[galaxy-dev] [hg] galaxy 3256: Removed SOLiD option from BWA, cleaned up Bowt...

details: http://www.bx.psu.edu/hg/galaxy/rev/4cd66d01aaf0 changeset: 3256:4cd66d01aaf0 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Fri Jan 22 10:49:38 2010 -0500 description: Removed SOLiD option from BWA, cleaned up Bowtie and BWA wrapper interfaces, and changed name of BWA index loc file diffstat: buildbot_setup.sh | 3 +- test-data/bwa_phiX_sanger.fastq | 4 - test-data/bwa_phiX_sanger_f.fastq | 4 - test-data/bwa_phiX_sanger_r.fastq | 4 - test-data/bwa_sanger.fastq | 76 --- test-data/bwa_sanger_f.fastq | 76 --- test-data/bwa_sanger_r.fastq | 76 --- test-data/bwa_solid.fastq | 576 ----------------------------- test-data/bwa_solid_f.fastq | 192 --------- test-data/bwa_solid_r.fastq | 192 --------- test-data/bwa_wrapper_in0.fastq | 576 ----------------------------- test-data/bwa_wrapper_in2.fastq | 580 +----------------------------- test-data/bwa_wrapper_in3.fastq | 196 +--------- test-data/bwa_wrapper_in4.fastq | 192 --------- test-data/bwa_wrapper_in5.fastq | 4 - test-data/bwa_wrapper_in6.fastq | 4 - test-data/bwa_wrapper_out0.sam | 1 - test-data/bwa_wrapper_out0b.sam | 144 ------- test-data/bwa_wrapper_out1.sam | 145 +------- test-data/bwa_wrapper_out2.sam | 97 +---- test-data/bwa_wrapper_out3.sam | 3 +- test-data/bwa_wrapper_out4.sam | 2 - tool-data/bwa_index.loc.sample | 29 + tools/sr_mapping/bowtie_color_wrapper.xml | 149 ++++-- tools/sr_mapping/bowtie_wrapper.py | 10 +- tools/sr_mapping/bowtie_wrapper.xml | 145 ++++-- tools/sr_mapping/bwa_wrapper.py | 196 +++++---- tools/sr_mapping/bwa_wrapper.xml | 353 ++++++----------- 28 files changed, 470 insertions(+), 3559 deletions(-) diffs (truncated from 4465 to 3000 lines): diff -r ea652508497a -r 4cd66d01aaf0 buildbot_setup.sh --- a/buildbot_setup.sh Fri Jan 22 08:47:05 2010 -0500 +++ b/buildbot_setup.sh Fri Jan 22 10:49:38 2010 -0500 @@ -21,6 +21,7 @@ /depot/data2/galaxy/blastdb.loc /depot/data2/galaxy/bowtie_indices.loc /depot/data2/galaxy/bowtie_indices_color.loc +/depot/data2/galaxy/bwa_index.loc /depot/data2/galaxy/encode_datasets.loc /galaxy/home/universe/encode_feature_partitions /depot/data2/galaxy/lastz_seqs.loc @@ -32,8 +33,6 @@ /depot/data2/galaxy/quality_scores.loc /depot/data2/galaxy/regions.loc /depot/data2/galaxy/sam_fa_indices.loc -/depot/data2/galaxy/sequence_index_base.loc -/depot/data2/galaxy/sequence_index_color.loc /depot/data2/galaxy/taxonomy /depot/data2/galaxy/twobit.loc " diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_phiX_sanger.fastq --- a/test-data/bwa_phiX_sanger.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@081017-and-081020:1:1:1715:1759 -GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC -+ -II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_phiX_sanger_f.fastq --- a/test-data/bwa_phiX_sanger_f.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@081017-and-081020:1:1:1715:1759/2 -ACGCTCCTTTAAAATATC -+/2 -IIIII$%*$G$A31I&&B diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_phiX_sanger_r.fastq --- a/test-data/bwa_phiX_sanger_r.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@081017-and-081020:1:1:1715:1759/1 -GGACTCAGATAGTAATCC -+/1 -II#IIIIIII$5+.(9II diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_sanger.fastq --- a/test-data/bwa_sanger.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -@HWI-EAS91_1_30788AAXX:1:1:1761:343 -AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAACNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG -+ -IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIHI""I""IIII"I"""""""IIIIIIHIIII""1III -@HWI-EAS91_1_30788AAXX:1:1:1578:331 -GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTTCNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII""II7I -@HWI-EAS91_1_30788AAXX:1:1:1647:512 -GTTCCATNNATCTGTGTGTCTATTTTTGTGCAAGTAANNCNNTGTTNANNNNNNNTGAAGAAGACANNAAGA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIGII""IIII -@HWI-EAS91_1_30788AAXX:1:1:1570:620 -GAGGTGTNNAAAATGAGAAAGGTCAAGGAGCATGTGCNNGNNTCAGNGNNNNNNNCACTGTACTGCNNGCTA -+ -IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIIIII""I""IIII"I"""""""IIII@4EIII:""I?E6 -@HWI-EAS91_1_30788AAXX:1:1:1599:330 -GTTGGAGNNTGTCAAATGCCTTCTCTGCATCTATTGCNNANNGCTTNCNNNNNNNATCCTACCAAANNTTCA -+ -IIIIIII""IIIIIIIIIIIIIIIIIII<III@IIII""I""IIII"I"""""""@IIHI16IF51""I:A< -@HWI-EAS91_1_30788AAXX:1:1:1652:270 -GCCAAGCNNAGCAAATGTTTGAAGTCTCTAGGAGTGANNANNTTCANTNNNNNNNTCTTCTCTCTTNNGTAT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6IIII""I""IIII"I"""""""IIIIIIIIIII""<D9I -@HWI-EAS91_1_30788AAXX:1:1:1746:351 -GCCTTCGNNAGGTCTCAGCGCTTTCTCTGTGTTCTTTNNANNATACNANNNNNNNAAACTAAAAAANNCAAA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""BIIIH:7IIII""I0>I -@HWI-EAS91_1_30788AAXX:1:1:1582:633 -GGATGTGNNGAAAGGAGAACCCTCATACACTGCTGGGNNTNNTCTGNTNNNNNNNATACCCTCAAGNNCCAT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIFIIIIIC3I""IIII -@HWI-EAS91_1_30788AAXX:1:1:1598:534 -GAATCATNNAATCCGCTTGGTTTGACACTTTGGATTTNNANNTCCANANNNNNNNGACTAAGAAACNNAGAT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""II.IIIICIII""IIII -@HWI-EAS91_1_30788AAXX:1:1:1572:324 -GGTGGTGNNGTCAGATCAGACAGGCTCCCAAGAAGCTNNTNNGCTTNGNNNNNNNTCAGTAAAGCGNNACAA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05III""I""IIII"I"""""""II3II-/EIGI""A84; -@HWI-EAS91_1_30788AAXX:1:1:1749:466 -GTTGTGTNNTTTCTTTCAATATTGTGATCTGGTTTAANNTNNATCCNCNNNNNNNGAGGCTTTTGTNNGGAC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""ICIIIIIGII@""EI1: -@HWI-EAS91_1_30788AAXX:1:1:1629:446 -GCAAAGGNNATGGGCAAAACAGTTCTTTGGTTAATGTNNTNNTAAANANNNNNNNTAAATCTTTCTNNAATG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIII?H<EII""I:I? -@HWI-EAS91_1_30788AAXX:1:1:1763:587 -GATACAGNNCTGTTTTCCTTATTAATTTCCAGTAGCTNNANNTTGTNTNNNNNNNAATCTTGAGTTNNGCCA -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII"")II? -@HWI-EAS91_1_30788AAXX:1:1:1616:363 -GATGAAANNCGGAAGCGATTGAAAAAATAGAAGGGGANNANNGAAANCNNNNNNNTGAACGATTTTNNATTT -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIIIII""I""IIII"I"""""""FI@7II1IIII""-III -@HWI-EAS91_1_30788AAXX:1:1:1768:715 -GTATCATNNCAGAAACACCATAAGTAGCTGCTTTTTANNANNTTAANANNNNNNNAACCCTTTATTNNTGAC -+ -IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIIIII""I""IIII"I"""""""IIIIIIIIIII""I9F< -@HWI-EAS91_1_30788AAXX:1:1:1572:270 -GATTAGGNNTGCAAAGAAACTGCGTTTCACAGGCCTCNNGNNGGCTNCNNNNNNNAGGGCGAGTTGNNCCCC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIIII""I""IIII":"""""""IIII5IIIBII""IIII -@HWI-EAS91_1_30788AAXX:1:1:1785:1272 -GTTNNNNNNATGCACATTNNATNAAATNNTTGCAGTGNNANNTGGGNCNNNNNNNCAAGTGAACTTNNACGT -+ -III""""""IIIIIIIII""FI"IIII""II+ICIII""I""IIII"I"""""""IIIIIIIIGII""I;I@ -@HWI-EAS91_1_30788AAXX:1:1:1673:514 -GTTTTGANNATGGTTTCTCTTCTGTTGTAACTCCATANNANNAAAANTNNNNNNNCGAACTGGTTCNNGAAC -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1II""I""IIII"I"""""""II%I'$+ACI/""3(.I -@HWI-EAS91_1_30788AAXX:1:1:1634:330 -GCTCTGCNNAGTGCTCTTACAGCCTAGTGGGAACATANNANNTGGANGNNNNNNNCTGTGGGGCACNNCTCG -+ -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8IIII""I""IIII"I"""""""IIIEIIIII8I""@7>I \ No newline at end of file diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_sanger_f.fastq --- a/test-data/bwa_sanger_f.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -@HWI-EAS91_1_30788AAXX:1:1:1761:343/2 -CNNANNGAGTNGNNNNNNNGCTTCCCACAGNNCTGG -+/2 -I""I""IIII"I"""""""IIIIIIHIIII""1III -@HWI-EAS91_1_30788AAXX:1:1:1578:331/2 -CNNANNTCTGNANNNNNNNTCTTTTTTCAGNNGTAG -+/2 -I""I""IIII"I"""""""IIIIIIIIIII""II7I -@HWI-EAS91_1_30788AAXX:1:1:1647:512/2 -ANNCNNTGTTNANNNNNNNTGAAGAAGACANNAAGA -+/2 -I""I""IIII"I"""""""IIIIIIIIGII""IIII -@HWI-EAS91_1_30788AAXX:1:1:1570:620/2 -CNNGNNTCAGNGNNNNNNNCACTGTACTGCNNGCTA -+/2 -I""I""IIII"I"""""""IIII@4EIII:""I?E6 -@HWI-EAS91_1_30788AAXX:1:1:1599:330/2 -CNNANNGCTTNCNNNNNNNATCCTACCAAANNTTCA -+/2 -I""I""IIII"I"""""""@IIHI16IF51""I:A< -@HWI-EAS91_1_30788AAXX:1:1:1652:270/2 -ANNANNTTCANTNNNNNNNTCTTCTCTCTTNNGTAT -+/2 -I""I""IIII"I"""""""IIIIIIIIIII""<D9I -@HWI-EAS91_1_30788AAXX:1:1:1746:351/2 -TNNANNATACNANNNNNNNAAACTAAAAAANNCAAA -+/2 -I""I""IIII"I"""""""BIIIH:7IIII""I0>I -@HWI-EAS91_1_30788AAXX:1:1:1582:633/2 -GNNTNNTCTGNTNNNNNNNATACCCTCAAGNNCCAT -+/2 -I""I""IIII"I"""""""IIFIIIIIC3I""IIII -@HWI-EAS91_1_30788AAXX:1:1:1598:534/2 -TNNANNTCCANANNNNNNNGACTAAGAAACNNAGAT -+/2 -I""I""IIII"I"""""""II.IIIICIII""IIII -@HWI-EAS91_1_30788AAXX:1:1:1572:324/2 -TNNTNNGCTTNGNNNNNNNTCAGTAAAGCGNNACAA -+/2 -I""I""IIII"I"""""""II3II-/EIGI""A84; -@HWI-EAS91_1_30788AAXX:1:1:1749:466/2 -ANNTNNATCCNCNNNNNNNGAGGCTTTTGTNNGGAC -+/2 -I""I""IIII"I"""""""ICIIIIIGII@""EI1: -@HWI-EAS91_1_30788AAXX:1:1:1629:446/2 -TNNTNNTAAANANNNNNNNTAAATCTTTCTNNAATG -+/2 -I""I""IIII"I"""""""IIIII?H<EII""I:I? -@HWI-EAS91_1_30788AAXX:1:1:1763:587/2 -TNNANNTTGTNTNNNNNNNAATCTTGAGTTNNGCCA -+/2 -I""I""IIII"I"""""""IIIIIIIIIII"")II? -@HWI-EAS91_1_30788AAXX:1:1:1616:363/2 -ANNANNGAAANCNNNNNNNTGAACGATTTTNNATTT -+/2 -I""I""IIII"I"""""""FI@7II1IIII""-III -@HWI-EAS91_1_30788AAXX:1:1:1768:715/2 -ANNANNTTAANANNNNNNNAACCCTTTATTNNTGAC -+/2 -I""I""IIII"I"""""""IIIIIIIIIII""I9F< -@HWI-EAS91_1_30788AAXX:1:1:1572:270/2 -CNNGNNGGCTNCNNNNNNNAGGGCGAGTTGNNCCCC -+/2 -I""I""IIII":"""""""IIII5IIIBII""IIII -@HWI-EAS91_1_30788AAXX:1:1:1785:1272/2 -GNNANNTGGGNCNNNNNNNCAAGTGAACTTNNACGT -+/2 -I""I""IIII"I"""""""IIIIIIIIGII""I;I@ -@HWI-EAS91_1_30788AAXX:1:1:1673:514/2 -ANNANNAAAANTNNNNNNNCGAACTGGTTCNNGAAC -+/2 -I""I""IIII"I"""""""II%I'$+ACI/""3(.I -@HWI-EAS91_1_30788AAXX:1:1:1634:330/2 -ANNANNTGGANGNNNNNNNCTGTGGGGCACNNCTCG -+/2 -I""I""IIII"I"""""""IIIEIIIII8I""@7>I diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_sanger_r.fastq --- a/test-data/bwa_sanger_r.