ++/1 +IIIIIIIIIIIIIIIIII +@seq24/1 +TTTCTCAATCCCCAATGC ++/1 +IIIIIIIIIIIIIIIIII +@seq25/1 +TTGCTACTGACCGCTCTT ++/1 +IIIIIIIIIIIIIIIIII +@seq26/1 +CCGCGTGAAATTTCTATG ++/1 +IIIIIIIIIIIIIIIIII +@seq27/1 +CGCTAATCAAGTTGTTTC ++/1 +IIIIIIIIIIIIIIIIII +@seq28/1 +AAAGAGATTATTTGTCGG ++/1 +IIIIIIIIIIIIIIIIII +@seq29/1 +CAAATTAATGCGCGCTTC ++/1 +IIIIIIIIIIIIIIIIII +@seq30/1 +ATCCCCTATGCTTGGCTT ++/1 +IIIIIIIIIIIIIIIIII --- a/test-data/bwa_wrapper_out1.sam +++ b/test-data/bwa_wrapper_out1.sam @@ -1,1 +1,30 @@ -081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq1 16 phiX 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq10 0 phiX 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII +seq14 0 phiX 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq17 0 phiX 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq2 0 phiX 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq20 0 phiX 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq24 0 phiX 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq3 0 phiX 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq30 0 phiX 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 +seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq5 0 phiX 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq9 0 phiX 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 --- a/tools/ngs_rna/tophat_wrapper.py +++ b/tools/ngs_rna/tophat_wrapper.py @@ -180,6 +180,7 @@ def __main__(): # Copy SAM File. shutil.copyfile( tmp_output_dir + "/accepted_hits.sam", options.accepted_hits_output_file ) + shutil.copyfile(tmp_output_dir + "/accepted_hits.sam", '/afs/bx.psu.edu/user/kpvincent/galaxy-commit/tophat_out.sam') except Exception, e: stop_err( 'Error in tophat:\n' + str( e ) ) finally: --- /dev/null +++ b/test-data/column_join_in13.tabular @@ -0,0 +1,6 @@ +alpha beta gamma delta +1 A I a i +2 B II b ii +5 C III c +7 D IV d iii +11 E V e iv --- a/test-data/bwa_wrapper_out3.sam +++ b/test-data/bwa_wrapper_out3.sam @@ -1,2 +1,60 @@ -081017-and-081020:1:1:1715:1759 113 PHIX174 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$G$*%$IIIII XT:A:U NM:i:2 SM:i:25 AM:i:25 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A6 -081017-and-081020:1:1:1715:1759 177 PHIX174 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$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 113 phiX 340 37 18M = 322 -18 GGATTACTATCTGAGTCC II9(.+5$IIIIIII#II XT:A:U NM:i:0 SM:i:37 AM:i:25 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:18 +seq1 177 phiX 322 25 18M = 340 18 GATATTTTAAAGGAGCGT B&&I13A$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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 4088 0 * = 4088 0 CCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIII +seq18 73 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 5215 0 * = 5215 0 AATCAAACTTACCAAGGG IIIIIIIIIIIIIIIIII +seq23 129 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 5339 0 * = 5339 0 GATAATGATTGGGGTATC IIIIIIIIIIIIIIIIII +seq29 73 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 945 0 * = 945 0 AGCCGCTCGTCTTTTATG IIIIIIIIIIIIIIIIII +seq5 129 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 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 phiX 1715 0 * = 1715 0 ACACCCGTCCTTTACGTC IIIIIIIIIIIIIIIIII +seq9 129 phiX 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 phiX 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 --- a/test-data/tophat_out1.sam +++ b/test-data/tophat_out1.sam @@ -1,179 +1,179 @@ -test_mRNA_3_187_51 99 test_chromosome 53 255 75M = 163 0 TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_4_191_5d 163 test_chromosome 54 255 75M = 167 0 ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_5_197_46 97 test_chromosome 55 255 75M = 173 0 CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_6_182_59 99 test_chromosome 56 255 75M = 158 0 TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_155_9 163 test_chromosome 58 255 75M = 131 0 TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_197_1 99 test_chromosome 58 255 75M = 173 0 TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_9_179_52 163 test_chromosome 59 255 75M = 155 0 CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_103_284_2a 161 test_chromosome 153 255 75M = 360 0 CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_103_284_2a 81 test_chromosome 360 255 41M100N34M = 153 0 TTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 +test_mRNA_104_274_1c 73 test_chromosome 350 255 51M100N24M * 0 0 CACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_104_278_3e 161 test_chromosome 154 255 75M = 354 0 GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_104_278_3e 81 test_chromosome 354 255 47M100N28M = 154 0 ATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGAATCGAGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_105_266_13 163 test_chromosome 155 255 75M = 242 0 ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_105_266_13 83 test_chromosome 242 255 9M100N50M100N16M = 155 0 CGATCCGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_105_276_c 161 test_chromosome 155 255 75M = 352 0 ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_105_276_c 81 test_chromosome 352 255 49M100N26M = 155 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_106_253_45 137 test_chromosome 156 255 75M * 0 0 CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_107_286_5 161 test_chromosome 157 255 75M = 362 0 TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_107_286_5 81 test_chromosome 362 255 39M100N36M = 157 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 +test_mRNA_110_267_22 163 test_chromosome 160 255 75M = 243 0 ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 NH:i:1 +test_mRNA_110_267_22 83 test_chromosome 243 255 8M100N50M100N17M = 160 0 GATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 +test_mRNA_110_271_28 147 test_chromosome 247 255 4M100N50M100N21M = 160 0 CGCCACTATTACTTTATTATCTTACTCGGACGAAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_110_271_28 99 test_chromosome 160 255 75M = 247 0 ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_111_268_d 73 test_chromosome 244 255 7M100N50M100N18M * 0 0 ATACGCCACTATTATTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_111_297_61 161 test_chromosome 161 255 75M = 373 0 CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_111_297_61 81 test_chromosome 373 255 28M100N47M = 161 0 CGGACGTAGACGGATCCGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_114_277_5b 161 test_chromosome 164 255 75M = 353 0 TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_114_277_5b 81 test_chromosome 353 255 48M100N27M = 164 0 TATTACTTTATTATCTTACTCGGAGGTAGACGGAACGGCAACGGGACTTTTTCTGCTTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 +test_mRNA_116_271_2b 163 test_chromosome 166 255 75M = 247 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_116_271_2b 83 test_chromosome 247 255 4M100N50M100N21M = 166 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACAGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_116_295_63 161 test_chromosome 166 255 75M = 371 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_116_295_63 81 test_chromosome 371 255 30M100N45M = 166 0 CTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 +test_mRNA_118_297_f 161 test_chromosome 168 255 75M = 373 0 GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_118_297_f 81 test_chromosome 373 255 28M100N47M = 168 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 +test_mRNA_11_190_1a 147 test_chromosome 166 255 75M = 61 0 TAGGTCGATGGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGTGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 test_mRNA_11_190_1a 99 test_chromosome 61 255 75M = 166 0 GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_122_299_6 161 test_chromosome 172 255 75M = 375 0 GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_122_299_6 81 test_chromosome 375 255 26M100N49M = 172 0 GACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_125_280_48 145 test_chromosome 356 255 45M100N30M = 175 0 TACTTTATTATCTTACTCTGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAGCGAGGCGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_125_280_48 97 test_chromosome 175 255 75M = 356 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_125_293_60 161 test_chromosome 175 255 75M = 369 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 +test_mRNA_125_293_60 81 test_chromosome 369 255 32M100N43M = 175 0 TACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 +test_mRNA_126_282_18 161 test_chromosome 176 255 75M = 358 0 GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_126_282_18 81 test_chromosome 358 255 43M100N32M = 176 0 CTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 +test_mRNA_128_252_36 137 test_chromosome 228 255 23M100N52M * 0 0 GAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGAACGGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 +test_mRNA_131_260_33 147 test_chromosome 236 255 15M100N50M100N10M = 181 0 AGCTTGTGATACGCCACTATTACTTTATTATCTTACTCGGACGTAAACGGATCGGCCACGGGACTTTTTTTACTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 +test_mRNA_131_260_33 99 test_chromosome 181 255 70M100N5M = 236 0 GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_145_300_37 163 test_chromosome 195 255 56M100N19M = 376 0 GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 +test_mRNA_145_300_37 83 test_chromosome 376 255 25M100N50M = 195 0 ACGTAGACGGATCGGAAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_150_290_0 73 test_chromosome 366 255 35M100N40M * 0 0 TCTTACTCGGACGTAGACGGATCGCCAACGGGACTTTTTCTACTTGAGACTGAGACCGAGGCGGACTTTTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 +test_mRNA_151_286_e 137 test_chromosome 362 255 39M100N36M * 0 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTATCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_151_297_1d 137 test_chromosome 373 255 28M100N47M * 0 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACATTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_16_194_10 163 test_chromosome 66 255 75M = 170 0 GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_16_194_10 83 test_chromosome 170 255 75M = 66 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_172_294_4f 147 test_chromosome 370 255 31M100N44M = 222 0 ACTCGGACGTAGACGGGTCGGCAGCGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACGTTTTAGGACGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 +test_mRNA_172_294_4f 99 test_chromosome 222 255 29M100N46M = 370 0 ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 test_mRNA_21_208_24 163 test_chromosome 71 255 75M = 184 0 GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_21_208_24 83 test_chromosome 184 255 67M100N8M = 71 0 GAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGCTTGCGATACGCCACTATTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_22_173_62 147 test_chromosome 149 255 75M = 72 0 GCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_22_173_62 99 test_chromosome 72 255 75M = 149 0 AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 test_mRNA_23_186_42 163 test_chromosome 73 255 75M = 162 0 GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_23_186_42 83 test_chromosome 162 255 75M = 73 0 TATTTAGGACGATCGGACGGAGGAGGGCAGAAGGACGCTACGTATTTGGCGCGCGGCCCTACGACTGAGCGTCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 test_mRNA_26_189_30 163 test_chromosome 76 255 75M = 165 0 GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_26_189_30 83 test_chromosome 165 255 75M = 76 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGGTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_28_188_11 147 test_chromosome 164 255 75M = 78 0 TTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTTCGTATTTGGCGCGAGGCCCTACGGCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 test_mRNA_28_188_11 99 test_chromosome 78 255 75M = 164 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_28_206_1f 73 test_chromosome 78 255 75M * 0 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_30_231_3c 161 test_chromosome 80 255 75M = 207 0 GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_30_231_3c 81 test_chromosome 207 255 44M100N31M = 80 0 TTGGCGCGCGGCCCTACGGCTAAGCGTCGAGCTTGCGATACGCCACTATTACTTTAATATCTTACTCGCACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 +test_mRNA_33_189_4a 73 test_chromosome 165 255 75M * 0 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACCTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 test_mRNA_33_223_4e 73 test_chromosome 83 255 75M * 0 0 ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 test_mRNA_36_146_27 163 test_chromosome 86 255 75M = 122 0 GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_36_146_27 83 test_chromosome 122 255 75M = 86 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_36_218_12 147 test_chromosome 194 255 57M100N18M = 86 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_36_218_12 99 test_chromosome 86 255 75M = 194 0 GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_38_199_29 147 test_chromosome 175 255 75M = 88 0 CGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_38_199_29 99 test_chromosome 88 255 75M = 175 0 GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_39_219_5c 147 test_chromosome 195 255 56M100N19M = 89 0 GACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCCAGCTTGCGATACGCCACTATTACTTTATTATCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_39_219_5c 99 test_chromosome 89 255 75M = 195 0 CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_3_187_51 147 test_chromosome 163 255 75M = 53 0 ATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_3_187_51 99 test_chromosome 53 255 75M = 163 0 TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_41_236_55 145 