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -@HWI-EAS91_1_30788AAXX:1:1:1761:343/1 -AAAAAAANNAAAAAAAAAAAAAAAAAAAAAAAAAAA -+/1 -IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIH -@HWI-EAS91_1_30788AAXX:1:1:1578:331/1 -GTATAGANNAATAAGAAAAAAAAAAATGAAGACTTT -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1647:512/1 -GTTCCATNNATCTGTGTGTCTATTTTTGTGCAAGTA -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1570:620/1 -GAGGTGTNNAAAATGAGAAAGGTCAAGGAGCATGTG -+/1 -IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1599:330/1 -GTTGGAGNNTGTCAAATGCCTTCTCTGCATCTATTG -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIII<III@III -@HWI-EAS91_1_30788AAXX:1:1:1652:270/1 -GCCAAGCNNAGCAAATGTTTGAAGTCTCTAGGAGTG -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6III -@HWI-EAS91_1_30788AAXX:1:1:1746:351/1 -GCCTTCGNNAGGTCTCAGCGCTTTCTCTGTGTTCTT -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1582:633/1 -GGATGTGNNGAAAGGAGAACCCTCATACACTGCTGG -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1598:534/1 -GAATCATNNAATCCGCTTGGTTTGACACTTTGGATT -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1572:324/1 -GGTGGTGNNGTCAGATCAGACAGGCTCCCAAGAAGC -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05II -@HWI-EAS91_1_30788AAXX:1:1:1749:466/1 -GTTGTGTNNTTTCTTTCAATATTGTGATCTGGTTTA -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1629:446/1 -GCAAAGGNNATGGGCAAAACAGTTCTTTGGTTAATG -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1763:587/1 -GATACAGNNCTGTTTTCCTTATTAATTTCCAGTAGC -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1616:363/1 -GATGAAANNCGGAAGCGATTGAAAAAATAGAAGGGG -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIIII -@HWI-EAS91_1_30788AAXX:1:1:1768:715/1 -GTATCATNNCAGAAACACCATAAGTAGCTGCTTTTT -+/1 -IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1572:270/1 -GATTAGGNNTGCAAAGAAACTGCGTTTCACAGGCCT -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII -@HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 -GTTNNNNNNATGCACATTNNATNAAATNNTTGCAGT -+/1 -III""""""IIIIIIIII""FI"IIII""II+ICII -@HWI-EAS91_1_30788AAXX:1:1:1673:514/1 -GTTTTGANNATGGTTTCTCTTCTGTTGTAACTCCAT -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1I -@HWI-EAS91_1_30788AAXX:1:1:1634:330/1 -GCTCTGCNNAGTGCTCTTACAGCCTAGTGGGAACAT -+/1 -IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8III diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_solid.fastq --- a/test-data/bwa_solid.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,576 +0,0 @@ -@1831_573_1004/1 -AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG -+ -><C&&9952+C>5<.?<79,=42<292:<(9/-7 -@1831_573_1050/1 -TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT -+ -;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -@1831_573_1067/1 -AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG -+ -++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -@1831_573_1219/1 -CGCCCTATAATAATACAGCGCGTTAGACCGCTCA -+ -@@=4/+)5)408?'665>*/5?<61';<3,:,5- -@1831_573_1242/1 -GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC -+ ->>::>17=A5?@@=;7A=;2.60>82<8=74+;; -@1831_573_1333/1 -AGAATCGTTACCACACACTGCGTCTGGGTATCCG -+ -='@#%3=.>)/34*117,,/6-4+.9742456<) -@1831_573_1362/1 -CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC -+ -B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -@1831_573_1448/1 -TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG -+ -7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ -@1831_573_1490/1 -CTCGTCATGTTACGCAAAGGCACGTCACAGCACC -+ -@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. -@1831_573_1523/1 -ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG -+ -,//*,#8''.6''6'2&27/80)%�'%#*,2' -@1831_573_1578/1 -CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC -+ -?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -@1831_573_1647/1 -AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT -+ -?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -@1831_573_1684/1 -TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT -+ ->1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -@1831_573_1769/1 -TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC -+ -54749&&767%/7;3$-7;3#,3//#,45/#&06 -@1831_573_1853/1 -CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC -+ -4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -@1831_573_1943/1 -ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC -+ ->/*1,),@-)'0*>5'$/?6@/.&?8/(')A43, -@1831_573_1977/1 -GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC -+ -@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -@1831_574_109/1 -TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT -+ -7651#4817>@65<2:84716=788<1995.7?6 -@1831_574_148/1 -CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC -+ -;->3;;3>//>0;;7=,=4-4/+>029<9<624; -@1831_574_185/1 -CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC -+ -<4;%%@7>#*>97%6;+8$#<07%1372$%<54# -@1831_574_243/1 -AGGCACCGTAACTCAGGACATTCTCGATTAGTTA -+ -@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 -@1831_574_257/1 -ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC -+ ->>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -@1831_574_293/1 -TGCTGCAAATAAACATACAGCCTTCTAATGACTA -+ -')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -@1831_574_389/1 -CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA -+ -)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -@1831_574_575/1 -TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG -+ -?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< -@1831_574_592/1 -TCATTTACCACGTCAGGGTCGGAGTCATTCATTA -+ -3-5)19,,<@>4067<2.-864346;9<1/;212 -@1831_574_617/1 -AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC -+ ->@?;>?=@==@>@=5?@+@:@40@><:0)')64- -@1831_574_725/1 -GACAAGATGGCTATTATTTACAATCCGATCTGCA -+ -'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -@1831_574_734/1 -CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG -+ --&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 -@1831_574_824/1 -AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT -+ -@@@;;),+@<-<7;<&89??&29?<$2:A<);8? -@1831_574_959/1 -CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC -+ -A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -@1831_574_1062/1 -ACCGGTAATATAAGGCAACATGATTACGGCCACG -+ -@821<//:136/8<1/5.427.;>288/0<1$)/ -@1831_574_1092/1 -GACTGGCGAAATCATCGCGGAAAAACCCCTATCA -+ -8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -@1831_574_1103/1 -ATCTCCTGATTAGACATATCTCCGTAGCTCACGC -+ -??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -@1831_574_1116/1 -CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC -+ -@++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -@1831_574_1194/1 -TTATCACATTTGGGGATCGGAAGGGACTACTTCG -+ -5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 -@1831_574_1204/1 -CTTACTGGTCTGCTGGACATATAGTGGCGATGAA -+ -A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* -@1831_574_1306/1 -ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA -+ -2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -@1831_574_1387/1 -GTACTTCTCAATGCTGCACTACTATGTACGCCCC -+ -?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -@1831_574_1431/1 -GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC -+ -7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -@1831_574_1560/1 -GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC -+ -))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -@1831_574_1591/1 -TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG -+ -=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 -@1831_574_1624/1 -ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG -+ -<6.&(,7-+))7..'/;43.)927.(<85&13-) -@1831_574_1826/1 -TACGTCGCGACCGAGCGTTATATAGTCTGACCCC -+ -@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -@1831_574_1903/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ -@1831_574_1961/1 -GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA -+ ->-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 -@1831_575_54/1 -TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA -+ -=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 -@1831_575_80/1 -TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT -+ -?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -@1831_575_192/1 -AACTACGCCCCTTAATTACACAGCGCGTTAGACC -+ -:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -@1831_575_197/1 -TTCGCCTACACTTAGATACCTCTTAAACTCAATG -+ --:?463@A:88?6?437<=.2&1.;@67.4@%2, -@1831_575_223/1 -ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA -+ -?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -@1831_575_420/1 -CCCACATGGAAAACACTCACCGCCGAACAGAGCG -+ -2?.>?(-''2+..@),$%1@;')1)?+)7.').. -@1831_575_434/1 -ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC -+ -@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -@1831_575_444/1 -TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA -+ -2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> -@1831_575_459/1 -CTTATCAGCACACGGTTTACCAGTCCGACTCCAA -+ -@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -@1831_575_506/1 -CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC -+ -?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -@1831_575_569/1 -AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT -+ -'9-,@29+479%&>9#&08=>7#9>,69/+'*3) -@1831_575_622/1 -CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC -+ -A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ -@1831_575_644/1 -CTTGAATGGCGATCTCGTCGAGGAAATACCACTA -+ -<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -@1831_575_663/1 -GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA -+ -@@@@A</;A>@6>0792<5966:?;25+:><1,+ -@1831_575_681/1 -TCTCCTGATTAGACATATCACTGTTGAACACAGC -+ -72?.)25;96-14'*.03'#4#++$)/8+%/((& -@1831_575_711/1 -TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC -+ -%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -@1831_575_730/1 -CACACAGGAACCATAGCGTATGTTATTCACCCCC -+ -%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -@1831_575_904/1 -ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC -+ -<><.689@@7@<54:4=@>69=:+6-=42;8<:# -@1831_575_938/1 -TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA -+ -:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 -@1831_575_970/1 -TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC -+ -@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 -@1831_575_991/1 -TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA -+ ->>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -@1831_575_1138/1 -TTGAAAGACCTGAACGCGATTTCATGTTTACTGC -+ -=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 -@1831_575_1157/1 -TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC -+ -B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 -@1831_575_1180/1 -GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA -+ -<B>5?':/78?;1;55:997@@>94=7<186->7 -@1831_575_1283/1 -GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT -+ -C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -@1831_575_1302/1 -CGACTATTCGTTTCGTCTAGAACGTGACACTAGC -+ -12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* -@1831_575_1310/1 -CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT -+ -<<>663?99@(@7=11@:@@/7??<@<;>'3-7; -@1831_575_1321/1 -CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG -+ -;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 -@1831_575_1373/1 -CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA -+ -@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< -@1831_575_1419/1 -TGGGGAATATAACAGCGTAGCGTTGAACACTAGA -+ -//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -@1831_575_1436/1 -TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC -+ -2@=;39*3<*4<:>52>>9'7:<='0=>1'136< -@1831_575_1442/1 -TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG -+ ->58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> -@1831_575_1454/1 -CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT -+ -4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -@1831_575_1500/1 -CACAAAAGGTCCCTACCTGTCTACCCTACATAGC -+ -?@@?A@?8<6<:985=99999==B3<5<<,7?>9 -@1831_575_1535/1 -CTCGACGATATGACCGCCAGCCACTTAACTCCGC -+ -B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< -@1831_575_1724/1 -TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA -+ -<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -@1831_575_1829/1 -CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC -+ -2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -@1831_575_1898/1 -CTTACCATATCATCTCAACCCATAACAGCACTTA -+ -B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -@1831_575_1964/1 -GACAGACCATGAGGCTGAAGACTACTAAGTGCGT -+ ->39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -@1831_576_32/1 -TACGCAACGATTTATGGCCTTATAATTGAGGCCA -+ -<>?>?=7<2)522;><<@40@>704<>5=23@+& -@1831_576_74/1 -ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA -+ -=@@?@>(??<B5?@@@9<@><+><;@';>6961? -@1831_576_86/1 -ATGAAAACGCATTAGGACAACCATAATGGCCTCA -+ -811)2:*.++5</:3+43924*))/:,6&29)2/ -@1831_576_89/1 -GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA -+ -)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -@1831_576_266/1 -ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT -+ -@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 -@1831_576_327/1 -GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA -+ -@?@6@@;<@?><@>==3@:==<3@@>53<9><6= -@1831_576_331/1 -GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -+ --2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -@1831_576_387/1 -ACACGCCATGATCCGATAAGAAGGGAACGTAAGG -+ -8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -@1831_576_406/1 -AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC -+ -4<>%%14:*4656)&<251&2+3#&19,6&4>5( -@1831_576_449/1 -CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA -+ -+'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -@1831_576_519/1 -TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC -+ -=46<97@>2/6?;2<4A881>9121+<1/4.9+7 -@1831_576_603/1 -CAATATGTCTTAGTCGTGACTCGGCAACTTATCC -+ -@46=@C.??<A79@@;-<@@>29B?>55<B7598 -@1831_576_655/1 -GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG -+ -@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -@1831_576_677/1 -TTTACTCAGTTGATACATCACTGTAGCACATAGG -+ -290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -@1831_576_718/1 -CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT -+ -4###$0###%(#########,####%####$### -@1831_576_722/1 -CGTATGATGGCGAGTCTTTATAATCCAATCTGAA -+ -*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -@1831_576_754/1 -AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA -+ -4//#(.$)'',>(
$<,##%((,#5?#0*%1* -@1831_576_815/1 -TAGGCCTGATATGACACGATCACAGTGCAACATC -+ -3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -@1831_576_882/1 -TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG -+ -26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -@1831_576_898/1 -AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT -+ -@@C2?C>?<>@886B?;?.??87=B<8<15??=. -@1831_576_923/1 -CTGGACATGAGAGACTGCACGCGGTACACGTCGG -+ -6.51=;.699<96>;;49<;;11;<@59:9=647 -@1831_576_930/1 -CTGGCATGTACGTCCATGTCAGACGAGCAGAACT -+ -#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -@1831_576_1019/1 -GATGCGCGCTGTCATGGCATCGAACCATCGGTCG -+ -<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -@1831_576_1068/1 -AAGAGTGACTCACTTACCGGGATGCGATGGAGCC -+ ->><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -@1831_576_1131/1 -AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA -+ -04@#@/@,4>9?2+?1571@',>=;(759;*92< -@1831_576_1168/1 -CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA -+ -@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -@1831_576_1207/1 -CAACCTGACTAAACGGGGATACGCTGGCGCTACA -+ -$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -@1831_576_1289/1 -TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT -+ -9<>1B@@;7@@663==28,5':8<<,.=2>>.50 -@1831_576_1329/1 -CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA -+ ->&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -@1831_576_1367/1 -GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT -+ -?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 -@1831_576_1416/1 -TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC -+ -';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ -@1831_576_1461/1 -GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA -+ -1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -@1831_576_1605/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -<@C@@>1;@:;<<@@9@???9<3?5-21=4877, -@1831_576_1664/1 -CGCGCACAACTCGCCATGATACGACAAGACCCGA -+ -@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -@1831_576_1671/1 -GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT -+ -@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -@1831_576_1729/1 -CGTTTCGTCTACAACGTGACACTAGCACAGTATA -+ -?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> -@1831_576_1880/1 -TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT -+ -515/792,:,7/%/05,%$):+#8%2(1754))3 -@1831_576_1982/1 -AATGTCGTCAGACGACTTTGGCGCGAAAACCATA -+ -@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ -@1831_576_1987/1 -AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA -+ -##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -@1831_576_2014/1 -CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT -+ -@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -@1831_576_2028/1 -ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA -+ -<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -@1831_577_40/1 -CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT -+ -2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 -@1831_577_119/1 -TCCCACAAGCCATTGACATGCTCGCTCTAAACAG -+ ->?C11)-1/)#;#/,850*+.