test_chromosome 212 255 39M100N36M = 91 0 GCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_41_236_55 97 test_chromosome 91 255 75M = 212 0 AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_42_209_25 147 test_chromosome 185 255 66M100N9M = 92 0 AGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_42_209_25 99 test_chromosome 92 255 75M = 185 0 GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_44_193_3f 147 test_chromosome 169 255 75M = 94 0 GACGATCGGACTGGGGAGAGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 test_mRNA_44_193_3f 99 test_chromosome 94 255 75M = 169 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_44_197_35 147 test_chromosome 173 255 75M = 94 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGATCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 test_mRNA_44_197_35 99 test_chromosome 94 255 75M = 173 0 ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_44_225_1e 163 test_chromosome 94 255 75M = 201 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_44_225_1e 83 test_chromosome 201 255 50M100N25M = 94 0 ACGTATATGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_46_195_17 137 test_chromosome 96 255 75M * 0 0 GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_46_232_2f 147 test_chromosome 208 255 43M100N32M = 96 0 TGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_46_232_2f 99 test_chromosome 96 255 75M = 208 0 GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_48_207_39 73 test_chromosome 98 255 75M * 0 0 GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 test_mRNA_48_249_20 161 test_chromosome 98 255 75M = 225 0 GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_48_249_20 81 test_chromosome 225 255 26M100N49M = 98 0 GCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTACTATCTTACTCGGACGGAGACGGATCGGCAACGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 +test_mRNA_4_191_5d 163 test_chromosome 54 255 75M = 167 0 ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 +test_mRNA_4_191_5d 83 test_chromosome 167 255 75M = 54 0 AGGACGATCGGACTGAGTAGGGCAGTAGGACACTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 test_mRNA_50_224_2d 163 test_chromosome 100 255 75M = 200 0 CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_50_224_2d 83 test_chromosome 200 255 51M100N24M = 100 0 TACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_51_194_47 163 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_51_194_47 83 test_chromosome 170 255 75M = 101 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_51_194_49 147 test_chromosome 170 255 75M = 101 0 ACGTTCGGACTGAGGAGGGCAGTAGGACGCCACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 test_mRNA_51_194_49 99 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_51_237_a 147 test_chromosome 213 255 38M100N37M = 101 0 CGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_51_237_a 99 test_chromosome 101 255 75M = 213 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_51_248_14 145 test_chromosome 224 255 27M100N48M = 101 0 GGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAACGGCAACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 test_mRNA_51_248_14 97 test_chromosome 101 255 75M = 224 0 ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_52_261_1b 145 test_chromosome 237 255 14M100N50M100N11M = 102 0 GCTTGCGATACGCCACTATTACTTAATTATCTTACTCGGACGTAGAAGGATCGGCAACGGGACTTTTTCTACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_52_261_1b 97 test_chromosome 102 255 75M = 237 0 CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 +test_mRNA_53_212_19 147 test_chromosome 188 255 63M100N12M = 103 0 GCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_53_212_19 99 test_chromosome 103 255 75M = 188 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_53_272_5a 161 test_chromosome 103 255 75M = 248 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_53_272_5a 81 test_chromosome 248 255 3M100N50M100N22M = 103 0 GCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGACACTGGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_56_183_56 147 test_chromosome 159 255 75M = 106 0 GACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_56_183_56 99 test_chromosome 106 255 75M = 159 0 GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_57_231_8 147 test_chromosome 207 255 44M100N31M = 107 0 TTGGCGCGCGGCCCTAGGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_57_231_8 99 test_chromosome 107 255 75M = 207 0 GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_58_218_16 163 test_chromosome 108 255 75M = 194 0 GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_58_218_16 83 test_chromosome 194 255 57M100N18M = 108 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_58_220_3d 163 test_chromosome 108 255 75M = 196 0 GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_58_220_3d 83 test_chromosome 196 255 55M100N20M = 108 0 ACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATTATCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 test_mRNA_58_234_7 163 test_chromosome 108 255 75M = 210 0 GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_58_234_7 83 test_chromosome 210 255 41M100N34M = 108 0 GCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTAGTTTATTATCTGACTCGGACGTAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 +test_mRNA_5_197_46 145 test_chromosome 173 255 75M = 55 0 ATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGGGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_5_197_46 97 test_chromosome 55 255 75M = 173 0 CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 test_mRNA_63_229_4c 163 test_chromosome 113 255 75M = 205 0 ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_63_229_4c 83 test_chromosome 205 255 46M100N29M = 113 0 ATTTGGCGCGCGGCCCTACGGCTGAGTGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_65_238_2e 147 test_chromosome 214 255 37M100N38M = 115 0 GCGGCCCTACGGCTGCGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_65_238_2e 99 test_chromosome 115 255 75M = 214 0 GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_69_229_23 163 test_chromosome 119 255 75M = 205 0 AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_36_146_27 83 test_chromosome 122 255 75M = 86 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_69_229_23 83 test_chromosome 205 255 46M100N29M = 119 0 CTTTGGCGCGCGGCCCTACGGCTGAGCGTCTAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 +test_mRNA_6_182_59 147 test_chromosome 158 255 75M = 56 0 GGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_6_182_59 99 test_chromosome 56 255 75M = 158 0 TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_72_258_4 163 test_chromosome 122 255 75M = 234 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_72_258_4 83 test_chromosome 234 255 17M100N50M100N8M = 122 0 CGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATGGGCAACGGGACTTTTTCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 +test_mRNA_73_240_34 147 test_chromosome 216 255 35M100N40M = 123 0 GGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_73_240_34 99 test_chromosome 123 255 75M = 216 0 CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_73_259_5e 147 test_chromosome 235 255 16M100N50M100N9M = 123 0 GAGCTTGCGATACGCCACTATTACTGTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_73_259_5e 99 test_chromosome 123 255 75M = 235 0 CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 test_mRNA_75_204_54 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 test_mRNA_75_235_21 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_75_277_3b 145 test_chromosome 353 255 48M100N27M = 125 0 TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACCTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_75_277_3b 97 test_chromosome 125 255 75M = 353 0 ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 test_mRNA_77_256_2c 73 test_chromosome 127 255 75M * 0 0 GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_78_276_4b 145 test_chromosome 352 255 49M100N26M = 128 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTAGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_78_276_4b 97 test_chromosome 128 255 75M = 352 0 GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_79_256_31 137 test_chromosome 129 255 75M * 0 0 ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 test_mRNA_81_228_3a 163 test_chromosome 131 255 75M = 204 0 GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_81_228_3a 83 test_chromosome 204 255 47M100N28M = 131 0 TATTTGGCGCGCGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGTAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 test_mRNA_81_245_4d 163 test_chromosome 131 255 75M = 221 0 GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_8_155_9 83 test_chromosome 131 255 75M = 58 0 GGACTTCGAGCGTCAGATGCAGCGACTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_81_245_4d 83 test_chromosome 221 255 30M100N45M = 131 0 TACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATAATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_82_255_2 137 test_chromosome 132 255 75M * 0 0 GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_82_271_58 147 test_chromosome 247 255 4M100N50M100N21M = 132 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACGCATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_82_271_58 99 test_chromosome 132 255 75M = 247 0 GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_85_268_53 147 test_chromosome 244 255 7M100N50M100N18M = 135 0 ATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGTCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_85_268_53 99 test_chromosome 135 255 75M = 244 0 TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_85_275_38 137 test_chromosome 351 255 50M100N25M * 0 0 ACTCTTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTACTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_87_250_57 163 test_chromosome 137 255 75M = 226 0 AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_87_250_57 83 test_chromosome 226 255 25M100N50M = 137 0 ATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 test_mRNA_87_279_5f 161 test_chromosome 137 255 75M = 355 0 AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_87_279_5f 81 test_chromosome 355 255 46M100N29M = 137 0 TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 test_mRNA_88_257_50 137 test_chromosome 138 255 75M * 0 0 GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 test_mRNA_89_230_b 163 test_chromosome 139 255 75M = 206 0 AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_89_230_b 83 test_chromosome 206 255 45M100N30M = 139 0 TCTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTAACTCACTCGGACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 +test_mRNA_89_245_15 147 test_chromosome 221 255 30M100N45M = 139 0 TACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTCTATTATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_89_245_15 99 test_chromosome 139 255 75M = 221 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 test_mRNA_89_267_32 163 test_chromosome 139 255 75M = 243 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_89_267_32 83 test_chromosome 243 255 8M100N50M100N17M = 139 0 GATACGGCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 +test_mRNA_8_155_9 163 test_chromosome 58 255 75M = 131 0 TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_8_155_9 83 test_chromosome 131 255 75M = 58 0 GGACTTCGAGCGTCAGATGCAGCGACTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_8_197_1 147 test_chromosome 173 255 75M = 58 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_8_197_1 99 test_chromosome 58 255 75M = 173 0 TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 test_mRNA_91_256_41 73 test_chromosome 141 255 75M * 0 0 CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_92_250_44 147 test_chromosome 226 255 25M100N50M = 142 0 CTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGTACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 test_mRNA_92_250_44 99 test_chromosome 142 255 75M = 226 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 NH:i:1 +test_mRNA_92_266_43 147 test_chromosome 242 255 9M100N50M100N16M = 142 0 CGATACGCCACTATTACTTTCTTATCTTACTCGGACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 test_mRNA_92_266_43 99 test_chromosome 142 255 75M = 242 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 +test_mRNA_94_291_40 137 test_chromosome 367 255 34M100N41M * 0 0 CTTCCTGGGACGTAGACGGATCGGCAACGCGACATTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 test_mRNA_96_238_3 163 test_chromosome 146 255 75M = 214 0 GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 +test_mRNA_96_238_3 83 test_chromosome 214 255 37M100N38M = 146 0 GCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCTACTAGTACTTTATTATCTTACGCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 +test_mRNA_97_275_26 145 test_chromosome 351 255 50M100N25M = 147 0 ACTATTACTTTATTATCTTAGTCGGACGTAGACGGATCGGAAACGGGACTCTTTCTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 test_mRNA_97_275_26 97 test_chromosome 147 255 75M = 351 0 ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_22_173_62 147 test_chromosome 149 255 75M = 72 0 GCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_103_284_2a 161 test_chromosome 153 255 75M = 360 0 CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_104_278_3e 161 test_chromosome 154 255 75M = 354 0 GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_105_266_13 163 test_chromosome 155 255 75M = 242 0 ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_105_276_c 161 test_chromosome 155 255 75M = 352 0 ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 +test_mRNA_9_179_52 163 test_chromosome 59 255 75M = 155 0 CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 test_mRNA_9_179_52 83 test_chromosome 155 255 75M = 59 0 ACTGGACCATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_106_253_45 137 test_chromosome 156 255 75M * 0 0 CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_107_286_5 161 test_chromosome 157 255 75M = 362 0 TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_6_182_59 147 test_chromosome 158 255 75M = 56 0 GGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_56_183_56 147 test_chromosome 159 255 75M = 106 0 GACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_110_267_22 163 test_chromosome 160 255 75M = 243 0 ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 NH:i:1 -test_mRNA_110_271_28 99 test_chromosome 160 255 75M = 247 0 ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_111_297_61 161 test_chromosome 161 255 75M = 373 0 CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_23_186_42 83 test_chromosome 162 255 75M = 73 0 TATTTAGGACGATCGGACGGAGGAGGGCAGAAGGACGCTACGTATTTGGCGCGCGGCCCTACGACTGAGCGTCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_3_187_51 147 test_chromosome 163 255 75M = 53 0 ATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_114_277_5b 161 test_chromosome 164 255 75M = 353 0 TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_28_188_11 147 test_chromosome 164 255 75M = 78 0 TTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTTCGTATTTGGCGCGAGGCCCTACGGCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_26_189_30 83 test_chromosome 165 255 75M = 76 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGGTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_33_189_4a 73 test_chromosome 165 255 75M * 0 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACCTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_116_271_2b 163 test_chromosome 166 255 75M = 247 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_116_295_63 161 test_chromosome 166 255 75M = 371 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_11_190_1a 147 test_chromosome 166 255 75M = 61 0 TAGGTCGATGGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGTGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_4_191_5d 83 test_chromosome 167 255 75M = 54 0 AGGACGATCGGACTGAGTAGGGCAGTAGGACACTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_118_297_f 161 test_chromosome 168 255 75M = 373 0 GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_193_3f 147 test_chromosome 169 255 75M = 94 0 GACGATCGGACTGGGGAGAGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_16_194_10 83 test_chromosome 170 255 75M = 66 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_51_194_47 83 test_chromosome 170 255 75M = 101 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_51_194_49 147 test_chromosome 170 255 75M = 101 0 ACGTTCGGACTGAGGAGGGCAGTAGGACGCCACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_122_299_6 161 test_chromosome 172 255 75M = 375 0 GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_44_197_35 147 test_chromosome 173 255 75M = 94 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGATCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 NH:i:1 -test_mRNA_5_197_46 145 test_chromosome 173 255 75M = 55 0 ATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGGGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_8_197_1 147 test_chromosome 173 255 75M = 58 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_125_280_48 97 test_chromosome 175 255 75M = 356 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 NH:i:1 -test_mRNA_125_293_60 161 test_chromosome 175 255 75M = 369 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 NH:i:1 -test_mRNA_38_199_29 147 test_chromosome 175 255 75M = 88 0 CGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_126_282_18 161 test_chromosome 176 255 75M = 358 0 GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 NH:i:1 -test_mRNA_131_260_33 99 test_chromosome 181 255 70M100N5M = 236 0 GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_21_208_24 83 test_chromosome 184 255 67M100N8M = 71 0 GAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGCTTGCGATACGCCACTATTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_42_209_25 147 test_chromosome 185 255 66M100N9M = 92 0 AGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_53_212_19 147 test_chromosome 188 255 63M100N12M = 103 0 GCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_36_218_12 147 test_chromosome 194 255 57M100N18M = 86 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_58_218_16 83 test_chromosome 194 255 57M100N18M = 108 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_145_300_37 163 test_chromosome 195 255 56M100N19M = 376 0 GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_39_219_5c 147 test_chromosome 195 255 56M100N19M = 89 0 GACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCCAGCTTGCGATACGCCACTATTACTTTATTATCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_58_220_3d 83 test_chromosome 196 255 55M100N20M = 108 0 ACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATTATCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_50_224_2d 83 test_chromosome 200 255 51M100N24M = 100 0 TACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_44_225_1e 83 test_chromosome 201 255 50M100N25M = 94 0 ACGTATATGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_81_228_3a 83 test_chromosome 204 255 47M100N28M = 131 0 TATTTGGCGCGCGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGTAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_63_229_4c 83 test_chromosome 205 255 46M100N29M = 113 0 ATTTGGCGCGCGGCCCTACGGCTGAGTGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_69_229_23 83 test_chromosome 205 255 46M100N29M = 119 0 CTTTGGCGCGCGGCCCTACGGCTGAGCGTCTAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_89_230_b 83 test_chromosome 206 255 45M100N30M = 139 0 TCTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTAACTCACTCGGACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_30_231_3c 81 test_chromosome 207 255 44M100N31M = 80 0 TTGGCGCGCGGCCCTACGGCTAAGCGTCGAGCTTGCGATACGCCACTATTACTTTAATATCTTACTCGCACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_57_231_8 147 test_chromosome 207 255 44M100N31M = 107 0 TTGGCGCGCGGCCCTAGGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_46_232_2f 147 test_chromosome 208 255 43M100N32M = 96 0 TGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_58_234_7 83 test_chromosome 210 255 41M100N34M = 108 0 GCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTAGTTTATTATCTGACTCGGACGTAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_41_236_55 145 test_chromosome 212 255 39M100N36M = 91 0 GCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_51_237_a 147 test_chromosome 213 255 38M100N37M = 101 0 CGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_65_238_2e 147 test_chromosome 214 255 37M100N38M = 115 0 GCGGCCCTACGGCTGCGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_96_238_3 83 test_chromosome 214 255 37M100N38M = 146 0 GCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCTACTAGTACTTTATTATCTTACGCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_73_240_34 147 test_chromosome 216 255 35M100N40M = 123 0 GGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_81_245_4d 83 test_chromosome 221 255 30M100N45M = 131 0 TACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATAATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_89_245_15 147 test_chromosome 221 255 30M100N45M = 139 0 TACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTCTATTATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_172_294_4f 99 test_chromosome 222 255 29M100N46M = 370 0 ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_51_248_14 145 test_chromosome 224 255 27M100N48M = 101 0 GGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAACGGCAACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_48_249_20 81 test_chromosome 225 255 26M100N49M = 98 0 GCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTACTATCTTACTCGGACGGAGACGGATCGGCAACGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_87_250_57 83 test_chromosome 226 255 25M100N50M = 137 0 ATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_92_250_44 147 test_chromosome 226 255 25M100N50M = 142 0 CTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGTACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_128_252_36 137 test_chromosome 228 255 23M100N52M * 0 0 GAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGAACGGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_72_258_4 83 test_chromosome 234 255 17M100N50M100N8M = 122 0 CGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATGGGCAACGGGACTTTTTCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_73_259_5e 147 test_chromosome 235 255 16M100N50M100N9M = 123 0 GAGCTTGCGATACGCCACTATTACTGTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_131_260_33 147 test_chromosome 236 255 15M100N50M100N10M = 181 0 AGCTTGTGATACGCCACTATTACTTTATTATCTTACTCGGACGTAAACGGATCGGCCACGGGACTTTTTTTACTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_52_261_1b 145 test_chromosome 237 255 14M100N50M100N11M = 102 0 GCTTGCGATACGCCACTATTACTTAATTATCTTACTCGGACGTAGAAGGATCGGCAACGGGACTTTTTCTACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_105_266_13 83 test_chromosome 242 255 9M100N50M100N16M = 155 0 CGATCCGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_92_266_43 147 test_chromosome 242 255 9M100N50M100N16M = 142 0 CGATACGCCACTATTACTTTCTTATCTTACTCGGACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_110_267_22 83 test_chromosome 243 255 8M100N50M100N17M = 160 0 GATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_89_267_32 83 test_chromosome 243 255 8M100N50M100N17M = 139 0 GATACGGCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_111_268_d 73 test_chromosome 244 255 7M100N50M100N18M * 0 0 ATACGCCACTATTATTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_85_268_53 147 test_chromosome 244 255 7M100N50M100N18M = 135 0 ATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGTCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_110_271_28 147 test_chromosome 247 255 4M100N50M100N21M = 160 0 CGCCACTATTACTTTATTATCTTACTCGGACGAAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_116_271_2b 83 test_chromosome 247 255 4M100N50M100N21M = 166 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACAGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_82_271_58 147 test_chromosome 247 255 4M100N50M100N21M = 132 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACGCATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_53_272_5a 81 test_chromosome 248 255 3M100N50M100N22M = 103 0 GCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGACACTGGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_104_274_1c 73 test_chromosome 350 255 51M100N24M * 0 0 CACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_85_275_38 137 test_chromosome 351 255 50M100N25M * 0 0 ACTCTTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTACTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_97_275_26 145 test_chromosome 351 255 50M100N25M = 147 0 ACTATTACTTTATTATCTTAGTCGGACGTAGACGGATCGGAAACGGGACTCTTTCTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_105_276_c 81 test_chromosome 352 255 49M100N26M = 155 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_78_276_4b 145 test_chromosome 352 255 49M100N26M = 128 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTAGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_114_277_5b 81 test_chromosome 353 255 48M100N27M = 164 0 TATTACTTTATTATCTTACTCGGAGGTAGACGGAACGGCAACGGGACTTTTTCTGCTTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NH:i:1 -test_mRNA_75_277_3b 145 test_chromosome 353 255 48M100N27M = 125 0 TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACCTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_104_278_3e 81 test_chromosome 354 255 47M100N28M = 154 0 ATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGAATCGAGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_87_279_5f 81 test_chromosome 355 255 46M100N29M = 137 0 TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_125_280_48 145 test_chromosome 356 255 45M100N30M = 175 0 TACTTTATTATCTTACTCTGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAGCGAGGCGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_126_282_18 81 test_chromosome 358 255 43M100N32M = 176 0 CTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_103_284_2a 81 test_chromosome 360 255 41M100N34M = 153 0 TTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_107_286_5 81 test_chromosome 362 255 39M100N36M = 157 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_151_286_e 137 test_chromosome 362 255 39M100N36M * 0 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTATCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_150_290_0 73 test_chromosome 366 255 35M100N40M * 0 0 TCTTACTCGGACGTAGACGGATCGCCAACGGGACTTTTTCTACTTGAGACTGAGACCGAGGCGGACTTTTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_94_291_40 137 test_chromosome 367 255 34M100N41M * 0 0 CTTCCTGGGACGTAGACGGATCGGCAACGCGACATTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NH:i:1 -test_mRNA_125_293_60 81 test_chromosome 369 255 32M100N43M = 175 0 TACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_172_294_4f 147 test_chromosome 370 255 31M100N44M = 222 0 ACTCGGACGTAGACGGGTCGGCAGCGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACGTTTTAGGACGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NH:i:1 -test_mRNA_116_295_63 81 test_chromosome 371 255 30M100N45M = 166 0 CTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_111_297_61 81 test_chromosome 373 255 28M100N47M = 161 0 CGGACGTAGACGGATCCGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_118_297_f 81 test_chromosome 373 255 28M100N47M = 168 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NH:i:1 -test_mRNA_151_297_1d 137 test_chromosome 373 255 28M100N47M * 0 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACATTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 -test_mRNA_122_299_6 81 test_chromosome 375 255 26M100N49M = 172 0 GACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NH:i:1 -test_mRNA_145_300_37 83 test_chromosome 376 255 25M100N50M = 195 0 ACGTAGACGGATCGGAAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NH:i:1 --- a/test-data/bwa_wrapper_in3.fastq +++ b/test-data/bwa_wrapper_in3.fastq @@ -1,4 +1,120 @@ -@081017-and-081020:1:1:1715:1759/1 -GGACTCAGATAGTAATCC -+/1 -II#IIIIIII$5+.