+$$5550+%-.40 -@1831_577_133/1 -TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG -+ -4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) -@1831_577_255/1 -ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG -+ -<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -@1831_577_281/1 -TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA -+ --:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? -@1831_577_288/1 -CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA -+ -;/79??&=B::298*6.7/+4&21,7,6?.7#'6 -@1831_577_322/1 -GAATGCTGGAGTACATTATGACAAACTATCGGAG -+ -=;>4506;255464-<#7+194&2<?65968)7/ -@1831_577_362/1 -CGATTAGTTACCACTCGTATTCGCACGCCCAGGA -+ -2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 -@1831_577_382/1 -GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA -+ -2957/:1))=76(*24;,3+:<.&.&-=1=2/5* -@1831_577_464/1 -TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG -+ -=<7/<826)>#.'&4204+5#/041.7*91&756 -@1831_577_488/1 -TGAATAGTTATGGCCAGAATGTCTGCACCGATAC -+ -48.,*>6566<?8=<=<2>6;94>;=9>@8924@ -@1831_577_511/1 -GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT -+ -7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -@1831_577_545/1 -ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT -+ -><<9?<>?A<481@<@8==@76/61<95.5988- -@1831_577_559/1 -GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG -+ -<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' -@1831_577_562/1 -GTTCCACTACGTTCCACGCAAAGGAATCCGAATC -+ -((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -@1831_577_637/1 -GCCTTCGCGGGAGCATATCAGTCGATACATCCCA -+ --,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, -@1831_577_641/1 -TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT -+ -47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -@1831_577_692/1 -CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA -+ -B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_solid_f.fastq --- a/test-data/bwa_solid_f.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -@1378_11_329/2 -GTTCGTGGCCGGTGGGTGTTTGGG -+ -###$$#$#$&#####$'$#$###$ -@1378_17_1788/2 -TGGGTGGATGTGTTGTCGTTCATG -+ -#$#$###$#$#######$#$#### -@1378_25_2035/2 -GTGCGTCGGGGAGGGTGCTGTCGG -+ -######%#$%#$$###($###&&% -@1378_28_770/2 -GGTTGGGAGTTGGCGCGCGTGGTT -+ -###$##%%$####%#%$#%%#($$ -@1378_33_1945/2 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -.6;?;55697>8779457986264 -@1378_34_789/2 -GGGCTTGCGTTAGTGAGAGGTTGT -+ -###%$%$%%###$####$###$#& -@1378_35_263/2 -GGCGGGGGGGGGGGGGGGGGGGGG -+ -$%%&,)3/)%$-6'$&5&#$''5. -@1378_43_186/2 -GCTAGGGTTTGGGTTTGCGGTGGG -+ -$%#$########%##%#$###'#' -@1378_51_1671/2 -GGTGTTGTTCGGATGTAGCGTGGG -+ -##%$$####$########$##0## -@1378_56_324/2 -GCTGGGTGATCTAAGGAATGTAAT -+ -#$#####$$$#$$$$##%###*(# -@1378_56_773/2 -TCTGGTCGGTTTCGGGGAGTGGAA -+ -##%%#&$###$#$##%$####%%$ -@1378_62_2027/2 -GTTGGCCTGGCCTGCCGTGCTGCG -+ -*##),/%##$)#%##1$#'%.#&# -@1378_62_2029/2 -GGCGGTGTGTGGTGCGGCTGTGCG -+ -/$$$=(####%####)$$%$-&%# -@1378_67_1795/2 -CGTGCCAACGACCGTCCTACGGAG -+ -@@.?7@@@.@:@A<<>>=>70<@7 -@1378_68_466/2 -GTGTCATCTGAGGTAAAGCATTGT -+ -/##$09#$#.=$#$76+$%1'### -@1378_68_1692/2 -TGTTCGATTTAGGTCTTGCCTCGC -+ -###%%$%%##%$#$##$###$$#$ -@1378_80_664/2 -TGTCTGCGTTGTATCTCTGGTGTA -+ -%##%,%$$#&$$###$#$%##'%# -@1378_85_1786/2 -CCCTAGGAGCGTATACCGGACGAG -+ -,'&/%/@,&1,&'/)&,6&&1)(( -@1378_86_1011/2 -AGGCGATGGGATATTATTTTACTT -+ -:$###)%##$9$###1$$#$2### -@1378_86_1789/2 -GGCCAGGTACTAATAAATTCAACA -+ -1.51/&%#'$,*?%#6&0$$5,20 -@1378_91_1596/2 -GCTTTTTCATTCGGTGCCTTTGGA -+ -'>%/3%=()8'#.%?50$&5>%)% -@1378_94_1595/2 -GCGGGTTAACCCAGTACCTCTGGC -+ -,8@6'>8<76>@@(->9)7'*941 -@1378_95_1039/2 -GTTCTGTGCCAGGTGAGGTACGGA -+ -&##,./#$&)6##+,'#$$0(##$ -@1378_95_1767/2 -CTAATTGACCGGGCAAGCTATTAA -+ -',,2'(10/>:=/7).3&%6&)&6 -@1378_96_1037/2 -CTGCTGGGCCATTTGACTTACTCA -+ -'$#+#(##-%5##+*&###-.$$$ -@1378_96_1764/2 -TCTTTGTAACCCACTTAGTATTTC -+ -4='28>.@4881B807:822>%)1 -@1378_98_1574/2 -AGGCGAGTGTGGGGGTTGTTTGAG -+ -+%%$#)##%##$####%###$%$# -@1378_107_1647/2 -GGTCTGGTTCTATGTTGGTCGACT -+ -###'$$#$$$(#%###(#$##$%# -@1378_111_829/2 -GGTCTTCTATGGTGCTAAATTAGT -+ -$##'&###$##)#%($#$%#$'%# -@1378_111_1900/2 -GCACGCCTTTGGGCTAAGCCGTAA -+ -)$)'#%$########$'#&%$#(# -@1378_112_1483/2 -TGGAGTGGTGTGTTTGCTGAGCCA -+ -#$#)#############$#%#%'% -@1378_125_1287/2 -TGACGTGGGTTGTCCCGTGAGATT -+ -##$%%#$###$##$$#&%##$(%% -@1378_126_468/2 -AAAAAACGGGCCGGGCGGACTAGG -+ -@@B@@@>@2>1+?:92)>@8&&<+ -@1378_127_664/2 -TCGCTTTGCCTATGTTTGTTCGGA -+ -#%$%#&##$%#%%###$$###)-' -@1378_129_463/2 -AAAAAAAAAAAAAAAAAAAAAAAA -+ -,)&20%8'(&35-***1-2&+510 -@1378_129_875/2 -GACCTTTACGTATTGGGGGTTGGC -+ -###)###+###$##$#&%##$,#$ -@1378_140_1251/2 -TTTCCTTCGTGTGCGTGCGGAGTG -+ -#%#%$##$$$######.$$$%#%( -@1378_141_809/2 -TCTCGTGGTTTCTTTTTTATGTGT -+ -##%)##$$#####%$#$#%%#'## -@1378_144_983/2 -GTTCGTTCGTGGTGTACGAGGGTG -+ -#(#%#####($#%##$$#%##%#) -@1378_153_270/2 -GGCCGTGTGCGGGTGTAGATTGGA -+ -%$##($######&##$&$$$$%## -@1378_155_1689/2 -CGCGTTCGGACAAAGCTAGCACCT -+ -@4@@=6=@@<4:@@681@@@.24. -@1378_157_1580/2 -GGGATTGAAGGGATGTATGCTAGG -+ -#%$&%#$$'%$%#$##*#%$$$$# -@1378_161_317/2 -AATCCATACCCACAAAAGCAGGCC -+ -.&%','(@''?7//+&)+2.+)0) -@1378_177_735/2 -CGAGCCCTAAACCATGAGATCGGA -+ -@@B>@AC9@A<B8@=9>7@5)>,0 -@1378_181_1684/2 -TTTCTGTTGTGGTTTTGTTGGGGT -+ -$##'$%'##%##$%$#$$####$* -@1378_187_1407/2 -TTGGGTGAAATCTTGTCGAGTGGA -+ -####&##$$###$#####%##%%) -@1378_203_721/2 -CCTTTACGATCATAAACCATGACC -+ -9<&./1&@;12')?<1',?/)&/. -@1378_206_2039/2 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -?=>>?=:;<>>4::<=56199(05 diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_solid_r.fastq --- a/test-data/bwa_solid_r.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -@1378_11_329/1 -AGACCGGGCGGGGTGGCGTTCGGT -+ -%##+'#######%###$#$##$(# -@1378_17_1788/1 -TGCCGTGTCTTGCTAACGCCGATT -+ -#'#$$#$###%%##$$$$###### -@1378_25_2035/1 -CTGCGTGTTGGTGTCTACTGGGGT -+ -#%#'##$#$##&%#%$$$%#%#'# -@1378_28_770/1 -CTGCTATGCCGGCCGCCTGCCCCT -+ -%##(#$$#%$#$%###$%%$##$# -@1378_33_1945/1 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -+9;64287788752796/576352 -@1378_34_789/1 -ATGGTGGCTGACGCGTTTGACTGT -+ -#$##%#$##$&$#%##$##$###$ -@1378_35_263/1 -GGGCGGGGGGCGGCGGGGGGGGGG -+ -),,#%'$)'-(%&%'%',%%&&(& -@1378_43_186/1 -ATACTAGTTGGGACGCGTTGTGCT -+ -#$(4%$########$#$###$$$# -@1378_51_1671/1 -TGGGTAGGTGCGGCTCTTGCGGTC -+ -##$#$%###%%#%#$##$$##### -@1378_56_324/1 -AGGCTTGGATTGTTGCGCTGACCT -+ -/+#**###%%##%#####$$$#$# -@1378_56_773/1 -TGTCGTGAGGTCACTTATCCCCAT -+ -&%#%##%%#####&#$%##$%##$ -@1378_62_2027/1 -CTTCCACGATCTGCTCGCTGTGGT -+ -(#&&$##$$#$%#%$$$#$###'# -@1378_62_2029/1 -TCTGGGCTGTCTTCGGGTCGGTGT -+ -$%$$####$##$$#)##%%#$### -@1378_67_1795/1 -TAGTGGGCTAGTCCGGGATCTACC -+ -B@C2@@?;-@@1>'A@@91@.@1' -@1378_68_466/1 -GTGATCGTCGGTGCCAGTCCCTGT -+ -#(%)+##$#$#%#+$%##$##### -@1378_68_1692/1 -GGTCTTCTGGGCACGGGCCAAGTT -+ -###)%'&%##$###%#######$# -@1378_80_664/1 -CTGCTTTGATCCCCGGTGGAGCAC -+ -7#%###$$6#######$##$$$## -@1378_85_1786/1 -ATACTATGTCGATCTGTAAAAAAA -+ -)&.)#3%@$&%-,2#&+.-%0&./ -@1378_86_1011/1 -CTACGTTATTGCTCTGTTTGTCCT -+ -######$%##$$$%###%#$#### -@1378_86_1789/1 -CGAATATCCCCTGGTTTAGAAGTA -+ -61?1;@/>@<=/(.7'(<5@=%$= -@1378_91_1596/1 -TTAGCGGTTGACTATCTGCTGACA -+ -*&+'#9'(%*'#//,&<),/)'*# -@1378_94_1595/1 -CGTGCGACAGCCCATGTTTTCAGA -+ --=..5,3826&*+.+#+#%%6;%# -@1378_95_1039/1 -CGGCGTCCATCTTCGCCTTGAGAT -+ -$##.#$##$$#%$#$%%$###$)$ -@1378_95_1767/1 -ACACGCACCATCTGGCGGCTAACC -+ -86<65<4<C27/$5+#;-$+#2%$ -@1378_96_1037/1 -ATCCCCCAAGATGCCTGTTGATTG -+ -$#$'##$$$#%$$#%###+##$#$ -@1378_96_1764/1 -TACACCGGAACCTTGCACTAAAGC -+ -6-9'<#+81?+*<8-=69&6;*3) -@1378_98_1574/1 -GTTCTGCCGGTGTCTGTGGCGGGC -+ -$$#+&$$####%$$$###$%#%%# -@1378_107_1647/1 -AGGCCTACTACGCGTCATTGATAG -+ -&#$$#$(.#%#$$####&$%##($ -@1378_111_829/1 -TGCGGCACTTGCTTCTTCGTATTT -+ -%#%##%#$%#$#%###$$##&#$$ -@1378_111_1900/1 -TCCCCTCGCTCGGCTCTGTGCTGT -+ -$&%*$#(#)##$#'##%(##$#$% -@1378_112_1483/1 -TGTCCAGCTATGCGGCTTCCTCCT -+ -%#$+#%#&#$#####%####%$## -@1378_125_1287/1 -TGTCTCTGGGGGGCCTGGTTAGGT -+ -$##13$'%#$###$$###$$$#&# -@1378_126_468/1 -TCTCCTGATTAGACATATCTCCGT -+ -7>@318?=,=8@49579?..7,7) -@1378_127_664/1 -AGAGGTTGGTGTCTTGTCGCAGCT -+ -##'#$######$$%######$$$# -@1378_129_463/1 -CCTGTGGGCCAAGCCCAATGAAAG -+ -8),,<6(--)<()5&.&/8+;.2+ -@1378_129_875/1 -TTTCTATGGCTTACGCTGTCTGCC -+ -#$($##%####%$#$#####$### -@1378_140_1251/1 -ATCCTAGCGCGGTGTCTTGGGGAC -+ -#$%1#$$$##$##$#$#$##$%$$ -@1378_141_809/1 -TGTCCTCCAGTGTCTGTTGGGTGT -+ -%&,-##$$#(%###$#$$'###'# -@1378_144_983/1 -AGCGCCCGGTTGGTGCGGCTCGTC -+ --$(&%*$#*#))#$$$#%%$#$## -@1378_153_270/1 -AGTCCTTGTCCCCTGGGTTTTCCC -+ -+''$#&%$%#$##&$$($#&#$$# -@1378_155_1689/1 -TTGGGAGGGAGAGAGACTAGACCG -+ -?4@@4<<??<?-@4@=4<5<?:/> -@1378_157_1580/1 -TGGGCCTCGGTGCCCTTGGTCTGT -+ -#%)$##'#$$$&#####%#$#$## -@1378_161_317/1 -TTGGCCGGCAACCCCGGTACCTAA -+ -7<,<'@)@>.)2@/')'&(?/-<( -@1378_177_735/1 -AGTACGCCATGTATTTGCGACCAG -+ -=?@?C<88@=>:7>@55/.,416, -@1378_181_1684/1 -CGACTCCCGCATTCACGGTCAAGT -+ -&*#,##$#&$*$$#$#$$$#%$## -@1378_187_1407/1 -TGGCGTCCACTCGTGGGTCTATCG -+ -$#$'%#$%$%&$%#####$#$#%# -@1378_203_721/1 -CCTAAATAACCCAGGGTAAAAGAT -+ -9<1+2+1@=259@+;2.71&@+2& -@1378_206_2039/1 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -9@?8>;>>><<994;=895895-8 diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_in0.fastq --- a/test-data/bwa_wrapper_in0.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,576 +0,0 @@ -@1831_573_1004/1 -AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG -+ -><C&&9952+C>5<.?<79,=42<292:<(9/-7 -@1831_573_1050/1 -TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT -+ -;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -@1831_573_1067/1 -AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG -+ -++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -@1831_573_1219/1 -CGCCCTATAATAATACAGCGCGTTAGACCGCTCA -+ -@@=4/+)5)408?'665>*/5?<61';<3,:,5- -@1831_573_1242/1 -GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC -+ ->>::>17=A5?@@=;7A=;2.60>82<8=74+;; -@1831_573_1333/1 -AGAATCGTTACCACACACTGCGTCTGGGTATCCG -+ -='@#%3=.>)/34*117,,/6-4+.9742456<) -@1831_573_1362/1 -CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC -+ -B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -@1831_573_1448/1 -TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG -+ -7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ -@1831_573_1490/1 -CTCGTCATGTTACGCAAAGGCACGTCACAGCACC -+ -@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. -@1831_573_1523/1 -ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG -+ -,//*,#8''.6''6'2&27/80)%�'%#*,2' -@1831_573_1578/1 -CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC -+ -?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -@1831_573_1647/1 -AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT -+ -?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -@1831_573_1684/1 -TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT -+ ->1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -@1831_573_1769/1 -TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC -+ -54749&&767%/7;3$-7;3#,3//#,45/#&06 -@1831_573_1853/1 -CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC -+ -4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -@1831_573_1943/1 -ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC -+ ->/*1,),@-)'0*>5'$/?6@/.&?8/(')A43, -@1831_573_1977/1 -GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC -+ -@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -@1831_574_109/1 -TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT -+ -7651#4817>@65<2:84716=788<1995.7?6 -@1831_574_148/1 -CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC -+ -;->3;;3>//>0;;7=,=4-4/+>029<9<624; -@1831_574_185/1 -CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC -+ -<4;%%@7>#*>97%6;+8$#<07%1372$%<54# -@1831_574_243/1 -AGGCACCGTAACTCAGGACATTCTCGATTAGTTA -+ -@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 -@1831_574_257/1 -ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC -+ ->>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -@1831_574_293/1 -TGCTGCAAATAAACATACAGCCTTCTAATGACTA -+ -')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -@1831_574_389/1 -CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA -+ -)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -@1831_574_575/1 -TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG -+ -?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< -@1831_574_592/1 -TCATTTACCACGTCAGGGTCGGAGTCATTCATTA -+ -3-5)19,,<@>4067<2.-864346;9<1/;212 -@1831_574_617/1 -AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC -+ ->@?;>?=@==@>@=5?@+@:@40@><:0)')64- -@1831_574_725/1 -GACAAGATGGCTATTATTTACAATCCGATCTGCA -+ -'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -@1831_574_734/1 -CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG -+ --&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 -@1831_574_824/1 -AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT -+ -@@@;;),+@<-<7;<&89??&29?<$2:A<);8? -@1831_574_959/1 -CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC -+ -A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -@1831_574_1062/1 -ACCGGTAATATAAGGCAACATGATTACGGCCACG -+ -@821<//:136/8<1/5.427.;>288/0<1$)/ -@1831_574_1092/1 -GACTGGCGAAATCATCGCGGAAAAACCCCTATCA -+ -8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -@1831_574_1103/1 -ATCTCCTGATTAGACATATCTCCGTAGCTCACGC -+ -??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -@1831_574_1116/1 -CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC -+ -@++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -@1831_574_1194/1 -TTATCACATTTGGGGATCGGAAGGGACTACTTCG -+ -5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 -@1831_574_1204/1 -CTTACTGGTCTGCTGGACATATAGTGGCGATGAA -+ -A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* -@1831_574_1306/1 -ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA -+ -2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -@1831_574_1387/1 -GTACTTCTCAATGCTGCACTACTATGTACGCCCC -+ -?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -@1831_574_1431/1 -GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC -+ -7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -@1831_574_1560/1 -GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC -+ -))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -@1831_574_1591/1 -TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG -+ -=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 -@1831_574_1624/1 -ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG -+ -<6.&(,7-+))7..'/;43.)927.(<85&13-) -@1831_574_1826/1 -TACGTCGCGACCGAGCGTTATATAGTCTGACCCC -+ -@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -@1831_574_1903/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ -@1831_574_1961/1 -GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA -+ ->-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 -@1831_575_54/1 -TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA -+ -=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 -@1831_575_80/1 -TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT -+ -?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -@1831_575_192/1 -AACTACGCCCCTTAATTACACAGCGCGTTAGACC -+ -:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -@1831_575_197/1 -TTCGCCTACACTTAGATACCTCTTAAACTCAATG -+ --:?463@A:88?6?437<=.2&1.;@67.4@%2, -@1831_575_223/1 -ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA -+ -?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -@1831_575_420/1 -CCCACATGGAAAACACTCACCGCCGAACAGAGCG -+ -2?.>?(-''2+..@),$%1@;')1)?+)7.').. -@1831_575_434/1 -ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC -+ -@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -@1831_575_444/1 -TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA -+ -2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> -@1831_575_459/1 -CTTATCAGCACACGGTTTACCAGTCCGACTCCAA -+ -@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -@1831_575_506/1 -CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC -+ -?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -@1831_575_569/1 -AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT -+ -'9-,@29+479%&>9#&08=>7#9>,69/+'*3) -@1831_575_622/1 -CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC -+ -A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ -@1831_575_644/1 -CTTGAATGGCGATCTCGTCGAGGAAATACCACTA -+ -<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -@1831_575_663/1 -GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA -+ -@@@@A</;A>@6>0792<5966:?;25+:><1,+ -@1831_575_681/1 -TCTCCTGATTAGACATATCACTGTTGAACACAGC -+ -72?.)25;96-14'*.03'#4#++$)/8+%/((& -@1831_575_711/1 -TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC -+ -%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -@1831_575_730/1 -CACACAGGAACCATAGCGTATGTTATTCACCCCC -+ -%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -@1831_575_904/1 -ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC -+ -<><.689@@7@<54:4=@>69=:+6-=42;8<:# -@1831_575_938/1 -TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA -+ -:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 -@1831_575_970/1 -TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC -+ -@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 -@1831_575_991/1 -TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA -+ ->>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -@1831_575_1138/1 -TTGAAAGACCTGAACGCGATTTCATGTTTACTGC -+ -=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 -@1831_575_1157/1 -TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC -+ -B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 -@1831_575_1180/1 -GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA -+ -<B>5?':/78?;1;55:997@@>94=7<186->7 -@1831_575_1283/1 -GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT -+ -C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -@1831_575_1302/1 -CGACTATTCGTTTCGTCTAGAACGTGACACTAGC -+ -12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* -@1831_575_1310/1 -CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT -+ -<<>663?99@(@7=11@:@@/7??