(9II +@seq1/2 +ACGCTCCTTTAAAATATC ++/2 +IIIII$%*$G$A31I&&B +@seq2/2 +CAGCTCGAGAAGCTCTTA ++/2 +IIIIIIIIIIIIIIIIII +@seq3/2 +CTACTGACCGCTCTCGTG ++/2 +IIIIIIIIIIIIIIIIII +@seq4/2 +TAGGTGGTCAACCATTTT ++/2 +IIIIIIIIIIIIIIIIII +@seq5/2 +TTTCTATGTGGCTTAATA ++/2 +IIIIIIIIIIIIIIIIII +@seq6/2 +GTAGGTGGTCAACAATTT ++/2 +IIIIIIIIIIIIIIIIII +@seq7/2 +TTTAATTGCAGGGGCTTC ++/2 +IIIIIIIIIIIIIIIIII +@seq8/2 +ATGCGCTCTATTCTCTGG ++/2 +IIIIIIIIIIIIIIIIII +@seq9/2 +TTCTGTTGGTGCTGATAT ++/2 +IIIIIIIIIIIIIIIIII +@seq10/2 +AGGGCGTTGAGTTCGATA ++/2 +IIIIIIIIIIIIIIIIII +@seq11/2 +ATCCCCAATGCTTGGCTT ++/2 +IIIII$%*$G$A31I&&B +@seq12/2 +GGATTGGCGTTTCCAACC ++/2 +IIIIIIIIIIIIIIIIII +@seq13/2 +CCCCAATCCTTGCCTTCC ++/2 +IIIAAIIIIIIIIIIIII +@seq14/2 +TGATATTTTGACTTTGAG ++/2 +IIIIIIIIIIIIIIIIII +@seq15/2 +TTACGAAACGCGACGCCG ++/2 +IIIIIIIIIIIIIIIIII +@seq16/2 +TTATTTTTCTCCAGCCAC ++/2 +IIIIIIIIIIIIIIIIII +@seq17/2 +AAACAATACTTTAGGCAT ++/2 +IIIIIIIIIIIIIIIIII +@seq18/2 +CCGTTCCATAAGCAGATG ++/2 +IIIIIIIIIIIIIIIIII +@seq19/2 +GAGCGTCCTGGTGCTGAT ++ +IIIIIIIIIIIIIIIIII +@seq20/2 +ACTCCGGTTATCGCTGGC ++/2 +IIIIIIIIIIIIIIIIII +@seq21/2 +TAAGCATTTGGTTCAGGG ++/2 +IIIII$%*$G$A31I&&B +@seq22/2 +GTTACGACGCGACGCCGT ++/2 +IIIIIIIIIIIIIIIIII +@seq23/2 +TTTAATAACCCTATAGAC ++/2 +IIIIIIIIIIIIIIIIII +@seq24/2 +CTTGGCTTCCCTAAGCAG ++/2 +IIIIIIIIIIIIIIIIII +@seq25/2 +CGTGCTCGTTGCTGCGTT ++/2 +IIIIIIIIIIIIIIIIII +@seq26/2 +AAGGATGTTTTCCGTTCT ++/2 +IIIIIIIIIIIIIIIIII +@seq27/2 +TGTTTGGTGCTGATATTG ++/2 +IIIIIIIIIIIIIIIIII +@seq28/2 +TCCAGCCACTAAAGTGAG ++/2 +IIIIIIIIIIIIIIIIII +@seq29/2 +GATAATGATTGGGGTATC ++/2 +IIIIIIIIIIIIIIIIII +@seq30/2 +ACCATAAGCAGATGGATA ++/2 +IIIIIIIIIIIIIIIIII --- /dev/null +++ b/test-data/column_join_in15.tabular @@ -0,0 +1,11 @@ +alpha beta gamma +2 BBB II3 bbb i3 +3 CCC III3 ccc ii3 +4 DDD IV2 ddd iii3 +5 EEE V3 eee +6 FFF VI3 fff iv3 +7 GGG VII3 ggg v3 +8 HHH VIII3 hhh +9 III IX3 iii vi3 +10 JJJ X3 jjj vii3 +11 LLL XI3 lll --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -263,7 +263,7 @@ <param name="input2" ftype="fastqsanger" value="tophat_in2.fq"/><param name="mate_inner_distance" value="20"/><param name="pSettingsType" value="preSet"/> - <output name="accepted_hits" file="tophat_out1.sam"/> + <output name="accepted_hits" file="tophat_out1.sam" sort="True"/><output name="coverage" file="tophat_out2.wig"/><output name="junctions" file="tophat_out3.bed"/></test> --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -108,9 +108,8 @@ BWA commands: bwa aln -t 4 phiX test-data/bwa_wrapper_in1.fastq > bwa_wrapper_out1.sai bwa samse phiX bwa_wrapper_out1.sai test-data/bwa_wrapper_in1.fastq >> bwa_wrapper_out1.sam - phiX.fasta is the prefix for the reference + phiX.fa is the prefix for the reference files (phiX.fa.amb, phiX.fa.ann, phiX.fa.bwt, ...) remove the comment lines (beginning with '@') from the resulting sam file - note that 'phiX' should be 'PHIX174' to match what's in the indexed file --><param name="refGenomeSource" value="indexed" /><param name="indices" value="phiX" /> @@ -118,7 +117,7 @@ <param name="input1" value="bwa_wrapper_in1.fastq" ftype="fastqsanger" /><param name="source_select" value="pre_set" /><param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out1.sam" ftype="sam" sort="true" /> + <output name="output" file="bwa_wrapper_out1.sam" ftype="sam" sort="True" /></test><test><param name="refGenomeSource" value="history" /> @@ -152,17 +151,16 @@ <param name="maxInsertSize" value="500" /><param name="maxOccurPairing" value="100000" /><param name="suppressHeader" value="true" /> - <output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="true" /> + <output name="output" file="bwa_wrapper_out2.sam" ftype="sam" sort="True" /></test><test><param name="refGenomeSource" value="indexed" /><param name="indices" value="phiX" /> @@ -187,7 +185,7 @@ <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" /> + <output name="output" file="bwa_wrapper_out3.sam" ftype="sam" sort="True" /></test></tests><help> --- a/test-data/phiX.fasta +++ b/test-data/phiX.fasta @@ -1,79 +1,109 @@ >phiX -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA - +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTG +ATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTA +CGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTA +TCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACT +AACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATA +TGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTT +CATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGT +TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA +TTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTG +ACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTG +CGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCT +TTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCAT +CCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGT +TCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGAC +GCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATG +TCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTT +GCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTG +GTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATT +ATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTA +CTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTC +CGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACAT +TTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTA +AGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACT +ACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATAC +CAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAAT +GAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAA +AAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAA +TGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTAT +GCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCg +TGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACC +GTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACA +GACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTA +TGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATT +CAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGA +CCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATG +TTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAG +TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCG +TACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTG +TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT +GCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTG +AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT +TGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTT +CAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTA +AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT +AATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGC +TAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTA +AATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACC +CTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGG +TTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCT +ACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTAT +TTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGG +CGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAG +GCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACC +GATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCA +AGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCT +GGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGG +CAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTG +CATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCT +GCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAAT +GCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAA +AAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTAC +TGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGC +AGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGT +CAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGC +TGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTT +CTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCT +GCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTA +ATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTT +TTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCC +TTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTA +AACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATG +CTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGAT +TCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTT +ACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCA +ACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAAT +GGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCT +GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAA +GAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGA +AATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGA +CGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATT +TTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAAT +GATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTAC +AGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTC +CTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGC +CAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGC +CTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTT +GGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGC +TGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGC +TGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTC +GGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCA +ACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCC +GACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCG +CGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA --- /dev/null +++ b/test-data/column_join_out5.tabular @@ -0,0 +1,12 @@ +1 i i2 0 +2 ii 0 i3 +3 0 ii2 ii3 +4 0 iii2 iii3 +5 0 0 0 +6 0 iv2 iv3 +7 iii 0 v3 +8 0 v2 0 +9 0 vi2 vi3 +10 0 vii2 vii3 +11 iv viii2 0 +alpha 0 epsilon 0 --- a/test-data/bwa_wrapper_in1.fastq +++ b/test-data/bwa_wrapper_in1.fastq @@ -1,4 +1,120 @@ -@081017-and-081020:1:1:1715:1759 +@seq1 GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC + II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B +@seq2 +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq3 +GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq4 +AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq5 +CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq6 +AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq7 +TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq8 +ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq9 +GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq10 +ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq11 +GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B +@seq12 +CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq13 +ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC ++ +IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII +@seq14 +CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq15 +CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq16 +TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq17 +GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq18 +TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq19 +TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq20 +CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq21 +CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B +@seq22 +AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq23 +TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq24 +TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq25 +TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq26 +CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq27 +CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq28 +AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq29 +CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq30 +ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII --- /dev/null +++ b/test-data/column_join_in14.tabular @@ -0,0 +1,11 @@ +alpha beta gamma delta epsilon +1 AA I2 aa i2 +2 BB II2 bb +3 CC III2 cc ii2 +4 DD IV2 dd iii2 +6 EE V2 ee iv2 +7 FF VI2 ff +8 GG VII2 gg v2 +9 HH VIII2 hh vi2 +10 II IX2 ii vii2 +11 JJ X2 jj viii2 --- a/test-data/bwa_wrapper_out2.sam +++ b/test-data/bwa_wrapper_out2.sam @@ -1,1 +1,30 @@ -081017-and-081020:1:1:1715:1759 16 phiX 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq1 16 phiX 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq10 0 phiX 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII +seq14 0 phiX 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq17 0 phiX 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq2 0 phiX 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq20 0 phiX 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq24 0 phiX 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq3 0 phiX 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq30 0 phiX 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 +seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq5 0 phiX 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq9 0 phiX 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27