<@<;>'3-7; -@1831_575_1321/1 -CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG -+ -;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 -@1831_575_1373/1 -CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA -+ -@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< -@1831_575_1419/1 -TGGGGAATATAACAGCGTAGCGTTGAACACTAGA -+ -//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -@1831_575_1436/1 -TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC -+ -2@=;39*3<*4<:>52>>9'7:<='0=>1'136< -@1831_575_1442/1 -TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG -+ ->58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> -@1831_575_1454/1 -CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT -+ -4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -@1831_575_1500/1 -CACAAAAGGTCCCTACCTGTCTACCCTACATAGC -+ -?@@?A@?8<6<:985=99999==B3<5<<,7?>9 -@1831_575_1535/1 -CTCGACGATATGACCGCCAGCCACTTAACTCCGC -+ -B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< -@1831_575_1724/1 -TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA -+ -<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -@1831_575_1829/1 -CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC -+ -2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -@1831_575_1898/1 -CTTACCATATCATCTCAACCCATAACAGCACTTA -+ -B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -@1831_575_1964/1 -GACAGACCATGAGGCTGAAGACTACTAAGTGCGT -+ ->39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -@1831_576_32/1 -TACGCAACGATTTATGGCCTTATAATTGAGGCCA -+ -<>?>?=7<2)522;><<@40@>704<>5=23@+& -@1831_576_74/1 -ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA -+ -=@@?@>(??<B5?@@@9<@><+><;@';>6961? -@1831_576_86/1 -ATGAAAACGCATTAGGACAACCATAATGGCCTCA -+ -811)2:*.++5</:3+43924*))/:,6&29)2/ -@1831_576_89/1 -GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA -+ -)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -@1831_576_266/1 -ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT -+ -@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 -@1831_576_327/1 -GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA -+ -@?@6@@;<@?><@>==3@:==<3@@>53<9><6= -@1831_576_331/1 -GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -+ --2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -@1831_576_387/1 -ACACGCCATGATCCGATAAGAAGGGAACGTAAGG -+ -8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -@1831_576_406/1 -AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC -+ -4<>%%14:*4656)&<251&2+3#&19,6&4>5( -@1831_576_449/1 -CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA -+ -+'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -@1831_576_519/1 -TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC -+ -=46<97@>2/6?;2<4A881>9121+<1/4.9+7 -@1831_576_603/1 -CAATATGTCTTAGTCGTGACTCGGCAACTTATCC -+ -@46=@C.??<A79@@;-<@@>29B?>55<B7598 -@1831_576_655/1 -GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG -+ -@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -@1831_576_677/1 -TTTACTCAGTTGATACATCACTGTAGCACATAGG -+ -290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -@1831_576_718/1 -CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT -+ -4###$0###%(#########,####%####$### -@1831_576_722/1 -CGTATGATGGCGAGTCTTTATAATCCAATCTGAA -+ -*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -@1831_576_754/1 -AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA -+ -4//#(.$)'',>(
$<,##%((,#5?#0*%1* -@1831_576_815/1 -TAGGCCTGATATGACACGATCACAGTGCAACATC -+ -3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -@1831_576_882/1 -TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG -+ -26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -@1831_576_898/1 -AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT -+ -@@C2?C>?<>@886B?;?.??87=B<8<15??=. -@1831_576_923/1 -CTGGACATGAGAGACTGCACGCGGTACACGTCGG -+ -6.51=;.699<96>;;49<;;11;<@59:9=647 -@1831_576_930/1 -CTGGCATGTACGTCCATGTCAGACGAGCAGAACT -+ -#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -@1831_576_1019/1 -GATGCGCGCTGTCATGGCATCGAACCATCGGTCG -+ -<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -@1831_576_1068/1 -AAGAGTGACTCACTTACCGGGATGCGATGGAGCC -+ ->><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -@1831_576_1131/1 -AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA -+ -04@#@/@,4>9?2+?1571@',>=;(759;*92< -@1831_576_1168/1 -CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA -+ -@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -@1831_576_1207/1 -CAACCTGACTAAACGGGGATACGCTGGCGCTACA -+ -$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -@1831_576_1289/1 -TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT -+ -9<>1B@@;7@@663==28,5':8<<,.=2>>.50 -@1831_576_1329/1 -CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA -+ ->&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -@1831_576_1367/1 -GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT -+ -?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 -@1831_576_1416/1 -TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC -+ -';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ -@1831_576_1461/1 -GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA -+ -1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -@1831_576_1605/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -<@C@@>1;@:;<<@@9@???9<3?5-21=4877, -@1831_576_1664/1 -CGCGCACAACTCGCCATGATACGACAAGACCCGA -+ -@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -@1831_576_1671/1 -GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT -+ -@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -@1831_576_1729/1 -CGTTTCGTCTACAACGTGACACTAGCACAGTATA -+ -?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> -@1831_576_1880/1 -TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT -+ -515/792,:,7/%/05,%$):+#8%2(1754))3 -@1831_576_1982/1 -AATGTCGTCAGACGACTTTGGCGCGAAAACCATA -+ -@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ -@1831_576_1987/1 -AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA -+ -##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -@1831_576_2014/1 -CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT -+ -@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -@1831_576_2028/1 -ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA -+ -<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -@1831_577_40/1 -CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT -+ -2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 -@1831_577_119/1 -TCCCACAAGCCATTGACATGCTCGCTCTAAACAG -+ ->?C11)-1/)#;#/,850*+.+$$5550+%-.40 -@1831_577_133/1 -TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG -+ -4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) -@1831_577_255/1 -ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG -+ -<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -@1831_577_281/1 -TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA -+ --:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? -@1831_577_288/1 -CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA -+ -;/79??&=B::298*6.7/+4&21,7,6?.7#'6 -@1831_577_322/1 -GAATGCTGGAGTACATTATGACAAACTATCGGAG -+ -=;>4506;255464-<#7+194&2<?65968)7/ -@1831_577_362/1 -CGATTAGTTACCACTCGTATTCGCACGCCCAGGA -+ -2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 -@1831_577_382/1 -GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA -+ -2957/:1))=76(*24;,3+:<.&.&-=1=2/5* -@1831_577_464/1 -TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG -+ -=<7/<826)>#.'&4204+5#/041.7*91&756 -@1831_577_488/1 -TGAATAGTTATGGCCAGAATGTCTGCACCGATAC -+ -48.,*>6566<?8=<=<2>6;94>;=9>@8924@ -@1831_577_511/1 -GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT -+ -7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -@1831_577_545/1 -ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT -+ -><<9?<>?A<481@<@8==@76/61<95.5988- -@1831_577_559/1 -GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG -+ -<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' -@1831_577_562/1 -GTTCCACTACGTTCCACGCAAAGGAATCCGAATC -+ -((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -@1831_577_637/1 -GCCTTCGCGGGAGCATATCAGTCGATACATCCCA -+ --,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, -@1831_577_641/1 -TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT -+ -47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -@1831_577_692/1 -CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA -+ -B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_in2.fastq --- a/test-data/bwa_wrapper_in2.fastq Fri Jan 22 08:47:05 2010 -0500 +++ b/test-data/bwa_wrapper_in2.fastq Fri Jan 22 10:49:38 2010 -0500 @@ -1,576 +1,4 @@ -@1831_573_1004/1 -AATACTTTCGGCGCCCTAAACCAGCTCACTGGGG -+ -><C&&9952+C>5<.?<79,=42<292:<(9/-7 -@1831_573_1050/1 -TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT -+ -;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -@1831_573_1067/1 -AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG -+ -++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -@1831_573_1219/1 -CGCCCTATAATAATACAGCGCGTTAGACCGCTCA -+ -@@=4/+)5)408?'665>*/5?<61';<3,:,5- -@1831_573_1242/1 -GCTGAATCGCACCTAGCAACTATAGCCGGGCCGC -+ ->>::>17=A5?