1 0

galaxy-dist commit 959157848189: (no commit message)
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282769169 14400 # Node ID 95915784818931029539fd058c328e45470d34c2 # Parent b1a9700382738ba805c20047f40541b06d33b04b (no commit message) --- a/tools/mutation/visualize.xml +++ b/tools/mutation/visualize.xml @@ -1,9 +1,16 @@ <tool id="mutation_visualize" name="Mutation Visualization" version="1.0.0"><description></description> - <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 $header_row</command> + <command interpreter="python">visualize.py --input-file=$input --output-file=$out_file1 --zoom=$zoom_value $header_row</command><inputs><param format="tabular" name="input" type="data" label="Compare sequences in"></param><param name="header_row" type="boolean" label="Header in dataset?" checked="yes" truevalue="" falsevalue="--noheaders"/> + <param name="zoom_value" type="select" label="Zoom"> + <option value="1">1x</option> + <option value="2">2x</option> + <option value="3">3x</option> + <option value="4">4x</option> + <option value="5">5x</option> + </param></inputs><outputs><data format="svg" name="out_file1" /> --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -17,21 +17,21 @@ import svgfig as svg COLS_PER_SAMPLE = 7 HEADER_COLS = 4 -SPACE_PAIRS = 0.8 -SPACE_SAMPLES = 1 +HEIGHT = 6 +WIDTH = 12 +BAR_WIDTH = 1.5 +GAP = 2 -HEIGHT = 4 -WIDTH = 8 colors = {'A':'blue', 'C':'green', 'G':'orange', 'T':'red'} bases = ['A', 'C', 'G', 'T' ] def mainsvg(opts): - s = svg.SVG('g') + s = svg.SVG('g', transform="translate(20,0)") # display legend - for i, b in enumerate(bases): + for i, b in enumerate( bases ): bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:3") s.append(svg.SVG("text", bt, x=12+(i*10), y=8, stroke="none", fill="black")) s.append(svg.SVG("rect", x=13+(i*10), y=5, width=4, height=3, @@ -71,10 +71,10 @@ def mainsvg(opts): #print 'position', position, ref, count # display positions - bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:3") - s.append(svg.SVG("text", bt, x=9, y=33+(count*5), stroke="none", fill="black")) - s.append(svg.SVG("rect", x=4, y=30+(count*5), width=10, height=4, - stroke='none', fill=colors[ref.upper()], fill_opacity=0.3)) + bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:4") + s.append(svg.SVG("text", bt, x=7, y=34+(count*(HEIGHT+GAP)), stroke="none", fill="black")) + s.append(svg.SVG("rect", x=0, y=30+(count*(HEIGHT+GAP)), width=14, height=HEIGHT, + stroke='none', fill=colors[ref.upper()], fill_opacity=0.2)) for sample_index in range(int((len(row)-HEADER_COLS)/COLS_PER_SAMPLE)): start_col = HEADER_COLS+(COLS_PER_SAMPLE*sample_index) @@ -88,10 +88,10 @@ def mainsvg(opts): #print 'sample_index', sample_index, total if total: - x = 16+(sample_index*10) - y = 30+(count*5) + x = 16+(sample_index*(WIDTH+GAP)) + y = 30+(count*(HEIGHT+GAP)) width = WIDTH - height = 4 + height = HEIGHT if imp == 1: fill_opacity = 0.1 @@ -104,18 +104,21 @@ def mainsvg(opts): stroke='none', fill='grey', fill_opacity=fill_opacity)) for base, value in enumerate([n_a, n_c, n_g, n_t]): width = int(math.ceil(value / total * WIDTH)) - s.append(svg.SVG("rect", x=x, y=y, width=width, height=1, + s.append(svg.SVG("rect", x=x, y=y, width=width, height=BAR_WIDTH, stroke='none', fill=colors[bases[base]], fill_opacity=0.6)) - y = y + 1 + y = y + BAR_WIDTH #print base, value, total, x, y, width count=count+1 - - w = str(int(700)) + "px" - h = str(int(1000)) + "px" - canv = svg.canvas(s, width=w, height=h, viewBox="0 0 200 300") + + #print x, y + + zoom = int(opts.zoom) + w = "%ipx" % (x*(10+zoom)) + h = "%ipx" % (y*(2+zoom)) + canv = svg.canvas(s, width=w, height=h, viewBox="0 0 %i %i" %(x+100, y+100)) canv.save(opts.output_file) @@ -123,6 +126,7 @@ if __name__ == '__main__': parser = optparse.OptionParser() parser.add_option('-i', '--input-file', dest='input_file', action='store') parser.add_option('-o', '--output-file', dest='output_file', action='store') + parser.add_option('-z', '--zoom', dest='zoom', action='store', default='1') parser.add_option('-n', '--noheaders', dest='header_row', action='store_false', default=True) (opts, args) = parser.parse_args() mainsvg(opts)

1 0

galaxy-dist commit b1a970038273: added svg datatype
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282753644 14400 # Node ID b1a9700382738ba805c20047f40541b06d33b04b # Parent d36d759bce05d7cd6db99b115ae8ebb549e09ce7 added svg datatype --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -105,6 +105,7 @@ <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/><datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> + <datatype extension="svg" type="galaxy.datatypes.images:Image" mimetype="image/svg+xml"/><datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/><datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/><datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>

1 0

galaxy-dist commit 7fa394981ef6: Bug fixes and basic zoom feature for mutation viz tool
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1282769259 14400 # Node ID 7fa394981ef6f8d079cd8dd776cba349baca958f # Parent 95915784818931029539fd058c328e45470d34c2 Bug fixes and basic zoom feature for mutation viz tool --- a/tools/mutation/visualize.py +++ b/tools/mutation/visualize.py @@ -85,8 +85,6 @@ def mainsvg(opts): total = int(row[start_col+4]) diff = int(row[start_col+5]) imp = int(row[start_col+6]) - - #print 'sample_index', sample_index, total if total: x = 16+(sample_index*(WIDTH+GAP)) y = 30+(count*(HEIGHT+GAP))