@@=;7A=;2.60>82<8=74+;; -@1831_573_1333/1 -AGAATCGTTACCACACACTGCGTCTGGGTATCCG -+ -='@#%3=.>)/34*117,,/6-4+.9742456<) -@1831_573_1362/1 -CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC -+ -B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -@1831_573_1448/1 -TCACGCCGGTCCTTGACTGGCGTTCTCTTCGAGG -+ -7=A)?,.@A@@:@@<=/7)@<-#8662%9613&+ -@1831_573_1490/1 -CTCGTCATGTTACGCAAAGGCACGTCACAGCACC -+ -@@@?,@??@$><=>+%/*>*1,)?26&12'9%7. -@1831_573_1523/1 -ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG -+ -,//*,#8''.6''6'2&27/80)%�'%#*,2' -@1831_573_1578/1 -CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC -+ -?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -@1831_573_1647/1 -AGGGGTTTACACTATTCGACTGGGTGAGAGGCGT -+ -?@@<@@???;A==@@;9?@?3=;6.4/;6:=/;4 -@1831_573_1684/1 -TTCAACTGCGTCGACGTAGCGCACAGGCGTCCGT -+ ->1:8<@39@@??9=;@@<>?@@<;<?7>76?9>? -@1831_573_1769/1 -TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC -+ -54749&&767%/7;3$-7;3#,3//#,45/#&06 -@1831_573_1853/1 -CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC -+ -4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -@1831_573_1943/1 -ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC -+ ->/*1,),@-)'0*>5'$/?6@/.&?8/(')A43, -@1831_573_1977/1 -GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC -+ -@?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -@1831_574_109/1 -TCGGTTGCGTTACTTCATGGGAGGGCTTTACATT -+ -7651#4817>@65<2:84716=788<1995.7?6 -@1831_574_148/1 -CGAACCTCGTATAACGGAGTAGTCGGAAACAGTC -+ -;->3;;3>//>0;;7=,=4-4/+>029<9<624; -@1831_574_185/1 -CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC -+ -<4;%%@7>#*>97%6;+8$#<07%1372$%<54# -@1831_574_243/1 -AGGCACCGTAACTCAGGACATTCTCGATTAGTTA -+ -@@@95@=9?*><45$<@<4%@9?7#=?>7&>?97 -@1831_574_257/1 -ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC -+ ->>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -@1831_574_293/1 -TGCTGCAAATAAACATACAGCCTTCTAATGACTA -+ -')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -@1831_574_389/1 -CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA -+ -)$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -@1831_574_575/1 -TTCTTGGCAAGCGCAGATTATGCGTTCCGCCTAG -+ -?@>=?@>8@@@=@6*%&<='5@<<',0<=4*5/< -@1831_574_592/1 -TCATTTACCACGTCAGGGTCGGAGTCATTCATTA -+ -3-5)19,,<@>4067<2.-864346;9<1/;212 -@1831_574_617/1 -AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC -+ ->@?;>?=@==@>@=5?@+@:@40@><:0)')64- -@1831_574_725/1 -GACAAGATGGCTATTATTTACAATCCGATCTGCA -+ -'>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -@1831_574_734/1 -CCTGTACGAAAGAACGTAGGCATGGGCTGGGGGG -+ --&.$2&<*(-%):/)%5:)/%7+,9034*A.?70 -@1831_574_824/1 -AGCGCAAATTATGCGTTCCGCCTAGCGGAGAACT -+ -@@@;;),+@<-<7;<&89??&29?<$2:A<);8? -@1831_574_959/1 -CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC -+ -A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -@1831_574_1062/1 -ACCGGTAATATAAGGCAACATGATTACGGCCACG -+ -@821<//:136/8<1/5.427.;>288/0<1$)/ -@1831_574_1092/1 -GACTGGCGAAATCATCGCGGAAAAACCCCTATCA -+ -8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -@1831_574_1103/1 -ATCTCCTGATTAGACATATCTCCGTAGCTCACGC -+ -??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -@1831_574_1116/1 -CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC -+ -@++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -@1831_574_1194/1 -TTATCACATTTGGGGATCGGAAGGGACTACTTCG -+ -5>;,??9@9@?@1@@=@3=@>@4?@@94?75/,6 -@1831_574_1204/1 -CTTACTGGTCTGCTGGACATATAGTGGCGATGAA -+ -A5A5B@5:;@@,.9?A1?#.?;3),>82%)='7* -@1831_574_1306/1 -ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA -+ -2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -@1831_574_1387/1 -GTACTTCTCAATGCTGCACTACTATGTACGCCCC -+ -?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -@1831_574_1431/1 -GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC -+ -7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -@1831_574_1560/1 -GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC -+ -))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -@1831_574_1591/1 -TGAGCACTTATGGCTAGGCGTAGGGGACCGTGAG -+ -=<A><?@78@<=;@&@6>8:?,><&&<7>8(8+9 -@1831_574_1624/1 -ACGGGAAGGGCTGGAATCTACCCAGTAGGCATTG -+ -<6.&(,7-+))7..'/;43.)927.(<85&13-) -@1831_574_1826/1 -TACGTCGCGACCGAGCGTTATATAGTCTGACCCC -+ -@<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -@1831_574_1903/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -956?@>;7@@@8:@>8><=9>9>@2=71?1:6;/ -@1831_574_1961/1 -GTTTCACTTCGGTTATTAAGAAACCCAAATGGAA -+ ->-07-@>(2'@<#064@%5%@@6.&<<(9)=:47 -@1831_575_54/1 -TTTCTTATGGGTAGAACAGCTGCCACTGACTGAA -+ -=@@68<2;<8;?@<>+9>7,,6972&57:4&9<8 -@1831_575_80/1 -TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT -+ -?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -@1831_575_192/1 -AACTACGCCCCTTAATTACACAGCGCGTTAGACC -+ -:8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -@1831_575_197/1 -TTCGCCTACACTTAGATACCTCTTAAACTCAATG -+ --:?463@A:88?6?437<=.2&1.;@67.4@%2, -@1831_575_223/1 -ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA -+ -?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -@1831_575_420/1 -CCCACATGGAAAACACTCACCGCCGAACAGAGCG -+ -2?.>?(-''2+..@),$%1@;')1)?+)7.').. -@1831_575_434/1 -ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC -+ -@@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -@1831_575_444/1 -TAGGCGACCGTGAGGACAAGAGCTGTTGCCTTGA -+ -2@@;<.=?@<+=:A<<@?<</>@><(<8>4&5;> -@1831_575_459/1 -CTTATCAGCACACGGTTTACCAGTCCGACTCCAA -+ -@@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -@1831_575_506/1 -CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC -+ -?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -@1831_575_569/1 -AGCAGACTGCTGTAACACGGTGTGGTGTAAGGAT -+ -'9-,@29+479%&>9#&08=>7#9>,69/+'*3) -@1831_575_622/1 -CCAAATCCGGCCCAGTAAGTGTCCTGTCGCACCC -+ -A8B=@@?<@?<>>=?96<497)<4/<':4+;74+ -@1831_575_644/1 -CTTGAATGGCGATCTCGTCGAGGAAATACCACTA -+ -<8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -@1831_575_663/1 -GGCAACTTATCCGCATTGGTCCCACTGGAGCGCA -+ -@@@@A</;A>@6>0792<5966:?;25+:><1,+ -@1831_575_681/1 -TCTCCTGATTAGACATATCACTGTTGAACACAGC -+ -72?.)25;96-14'*.03'#4#++$)/8+%/((& -@1831_575_711/1 -TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC -+ -%+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -@1831_575_730/1 -CACACAGGAACCATAGCGTATGTTATTCACCCCC -+ -%8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -@1831_575_904/1 -ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC -+ -<><.689@@7@<54:4=@>69=:+6-=42;8<:# -@1831_575_938/1 -TCATCAGGGAAGGCTAGGGGTTTACACTATTCGA -+ -:@@:?@;=8;>=;;:=<93<4.;<6:2<9;4)87 -@1831_575_970/1 -TGACTCCTACAGTCTTTATAGTACCGAGGGAGGC -+ -@=@=;@@><@@:9<:=?;>@=?9>>?@:2===<5 -@1831_575_991/1 -TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA -+ ->>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -@1831_575_1138/1 -TTGAAAGACCTGAACGCGATTTCATGTTTACTGC -+ -=0;%1936+?96?,?5<:2>@6@<:;4>.7;*:1 -@1831_575_1157/1 -TCGCTGTTTAGATTTCGGGAGGGTACTTCAGTGC -+ -B@B>?A?A@?9'?;?&8?@@6;<@=+<:99+965 -@1831_575_1180/1 -GAATTCACGGCAGTGTTATCACCGTTTCCTTCCA -+ -<B>5?':/78?;1;55:997@@>94=7<186->7 -@1831_575_1283/1 -GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT -+ -C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -@1831_575_1302/1 -CGACTATTCGTTTCGTCTAGAACGTGACACTAGC -+ -12>/#2'&-2&%'7+$%*#$/1(&&12/$,2,,* -@1831_575_1310/1 -CTTGCTCTCGAGCTATGCCTCAGGACACGCCCTT -+ -<<>663?99@(@7=11@:@@/7??<@<;>'3-7; -@1831_575_1321/1 -CAACACAGTTGAACGGCGGAGGAGTAAAGATGCG -+ -;B@?@>=A@<A?>@>?6>@5>'4@9?)7@7?/89 -@1831_575_1373/1 -CGCTACCGGTTCCAACGGCTGCCTGACTCGCGGA -+ -@@@>@;=9<@??7@>@:@;@;17?630/7=4,2< -@1831_575_1419/1 -TGGGGAATATAACAGCGTAGCGTTGAACACTAGA -+ -//3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -@1831_575_1436/1 -TGCATCTAGCGCGTATTGCGAGCCTTACGGATTC -+ -2@=;39*3<*4<:>52>>9'7:<='0=>1'136< -@1831_575_1442/1 -TCTGACAAGGTTCCTGCACCTGCGTCTGAGAGGG -+ ->58<?7>+1B6-/9<<:5?>A:1@?539.@4/1> -@1831_575_1454/1 -CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT -+ -4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -@1831_575_1500/1 -CACAAAAGGTCCCTACCTGTCTACCCTACATAGC -+ -?@@?A@?8<6<:985=99999==B3<5<<,7?>9 -@1831_575_1535/1 -CTCGACGATATGACCGCCAGCCACTTAACTCCGC -+ -B=@<@@B?:A@@=>@?68@=?@5?7;:6<<;>5< -@1831_575_1724/1 -TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA -+ -<B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -@1831_575_1829/1 -CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC -+ -2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -@1831_575_1898/1 -CTTACCATATCATCTCAACCCATAACAGCACTTA -+ -B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -@1831_575_1964/1 -GACAGACCATGAGGCTGAAGACTACTAAGTGCGT -+ ->39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -@1831_576_32/1 -TACGCAACGATTTATGGCCTTATAATTGAGGCCA -+ -<>?>?=7<2)522;><<@40@>704<>5=23@+& -@1831_576_74/1 -ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA -+ -=@@?@>(??<B5?@@@9<@><+><;@';>6961? -@1831_576_86/1 -ATGAAAACGCATTAGGACAACCATAATGGCCTCA -+ -811)2:*.++5</:3+43924*))/:,6&29)2/ -@1831_576_89/1 -GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA -+ -)69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -@1831_576_266/1 -ATGGGGTCACTCGACCTAATCCCGCGGCTTTGGT -+ -@@?