1 0

galaxy-dist commit 5d3e57e28fb7: Enhance grid framework to enable custom column sorting. Sort criteria are now mapped to a column, and the column defines the sorting to be done on the grid query. Default sorting behavior has not changed. In addition, column's model_class attribute now defaults to the grid's model_class; this should make column definitions more intuitive and shorter.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1282595659 14400 # Node ID 5d3e57e28fb7fa524a47d3a9b7e99f73ebca6676 # Parent 60448575467fef8f6a42d83906ee2a622511c541 Enhance grid framework to enable custom column sorting. Sort criteria are now mapped to a column, and the column defines the sorting to be done on the grid query. Default sorting behavior has not changed. In addition, column's model_class attribute now defaults to the grid's model_class; this should make column definitions more intuitive and shorter. Used custom sorting functionality to enable (a) case-insensitive sorting of text fields and (b) case-insensitive sorting of published item by username. --- a/templates/history/list_published.mako +++ b/templates/history/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -107,14 +107,14 @@ class HistoryDatasetAssociationListGrid( title = "Saved Datasets" model_class = model.HistoryDatasetAssociation template='/dataset/grid.mako' - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ - grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, + grids.TextColumn( "Name", key="name", # Link name to dataset's history. - link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -38,16 +38,15 @@ class HistoryListGrid( grids.Grid ): title = "Saved Histories" model_class = model.History template='/history/grid.mako' - default_sort_key = "-create_time" + default_sort_key = "-update_time" columns = [ - NameColumn( "Name", key="name", model_class=model.History, + NameColumn( "Name", key="name", link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, \ - model_tag_association_class=model.HistoryTagAssociation, \ + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, \ filterable="advanced", grid_name="HistoryListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. @@ -130,10 +129,10 @@ class HistoryAllPublishedGrid( grids.Gri default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), + NameURLColumn( "Name", key="name", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -37,8 +37,8 @@ class StoredWorkflowListGrid( grids.Grid default_filter = { "name" : "All", "tags": "All" } default_sort_key = "-update_time" columns = [ - grids.TextColumn( "Name", key="name", model_class=model.StoredWorkflow, attach_popup=True, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), + grids.TextColumn( "Name", key="name", attach_popup=True, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", "tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="StoredWorkflowListGrid" ), StepsColumn( "Steps" ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -67,10 +67,10 @@ class StoredWorkflowAllPublishedGrid( gr default_filter = dict( public_url="All", username="All", tags="All" ) use_async = True columns = [ - grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.PublicURLColumn( "Name", key="name", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/templates/visualization/list_published.mako +++ b/templates/visualization/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/templates/workflow/list_published.mako +++ b/templates/workflow/list_published.mako @@ -28,7 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${unicode( grid, 'utf-8' )} + ${h.to_unicode( grid )} </div></div> --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -12,11 +12,11 @@ class VisualizationListGrid( grids.Grid default_sort_key = "-update_time" default_filter = dict( title="All", deleted="False", tags="All", sharing="All" ) columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Visualization, attach_popup=True, + grids.TextColumn( "Title", key="title", attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), - grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), + grids.TextColumn( "Dbkey", key="dbkey" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -47,10 +47,10 @@ class VisualizationAllPublishedGrid( gri default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - grids.PublicURLColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Visualization, model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), + grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/templates/page/index.mako +++ b/templates/page/index.mako @@ -15,7 +15,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} + ${h.to_unicode( grid )} <br><br><h2>Pages shared with you by others</h2> --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -25,11 +25,11 @@ class PageListGrid( grids.Grid ): default_filter = { "published" : "All", "tags" : "All", "title" : "All", "sharing" : "All" } default_sort_key = "-create_time" columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), + grids.TextColumn( "Title", key="title", attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] @@ -61,10 +61,10 @@ class PageAllPublishedGrid( grids.Grid ) default_sort_key = "-update_time" default_filter = dict( title="All", username="All" ) columns = [ - grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), - grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), + grids.PublicURLColumn( "Title", key="title", filterable="advanced" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.OwnerColumn( "Owner", key="owner", model_class=model.User, filterable="advanced" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( @@ -107,12 +107,12 @@ class HistorySelectionGrid( ItemSelectio title = "Saved Histories" model_class = model.History columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -130,12 +130,12 @@ class HistoryDatasetAssociationSelection title = "Saved Datasets" model_class = model.HistoryDatasetAssociation columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.HistoryDatasetAssociation, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -155,12 +155,12 @@ class WorkflowSelectionGrid( ItemSelecti title = "Saved Workflows" model_class = model.StoredWorkflow columns = [ - ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), + ItemSelectionGrid.NameColumn( "Name", key="name", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.StoredWorkflow, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -175,12 +175,12 @@ class PageSelectionGrid( ItemSelectionGr title = "Saved Pages" model_class = model.Page columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced"), + grids.TextColumn( "Title", key="title", filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False, visible=False ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False, visible=False ), ] columns.append( grids.MulticolFilterColumn( @@ -195,10 +195,10 @@ class VisualizationSelectionGrid( ItemSe title = "Saved Visualizations" model_class = model.Visualization columns = [ - grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), - grids.TextColumn( "Type", key="type", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), - grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), + grids.TextColumn( "Title", key="title", filterable="advanced" ), + grids.TextColumn( "Type", key="type" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.SharingStatusColumn( "Sharing", key="sharing", filterable="advanced", sortable=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] columns.append( @@ -299,8 +299,8 @@ class PageController( BaseController, Sh return self.sharing( trans, **kwargs ) session.flush() - # Build grid HTML and make sure to encode in utf-8 to support unicode characters. - grid = unicode( self._page_list( trans, *args, **kwargs ), 'utf-8' ) + # Build grid HTML. + grid = self._page_list( trans, *args, **kwargs ) # Build list of pages shared with user. shared_by_others = trans.sa_session \ @@ -316,7 +316,7 @@ class PageController( BaseController, Sh @web.expose def list_published( self, trans, *args, **kwargs ): - grid = unicode( self._all_published_list( trans, *args, **kwargs ), 'utf-8' ) + grid = self._all_published_list( trans, *args, **kwargs ) if 'async' in kwargs: return grid else: --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -4,6 +4,7 @@ from galaxy.web.framework.helpers import from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string from galaxy.util.odict import odict +from galaxy.web.framework.helpers import to_unicode import sys, logging, math @@ -41,12 +42,25 @@ class Grid( object ): if operation.allow_multiple: self.has_multiple_item_operations = True break + + # If a column does not have a model class, set the column's model class + # to be the grid's model class. + for column in self.columns: + if not column.model_class: + column.model_class = self.model_class + def __call__( self, trans, **kwargs ): + # + # Get basics. + # webapp = kwargs.get( 'webapp', 'galaxy' ) status = kwargs.get( 'status', None ) message = kwargs.get( 'message', None ) + + # # Build a base filter and sort key that is the combination of the saved state and defaults. # Saved state takes preference over defaults. + # base_filter = {} if self.default_filter: # default_filter is a dictionary that provides a default set of filters based on the grid's columns. @@ -70,8 +84,11 @@ class Grid( object ): use_default_filter = False if use_default_filter_str: use_default_filter = ( use_default_filter_str.lower() == 'true' ) + + # # Process filtering arguments to (a) build a query that represents the filter and (b) builds a - # dictionary that denotes the current filter. + # dictionary that denotes the current filter. + # cur_filter_dict = {} for column in self.columns: if column.key: @@ -134,23 +151,39 @@ class Grid( object ): if not isinstance( column_filter, basestring ): column_filter = unicode(column_filter) extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") + + # # Process sort arguments. + # sort_key = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key - if sort_key: + + if sort_key: if sort_key.startswith( "-" ): - # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... - query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) + ascending = False + column_key = sort_key[1:] else: - # See reason for not using lower() to do case-insensitive sorting. - query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) - extra_url_args['sort'] = sort_key + ascending = True + column_key = sort_key + + # Sort key is a column key. + for column in self.columns: + if column.key == column_key: + query = column.sort( query, ascending ) + break + extra_url_args['sort'] = sort_key + + # # There might be a current row + # current_item = self.get_current_item( trans, **kwargs ) + + # # Process page number. + # if self.use_paging: if 'page' in kwargs: if kwargs['page'] == 'all': @@ -175,7 +208,10 @@ class Grid( object ): # Defaults. page_num = 1 num_pages = 1 + + # # Preserve grid state: save current filter and sort key. + # if self.preserve_state: pref_name = unicode( self.__class__.__name__ + self.cur_filter_pref_name ) trans.get_user().preferences[pref_name] = unicode( to_json_string( cur_filter_dict ) ) @@ -191,7 +227,10 @@ class Grid( object ): params['async'] = ( 'async' in kwargs ) params['webapp'] = webapp trans.log_action( trans.get_user(), unicode( "grid.view" ), context, params ) + + # # Render grid. + # def url( *args, **kwargs ): # Only include sort/filter arguments if not linking to another # page. This is a bit of a hack. @@ -211,9 +250,14 @@ class Grid( object ): else: new_kwargs[ 'id' ] = trans.security.encode_id( id ) return url_for( **new_kwargs ) - use_panels = ( 'use_panels' in kwargs ) and ( kwargs['use_panels'] in [ True, 'True', 'true' ] ) - async_request = ( ( self.use_async ) and ( 'async' in kwargs ) and ( kwargs['async'] in [ True, 'True', 'true'] ) ) - return trans.fill_template( iff( async_request, self.async_template, self.template), + use_panels = ( kwargs.get( 'use_panels', False ) in [ True, 'True', 'true' ] ) + async_request = ( ( self.use_async ) and ( kwargs.get( 'async', False ) in [ True, 'True', 'true'] ) ) + # Currently, filling the template returns a str object; this requires decoding the string into a + # unicode object within mako templates. What probably should be done is to return the template as + # utf-8 unicode; however, this would require encoding the object as utf-8 before returning the grid + # results via a controller method, which is require substantial changes. Hence, for now, return grid + # as str. + return trans.fill_template( iff( async_request, self.async_template, self.template ), grid=self, query=query, cur_page_num = page_num, @@ -258,11 +302,14 @@ class Grid( object ): return query class GridColumn( object ): - def __init__( self, label, grid=None, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, - # Valid values for filterable are ['standard', 'advanced', None] - filterable=None, sortable=True ): + def __init__( self, label, key=None, model_class=None, method=None, format=None, \ + link=None, attach_popup=False, visible=True, ncells=1, \ + # Valid values for filterable are ['standard', 'advanced', None] + filterable=None, sortable=True ): + """ + Create a grid column. + """ self.label = label - self.grid = grid self.key = key self.model_class = model_class self.method = method @@ -272,12 +319,9 @@ class GridColumn( object ): self.visible = visible self.ncells = ncells self.filterable = filterable - # Currently can only sort of columns that have a database - # representation, not purely derived. - if self.key and sortable: - self.sortable = True - else: - self.sortable = False + # Column must have a key to be sortable. + self.sortable = ( self.key is not None and sortable ) + def get_value( self, trans, grid, item ): if self.method: value = getattr( grid, self.method )( trans, item ) @@ -288,10 +332,12 @@ class GridColumn( object ): if self.format: value = self.format( value ) return value + def get_link( self, trans, grid, item ): if self.link and self.link( item ): return self.link( item ) return None + def filter( self, trans, user, query, column_filter ): """ Modify query to reflect the column filter. """ if column_filter == "All": @@ -301,6 +347,7 @@ class GridColumn( object ): elif column_filter == "False": query = query.filter_by( **{ self.key: False } ) return query + def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ accepted_filters_vals = [ "False", "True", "All" ] @@ -309,6 +356,15 @@ class GridColumn( object ): args = { self.key: val } accepted_filters.append( GridColumnFilter( val, args) ) return accepted_filters + + def sort( self, query, ascending ): + """ Sort query using this column. """ + if ascending: + query = query.order_by( self.model_class.table.c.get( self.key ).asc() ) + else: + query = query.order_by( self.model_class.table.c.get( self.key ).desc() ) + return query + class TextColumn( GridColumn ): """ Generic column that employs freetext and, hence, supports freetext, case-independent filtering. """ @@ -332,6 +388,14 @@ class TextColumn( GridColumn ): """ Returns a SQLAlchemy criterion derived for a single filter. Single filter is the most basic filter--usually a string--and cannot be a list. """ model_class_key_field = getattr( self.model_class, self.key ) return func.lower( model_class_key_field ).like( "%" + a_filter.lower() + "%" ) + + def sort( self, query, ascending ): + """ Sort column using case-insensitive alphabetical sorting. """ + if ascending: + query = query.order_by( func.lower ( self.model_class.table.c.get( self.key ) ).asc() ) + else: + query = query.order_by( func.lower( self.model_class.table.c.get( self.key ) ).desc() ) + return query class IntegerColumn( TextColumn ): """ @@ -357,7 +421,7 @@ class IntegerColumn( TextColumn ): class OwnerAnnotationColumn( TextColumn, UsesAnnotations ): """ Column that displays and filters item owner's annotations. """ - def __init__( self, col_name, key, model_class, model_annotation_association_class, filterable ): + def __init__( self, col_name, key, model_class=None, model_annotation_association_class=None, filterable=None ): GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) self.sortable = False self.model_annotation_association_class = model_annotation_association_class @@ -375,11 +439,9 @@ class OwnerAnnotationColumn( TextColumn, class CommunityTagsColumn( TextColumn ): """ Column that supports community tags. """ - def __init__( self, col_name, key, model_class, model_tag_association_class, filterable, grid_name=None ): - GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable ) + def __init__( self, col_name, key, model_class=None, model_tag_association_class=None, filterable=None, grid_name=None ): + GridColumn.__init__( self, col_name, key=key, model_class=model_class, filterable=filterable, sortable=False ) self.model_tag_association_class = model_tag_association_class - # Tags cannot be sorted. - self.sortable = False # Column-specific attributes. self.grid_name = grid_name def get_value( self, trans, grid, item ): @@ -464,6 +526,15 @@ class OwnerColumn( TextColumn ): """ Column that lists item's owner. """ def get_value( self, trans, grid, item ): return item.user.username + + def sort( self, query, ascending ): + """ Sort column using case-insensitive alphabetical sorting on item's username. """ + if ascending: + query = query.order_by( func.lower ( self.model_class.username ).asc() ) + else: + query = query.order_by( func.lower( self.model_class.username ).desc() ) + return query + class PublicURLColumn( TextColumn ): """ Column displays item's public URL based on username and slug. """ @@ -474,7 +545,7 @@ class PublicURLColumn( TextColumn ): # TODO: provide link to set username. return None elif not item.user.slug: - # TODO: provide link to set slg + # TODO: provide link to set slug. return None class DeletedColumn( GridColumn ): --- a/templates/page/list_published.mako +++ b/templates/page/list_published.mako @@ -28,6 +28,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} - + ${h.to_unicode( grid )} + </div> + </div></%def> --- a/templates/visualization/list.mako +++ b/templates/visualization/list.mako @@ -13,7 +13,7 @@ <div style="overflow: auto; height: 100%;"><div class="page-container" style="padding: 10px;"> - ${grid} + ${h.to_unicode( grid )} <br><br><h2>Visualizations shared with you by others</h2>

1 0

galaxy-dist commit d36d759bce05: Fix left padding issues on the edit attributes form
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1282674785 14400 # Node ID d36d759bce05d7cd6db99b115ae8ebb549e09ce7 # Parent 5d3e57e28fb7fa524a47d3a9b7e99f73ebca6676 Fix left padding issues on the edit attributes form --- a/templates/dataset/edit_attributes.mako +++ b/templates/dataset/edit_attributes.mako @@ -82,11 +82,13 @@ </form><form name="auto_detect" action="${h.url_for( controller='root', action='edit' )}" method="post"><input type="hidden" name="id" value="${data.id}"/> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="detect" value="${_('Auto-detect')}"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - This will inspect the dataset and attempt to correct the above column values if they are not accurate. + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="detect" value="${_('Auto-detect')}"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + This will inspect the dataset and attempt to correct the above column values if they are not accurate. + </div></div></form> %if data.missing_meta(): @@ -190,9 +192,9 @@ <form name="copy_hda" action="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" method="post"><div class="form-row"><input type="submit" name="change" value="Copy history item"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Make a copy of this history item in your current history or any of your active histories. + <div class="toolParamHelp" style="clear: both;"> + Make a copy of this history item in your current history or any of your active histories. + </div></div></form></div>

1 0

galaxy-dist commit 60448575467f: Merge.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Dannon Baker <dannonbaker(a)me.com> # Date 1282572917 14400 # Node ID 60448575467fef8f6a42d83906ee2a622511c541 # Parent 26a0b620490dd8698deb907ecaa540e7fa19a6ee # Parent 9bcd722236bd7d74784d7317bbe53fa3f050d101 Merge.

1 0

galaxy-dist commit 7242f2dffed3: Fixed another bug in column join so it will handle filling empty columns properly
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kelly Vincent <kpvincent(a)bx.psu.edu> # Date 1282338256 14400 # Node ID 7242f2dffed302ad6d0d727e43ede1ed65c39463 # Parent 8a3d3fba037061a818b4417978542ae7b71f2e1a Fixed another bug in column join so it will handle filling empty columns properly --- a/tools/new_operations/column_join.py +++ b/tools/new_operations/column_join.py @@ -241,10 +241,14 @@ def __main__(): new_split_line = split_line[:] split_line = [] for i, item in enumerate( new_split_line ): - if item: + col = i + 1 + if not item: + try: + split_line.append( fill_empty[ i + 1 ] ) + except KeyError: + split_line.append( item ) + else: split_line.append( item ) - else: - split_line.append( fill_empty[ i + 1 ] ) # add actual data to be output below if ''.join( split_line ): for col in cols: @@ -265,9 +269,11 @@ def __main__(): fout.write( '%s%s' % ( delimiter, delimiter.join( current_data ) ) ) elif current_data: fout.write( '%s%s%s' % ( current, delimiter, delimiter.join( current_data ) ) ) + last_lines = ''.join( current_lines ) + else: + last_lines = None last_loc = loc old_current = current - last_lines = ''.join( current_lines ) first_line = False # fill trailing empty columns for final line if last_loc < len( inputs ) - 1:

1 0

galaxy-dist commit 9bcd722236bd: Refactoring of grid framework in preparation for enhancing sorting. Removed unused keyword 'encoded_sort_key' and made all GridColumn constructor keyword parameters explicit.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1282492757 14400 # Node ID 9bcd722236bd7d74784d7317bbe53fa3f050d101 # Parent 3ab68d0ba173ea4b21317c79fdea907bd91f5a81 Refactoring of grid framework in preparation for enhancing sorting. Removed unused keyword 'encoded_sort_key' and made all GridColumn constructor keyword parameters explicit. --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -114,7 +114,7 @@ class HistoryDatasetAssociationListGrid( link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced", attach_popup=True ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced", grid_name="HistoryDatasetAssocationListGrid" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -44,7 +44,9 @@ class HistoryListGrid( grids.Grid ): link=( lambda history: iff( history.deleted, None, dict( operation="Switch", id=history.id ) ) ), attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="HistoryListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, \ + model_tag_association_class=model.HistoryTagAssociation, \ + filterable="advanced", grid_name="HistoryListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.History, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -131,7 +133,7 @@ class HistoryAllPublishedGrid( grids.Gri NameURLColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.History, model_annotation_association_class=model.HistoryAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced", grid_name="PublicHistoryListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/workflow.py +++ b/lib/galaxy/web/controllers/workflow.py @@ -70,7 +70,7 @@ class StoredWorkflowAllPublishedGrid( gr grids.PublicURLColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.StoredWorkflow, model_annotation_association_class=model.StoredWorkflowAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced", grid_name="PublicWorkflowListGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/visualization.py +++ b/lib/galaxy/web/controllers/visualization.py @@ -15,7 +15,7 @@ class VisualizationListGrid( grids.Grid grids.TextColumn( "Title", key="title", model_class=model.Visualization, attach_popup=True, link=( lambda item: dict( controller="tracks", action="browser", id=item.id ) ) ), grids.TextColumn( "Dbkey", key="dbkey", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -50,7 +50,7 @@ class VisualizationAllPublishedGrid( gri grids.PublicURLColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Visualization, model_annotation_association_class=model.VisualizationAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( --- a/lib/galaxy/web/controllers/page.py +++ b/lib/galaxy/web/controllers/page.py @@ -27,7 +27,8 @@ class PageListGrid( grids.Grid ): columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, attach_popup=True, filterable="advanced" ), URLColumn( "Public URL" ), - grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), + grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Page, filterable="advanced", sortable=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), @@ -63,7 +64,7 @@ class PageAllPublishedGrid( grids.Grid ) grids.PublicURLColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), grids.OwnerAnnotationColumn( "Annotation", key="annotation", model_class=model.Page, model_annotation_association_class=model.PageAnnotationAssociation, filterable="advanced" ), grids.OwnerColumn( "Owner", key="username", model_class=model.User, filterable="advanced", sortable=False ), - grids.CommunityTagsColumn( "Community Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), + grids.CommunityTagsColumn( "Community Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced", grid_name="PageAllPublishedGrid" ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ) ] columns.append( @@ -107,7 +108,7 @@ class HistorySelectionGrid( ItemSelectio model_class = model.History columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.History, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.History, model_tag_association_class=model.HistoryTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -130,7 +131,7 @@ class HistoryDatasetAssociationSelection model_class = model.HistoryDatasetAssociation columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.HistoryDatasetAssociation, model_tag_association_class=model.HistoryDatasetAssociationTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -155,7 +156,7 @@ class WorkflowSelectionGrid( ItemSelecti model_class = model.StoredWorkflow columns = [ ItemSelectionGrid.NameColumn( "Name", key="name", model_class=model.StoredWorkflow, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.StoredWorkflow, model.StoredWorkflowTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.StoredWorkflow, model_tag_association_class=model.StoredWorkflowTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -175,7 +176,7 @@ class PageSelectionGrid( ItemSelectionGr model_class = model.Page columns = [ grids.TextColumn( "Title", key="title", model_class=model.Page, filterable="advanced" ), - grids.IndividualTagsColumn( "Tags", "tags", model.Page, model.PageTagAssociation, filterable="advanced"), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Page, model_tag_association_class=model.PageTagAssociation, filterable="advanced"), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. grids.DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), @@ -196,7 +197,7 @@ class VisualizationSelectionGrid( ItemSe columns = [ grids.TextColumn( "Title", key="title", model_class=model.Visualization, filterable="advanced" ), grids.TextColumn( "Type", key="type", model_class=model.Visualization ), - grids.IndividualTagsColumn( "Tags", "tags", model.Visualization, model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), + grids.IndividualTagsColumn( "Tags", key="tags", model_class=model.Visualization, model_tag_association_class=model.VisualizationTagAssociation, filterable="advanced", grid_name="VisualizationListGrid" ), grids.SharingStatusColumn( "Sharing", key="sharing", model_class=model.Visualization, filterable="advanced", sortable=False ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -140,15 +140,14 @@ class Grid( object ): sort_key = kwargs['sort'] elif base_sort_key: sort_key = base_sort_key - encoded_sort_key = sort_key if sort_key: if sort_key.startswith( "-" ): # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) else: - # See reason for not using lower() to do case-insensitive search. + # See reason for not using lower() to do case-insensitive sorting. query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) - extra_url_args['sort'] = encoded_sort_key + extra_url_args['sort'] = sort_key # There might be a current row current_item = self.get_current_item( trans, **kwargs ) # Process page number. @@ -222,7 +221,6 @@ class Grid( object ): default_filter_dict=self.default_filter, cur_filter_dict=cur_filter_dict, sort_key=sort_key, - encoded_sort_key=encoded_sort_key, current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, @@ -260,10 +258,11 @@ class Grid( object ): return query class GridColumn( object ): - def __init__( self, label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, + def __init__( self, label, grid=None, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, # Valid values for filterable are ['standard', 'advanced', None] filterable=None, sortable=True ): self.label = label + self.grid = grid self.key = key self.model_class = model_class self.method = method --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -255,7 +255,7 @@ } // Add sort argument to URL args. - url_args['sort'] = "${encoded_sort_key}"; + url_args['sort'] = "${sort_key}"; // Add async keyword to URL args. url_args['async'] = true;

1 0

galaxy-dist commit 3ab68d0ba173: Fixes for performance problems with display link generation.
by commits-noreply＠bitbucket.org 08 Sep '10

08 Sep '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor <james(a)jamestaylor.org> # Date 1282421852 14400 # Node ID 3ab68d0ba173ea4b21317c79fdea907bd91f5a81 # Parent 7242f2dffed302ad6d0d727e43ede1ed65c39463 Fixes for performance problems with display link generation. 1) In "ucsc_links", "generate_display_viewport" was being called before the check for configured UCSC browsers matching the dataset's build. Thus, Galaxy would scan the start of the file for every dataset, regardless of whether UCSC links were displayed in the UI 2) When generating the viewport, if an exception was thrown parsing the chrom/start/end columns (for example, if the metadata was set wrong causing a non-numeric string to be found in the start column) the loop would continue WITHOUT executing the scan to end of line and update of the number of lines processed. Thus, on any file with incorrect metadata, every line of the file would be read and split. --- a/lib/galaxy/datatypes/interval.py +++ b/lib/galaxy/datatypes/interval.py @@ -1,7 +1,7 @@ """ Interval datatypes +""" -""" import pkg_resources pkg_resources.require( "bx-python" ) @@ -20,10 +20,8 @@ import math log = logging.getLogger(__name__) -# -# contain the meta columns and the words that map to it -# list aliases on the right side of the : in decreasing order of priority -# +# Contains the meta columns and the words that map to it; list aliases on the +# right side of the : in decreasing order of priority alias_spec = { 'chromCol' : [ 'chrom' , 'CHROMOSOME' , 'CHROM', 'Chromosome Name' ], 'startCol' : [ 'start' , 'START', 'chromStart', 'txStart', 'Start Position (bp)' ], @@ -38,9 +36,11 @@ for key, value in alias_spec.items(): for elem in value: alias_helper[elem] = key -#Constants for configuring viewport generation -VIEWPORT_READLINE_BUFFER_SIZE = 1048576 #1MB -VIEWPORT_MAX_READS_PER_LINE = 10 # If a line is greater than VIEWPORT_MAX_READS_PER_LINE * VIEWPORT_READLINE_BUFFER_SIZE bytes in size, then we will not generate a viewport for that dataset +# Constants for configuring viewport generation: If a line is greater than +# VIEWPORT_MAX_READS_PER_LINE * VIEWPORT_READLINE_BUFFER_SIZE bytes in size, +# then we will not generate a viewport for that dataset +VIEWPORT_READLINE_BUFFER_SIZE = 1048576 # 1MB +VIEWPORT_MAX_READS_PER_LINE = 10 class Interval( Tabular ): """Tab delimited data containing interval information""" @@ -150,55 +150,66 @@ class Interval( Tabular ): and dataset.metadata.endCol except: return False + def get_estimated_display_viewport( self, dataset, chrom_col = None, start_col = None, end_col = None ): """Return a chrom, start, stop tuple for viewing a file.""" viewport_feature_count = 100 # viewport should check at least 100 features; excludes comment lines max_line_count = max( viewport_feature_count, 500 ) # maximum number of lines to check; includes comment lines - if self.displayable( dataset ): - try: - chrom = None - start = sys.maxint - end = 0 - if chrom_col is None: - chrom_col = int( dataset.metadata.chromCol ) - 1 - if start_col is None: - start_col = int( dataset.metadata.startCol ) - 1 - if end_col is None: - end_col = int( dataset.metadata.endCol ) - 1 - max_col = max( chrom_col, start_col, end_col ) - fh = open( dataset.file_name ) - while True: + if not self.displayable( dataset ): + return ( None, None, None ) + try: + # If column indexes were not passwed, determine from metadata + if chrom_col is None: + chrom_col = int( dataset.metadata.chromCol ) - 1 + if start_col is None: + start_col = int( dataset.metadata.startCol ) - 1 + if end_col is None: + end_col = int( dataset.metadata.endCol ) - 1 + # Scan lines of file to find a reasonable chromosome and range + chrom = None + start = sys.maxint + end = 0 + max_col = max( chrom_col, start_col, end_col ) + fh = open( dataset.file_name ) + while True: + line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) + # Stop if at end of file + if not line: + break + # Skip comment lines + if not line.startswith( '#' ): + try: + fields = line.rstrip().split( '\t' ) + if len( fields ) > max_col: + if chrom is None or chrom == fields[ chrom_col ]: + start = min( start, int( fields[ start_col ] ) ) + end = max( end, int( fields[ end_col ] ) ) + # Set chrom last, in case start and end are not integers + chrom = fields[ chrom_col ] + viewport_feature_count -= 1 + except Exception, e: + # Most likely a non-integer field has been encountered + # for start / stop. Just ignore and make sure we finish + # reading the line and decrementing the counters. + pass + # Make sure we are at the next new line + readline_count = VIEWPORT_MAX_READS_PER_LINE + while line.rstrip( '\n\r' ) == line: + assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) if not line: break #EOF - if not line.startswith( '#' ): - try: - fields = line.rstrip().split( '\t' ) - if len( fields ) > max_col: - if chrom is None or chrom == fields[ chrom_col ]: - start = min( start, int( fields[ start_col ] ) ) - end = max( end, int( fields[ end_col ] ) ) - chrom = fields[ chrom_col ] #set chrom last, in case start and end are not integers - viewport_feature_count -= 1 - except Exception: - #most likely a non-integer field has been encountered for start / stop - continue - #make sure we are at the next new line - readline_count = VIEWPORT_MAX_READS_PER_LINE - while line.rstrip( '\n\r' ) == line: - assert readline_count > 0, Exception( 'Viewport readline count exceeded for dataset %s.' % dataset.id ) - line = fh.readline( VIEWPORT_READLINE_BUFFER_SIZE ) - if not line: break #EOF - readline_count -= 1 - max_line_count -= 1 - if not viewport_feature_count or not max_line_count: - #exceeded viewport or total line count to check - break - if chrom is not None: - return ( chrom, str( start ), str( end ) ) #Necessary to return strings? - except Exception, e: - #unexpected error, possibly missing metadata - log.exception( str( e ) ) - return ( None, None, None ) #could not determine viewport + readline_count -= 1 + max_line_count -= 1 + if not viewport_feature_count or not max_line_count: + #exceeded viewport or total line count to check + break + if chrom is not None: + return ( chrom, str( start ), str( end ) ) # Necessary to return strings? + except Exception, e: + # Unexpected error, possibly missing metadata + log.exception( "Exception caught attempting to generate viewport for dataset '%d'", dataset.id ) + return ( None, None, None ) + def as_ucsc_display_file( self, dataset, **kwd ): """Returns file contents with only the bed data""" fd, temp_name = tempfile.mkstemp() @@ -252,22 +263,39 @@ class Interval( Tabular ): out = "Can't create peek %s" % str( exc ) return out def ucsc_links( self, dataset, type, app, base_url ): + """ + Generate links to UCSC genome browser sites based on the dbkey + and content of dataset. + """ + # Filter UCSC sites to only those that are supported by this build and + # enabled. + valid_sites = [ ( name, url ) + for name, url in util.get_ucsc_by_build( dataset.dbkey ) + if name in app.config.ucsc_display_sites ] + if not valid_sites: + return [] + # If there are any valid sites, we need to generate the estimated + # viewport + chrom, start, stop = self.get_estimated_display_viewport( dataset ) + if chrom is None: + return [] + # Accumulate links for valid sites ret_val = [] - chrom, start, stop = self.get_estimated_display_viewport( dataset ) - if chrom is not None: - for site_name, site_url in util.get_ucsc_by_build(dataset.dbkey): - if site_name in app.config.ucsc_display_sites: - # HACK: UCSC doesn't support https, so force http even - # if our URL scheme is https. Making this work - # requires additional hackery in your upstream proxy. - # If UCSC ever supports https, remove this hack. - internal_url = "%s" % url_for( controller='/dataset', dataset_id=dataset.id, action='display_at', filename='ucsc_' + site_name ) - if base_url.startswith( 'https://' ): - base_url = base_url.replace( 'https', 'http', 1 ) - display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" % (base_url, url_for( controller='root' ), dataset.id, type) ) - redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" % (site_url, dataset.dbkey, chrom, start, stop ) ) - link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) - ret_val.append( (site_name, link) ) + for site_name, site_url in valid_sites: + internal_url = url_for( controller='/dataset', dataset_id=dataset.id, + action='display_at', filename='ucsc_' + site_name ) + # HACK: UCSC doesn't support https, so force http even if our URL + # scheme is https. Making this work requires additional + # hackery in your upstream proxy. If UCSC ever supports + # https, remove this hack. + if base_url.startswith( 'https://' ): + base_url = base_url.replace( 'https', 'http', 1 ) + display_url = urllib.quote_plus( "%s%s/display_as?id=%i&display_app=%s&authz_method=display_at" + % (base_url, url_for( controller='root' ), dataset.id, type) ) + redirect_url = urllib.quote_plus( "%sdb=%s&position=%s:%s-%s&hgt.customText=%%s" + % (site_url, dataset.dbkey, chrom, start, stop ) ) + link = '%s?redirect_url=%s&display_url=%s' % ( internal_url, redirect_url, display_url ) + ret_val.append( ( site_name, link ) ) return ret_val def validate( self, dataset ): """Validate an interval file using the bx GenomicIntervalReader"""

1 0