=;<?7=@>9,>@1$&&89$/:>7'3178%&6 -@1831_576_327/1 -GCCGTTCTACTCTAGCTGCAACTTGCGATTGCTA -+ -@?@6@@;<@?><@>==3@:==<3@@>53<9><6= -@1831_576_331/1 -GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -+ --2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -@1831_576_387/1 -ACACGCCATGATCCGATAAGAAGGGAACGTAAGG -+ -8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -@1831_576_406/1 -AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC -+ -4<>%%14:*4656)&<251&2+3#&19,6&4>5( -@1831_576_449/1 -CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA -+ -+'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -@1831_576_519/1 -TACCTGCCTACTACTTGCTCTCGAGCTATGCCTC -+ -=46<97@>2/6?;2<4A881>9121+<1/4.9+7 -@1831_576_603/1 -CAATATGTCTTAGTCGTGACTCGGCAACTTATCC -+ -@46=@C.??<A79@@;-<@@>29B?>55<B7598 -@1831_576_655/1 -GAACAGTCTATAGTGGCGGGAATCTCGTCGTCAG -+ -@AA9@@<6*>@@5/<@>9'=;>7+@?9>/9;+,% -@1831_576_677/1 -TTTACTCAGTTGATACATCACTGTAGCACATAGG -+ -290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -@1831_576_718/1 -CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT -+ -4###$0###%(#########,####%####$### -@1831_576_722/1 -CGTATGATGGCGAGTCTTTATAATCCAATCTGAA -+ -*,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -@1831_576_754/1 -AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA -+ -4//#(.$)'',>(
$<,##%((,#5?#0*%1* -@1831_576_815/1 -TAGGCCTGATATGACACGATCACAGTGCAACATC -+ -3>@?9>@?B=>=;>A???=>:25=4.25?6<57. -@1831_576_882/1 -TGTAAGACGGTGAGGTGTAAGGATCAGACCACGG -+ -26?8?@:4>@>96??<<=5'1<>9846=<9<1>8 -@1831_576_898/1 -AGTACTGTCGCGCATTGGGGTCCTGGTCGTTGCT -+ -@@C2?C>?<>@886B?;?.??87=B<8<15??=. -@1831_576_923/1 -CTGGACATGAGAGACTGCACGCGGTACACGTCGG -+ -6.51=;.699<96>;;49<;;11;<@59:9=647 -@1831_576_930/1 -CTGGCATGTACGTCCATGTCAGACGAGCAGAACT -+ -#*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -@1831_576_1019/1 -GATGCGCGCTGTCATGGCATCGAACCATCGGTCG -+ -<$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -@1831_576_1068/1 -AAGAGTGACTCACTTACCGGGATGCGATGGAGCC -+ ->><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -@1831_576_1131/1 -AGTTCGGGAAGGGCTGGAATCTACCCAGTAGGCA -+ -04@#@/@,4>9?2+?1571@',>=;(759;*92< -@1831_576_1168/1 -CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA -+ -@CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -@1831_576_1207/1 -CAACCTGACTAAACGGGGATACGCTGGCGCTACA -+ -$>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -@1831_576_1289/1 -TAGCGCAAGTCCAGAATGTTCATAGACTCGCGAT -+ -9<>1B@@;7@@663==28,5':8<<,.=2>>.50 -@1831_576_1329/1 -CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA -+ ->&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -@1831_576_1367/1 -GGTCTCATCCGTTCCAATCGGGACTTTGACCAGT -+ -?@@<>@@=@<@<=@>@??9:?<=>=<8;59@787 -@1831_576_1416/1 -TAGCGTTCAACGTCGATCTCATCTTGCCGATGGC -+ -';?..1.<@'.=+6.5?7<0-?7;(%=>56.98@ -@1831_576_1461/1 -GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA -+ -1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -@1831_576_1605/1 -AGTGCAACATCTGCTTTGCTTATCAGCACACGGC -+ -<@C@@>1;@:;<<@@9@???9<3?5-21=4877, -@1831_576_1664/1 -CGCGCACAACTCGCCATGATACGACAAGACCCGA -+ -@?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -@1831_576_1671/1 -GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT -+ -@?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -@1831_576_1729/1 -CGTTTCGTCTACAACGTGACACTAGCACAGTATA -+ -?@?<?<@>A?/==?>?7>?@8<?@>99;><+0=> -@1831_576_1880/1 -TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT -+ -515/792,:,7/%/05,%$):+#8%2(1754))3 -@1831_576_1982/1 -AATGTCGTCAGACGACTTTGGCGCGAAAACCATA -+ -@@?@,A><@9@=?@9B=8<6@@6@2<A?>.7<+@ -@1831_576_1987/1 -AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA -+ -##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -@1831_576_2014/1 -CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT -+ -@@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -@1831_576_2028/1 -ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA -+ -<>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -@1831_577_40/1 -CCCCGCGTTACGAACGAGAGAAATCTCTTATAAT -+ -2/4('.')(<*?#$)%&<,/39<(.2,+<=@611 -@1831_577_119/1 -TCCCACAAGCCATTGACATGCTCGCTCTAAACAG -+ ->?C11)-1/)#;#/,850*+.+$$5550+%-.40 -@1831_577_133/1 -TGCTTGTACGGTCTAACGGGGTATGGGTTTCTGG -+ -4@>>?=1?:+>@07@@><>@*<+1@15)96'2$) -@1831_577_255/1 -ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG -+ -<=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -@1831_577_281/1 -TATGTACGTCGCGTACACTCCGGGGCCCGCAAAA -+ --:B;8@=;>7@>4?=?+659?;5<7?;9@8(>:? -@1831_577_288/1 -CATCCGAGGCTATCAAGGCGTAAGCACTGACCTA -+ -;/79??&=B::298*6.7/+4&21,7,6?.7#'6 -@1831_577_322/1 -GAATGCTGGAGTACATTATGACAAACTATCGGAG -+ -=;>4506;255464-<#7+194&2<?65968)7/ -@1831_577_362/1 -CGATTAGTTACCACTCGTATTCGCACGCCCAGGA -+ -2B?:@?@<?958=,3:,90:&'-99,6<5.($+6 -@1831_577_382/1 -GTCGCGTATTCCCCGATGCTATGTAGACTTGCAA -+ -2957/:1))=76(*24;,3+:<.&.&-=1=2/5* -@1831_577_464/1 -TAGAGGCACCCTAACTCAGGGCTTTCTCGATTAG -+ -=<7/<826)>#.'&4204+5#/041.7*91&756 -@1831_577_488/1 -TGAATAGTTATGGCCAGAATGTCTGCACCGATAC -+ -48.,*>6566<?8=<=<2>6;94>;=9>@8924@ -@1831_577_511/1 -GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT -+ -7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -@1831_577_545/1 -ACCGCTCTTTGGGTATGGGGCAATCTGGCATGTT -+ -><<9?<>?A<481@<@8==@76/61<95.5988- -@1831_577_559/1 -GTGCCACTATGTTCGACAGACCCTAAGGCGGAAG -+ -<@;??@>@?/2<.@1=>12=61/;=?.&2+92)' -@1831_577_562/1 -GTTCCACTACGTTCCACGCAAAGGAATCCGAATC -+ -((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -@1831_577_637/1 -GCCTTCGCGGGAGCATATCAGTCGATACATCCCA -+ --,4#>:-6+:8,&(5;3=0>7=68&1/9&'?;4, -@1831_577_641/1 -TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT -+ -47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -@1831_577_692/1 -CCGGTGAGAATTACATCGCGAGTACGCCCAAGGA -+ -B,@?@B(@A?@+@@>@+?=>@'=<@<=<9=?75< +@081017-and-081020:1:1:1715:1759/2 +ACGCTCCTTTAAAATATC ++/2 +IIIII$%*$G$A31I&&B diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_in3.fastq --- a/test-data/bwa_wrapper_in3.fastq Fri Jan 22 08:47:05 2010 -0500 +++ b/test-data/bwa_wrapper_in3.fastq Fri Jan 22 10:49:38 2010 -0500 @@ -1,192 +1,4 @@ -@1378_11_329/2 -GTTCGTGGCCGGTGGGTGTTTGGG -+ -###$$#$#$&#####$'$#$###$ -@1378_17_1788/2 -TGGGTGGATGTGTTGTCGTTCATG -+ -#$#$###$#$#######$#$#### -@1378_25_2035/2 -GTGCGTCGGGGAGGGTGCTGTCGG -+ -######%#$%#$$###($###&&% -@1378_28_770/2 -GGTTGGGAGTTGGCGCGCGTGGTT -+ -###$##%%$####%#%$#%%#($$ -@1378_33_1945/2 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -.6;?;55697>8779457986264 -@1378_34_789/2 -GGGCTTGCGTTAGTGAGAGGTTGT -+ -###%$%$%%###$####$###$#& -@1378_35_263/2 -GGCGGGGGGGGGGGGGGGGGGGGG -+ -$%%&,)3/)%$-6'$&5&#$''5. -@1378_43_186/2 -GCTAGGGTTTGGGTTTGCGGTGGG -+ -$%#$########%##%#$###'#' -@1378_51_1671/2 -GGTGTTGTTCGGATGTAGCGTGGG -+ -##%$$####$########$##0## -@1378_56_324/2 -GCTGGGTGATCTAAGGAATGTAAT -+ -#$#####$$$#$$$$##%###*(# -@1378_56_773/2 -TCTGGTCGGTTTCGGGGAGTGGAA -+ -##%%#&$###$#$##%$####%%$ -@1378_62_2027/2 -GTTGGCCTGGCCTGCCGTGCTGCG -+ -*##),/%##$)#%##1$#'%.#&# -@1378_62_2029/2 -GGCGGTGTGTGGTGCGGCTGTGCG -+ -/$$$=(####%####)$$%$-&%# -@1378_67_1795/2 -CGTGCCAACGACCGTCCTACGGAG -+ -@@.?7@@@.@:@A<<>>=>70<@7 -@1378_68_466/2 -GTGTCATCTGAGGTAAAGCATTGT -+ -/##$09#$#.=$#$76+$%1'### -@1378_68_1692/2 -TGTTCGATTTAGGTCTTGCCTCGC -+ -###%%$%%##%$#$##$###$$#$ -@1378_80_664/2 -TGTCTGCGTTGTATCTCTGGTGTA -+ -%##%,%$$#&$$###$#$%##'%# -@1378_85_1786/2 -CCCTAGGAGCGTATACCGGACGAG -+ -,'&/%/@,&1,&'/)&,6&&1)(( -@1378_86_1011/2 -AGGCGATGGGATATTATTTTACTT -+ -:$###)%##$9$###1$$#$2### -@1378_86_1789/2 -GGCCAGGTACTAATAAATTCAACA -+ -1.51/&%#'$,*?%#6&0$$5,20 -@1378_91_1596/2 -GCTTTTTCATTCGGTGCCTTTGGA -+ -'>%/3%=()8'#.%?50$&5>%)% -@1378_94_1595/2 -GCGGGTTAACCCAGTACCTCTGGC -+ -,8@6'>8<76>@@(->9)7'*941 -@1378_95_1039/2 -GTTCTGTGCCAGGTGAGGTACGGA -+ -&##,./#$&)6##+,'#$$0(##$ -@1378_95_1767/2 -CTAATTGACCGGGCAAGCTATTAA -+ -',,2'(10/>:=/7).3&%6&)&6 -@1378_96_1037/2 -CTGCTGGGCCATTTGACTTACTCA -+ -'$#+#(##-%5##+*&###-.$$$ -@1378_96_1764/2 -TCTTTGTAACCCACTTAGTATTTC -+ -4='28>.@4881B807:822>%)1 -@1378_98_1574/2 -AGGCGAGTGTGGGGGTTGTTTGAG -+ -+%%$#)##%##$####%###$%$# -@1378_107_1647/2 -GGTCTGGTTCTATGTTGGTCGACT -+ -###'$$#$$$(#%###(#$##$%# -@1378_111_829/2 -GGTCTTCTATGGTGCTAAATTAGT -+ -$##'&###$##)#%($#$%#$'%# -@1378_111_1900/2 -GCACGCCTTTGGGCTAAGCCGTAA -+ -)$)'#%$########$'#&%$#(# -@1378_112_1483/2 -TGGAGTGGTGTGTTTGCTGAGCCA -+ -#$#)#############$#%#%'% -@1378_125_1287/2 -TGACGTGGGTTGTCCCGTGAGATT -+ -##$%%#$###$##$$#&%##$(%% -@1378_126_468/2 -AAAAAACGGGCCGGGCGGACTAGG -+ -@@B@@@>@2>1+?:92)>@8&&<+ -@1378_127_664/2 -TCGCTTTGCCTATGTTTGTTCGGA -+ -#%$%#&##$%#%%###$$###)-' -@1378_129_463/2 -AAAAAAAAAAAAAAAAAAAAAAAA -+ -,)&20%8'(&35-***1-2&+510 -@1378_129_875/2 -GACCTTTACGTATTGGGGGTTGGC -+ -###)###+###$##$#&%##$,#$ -@1378_140_1251/2 -TTTCCTTCGTGTGCGTGCGGAGTG -+ -#%#%$##$$$######.$$$%#%( -@1378_141_809/2 -TCTCGTGGTTTCTTTTTTATGTGT -+ -##%)##$$#####%$#$#%%#'## -@1378_144_983/2 -GTTCGTTCGTGGTGTACGAGGGTG -+ -#(#%#####($#%##$$#%##%#) -@1378_153_270/2 -GGCCGTGTGCGGGTGTAGATTGGA -+ -%$##($######&##$&$$$$%## -@1378_155_1689/2 -CGCGTTCGGACAAAGCTAGCACCT -+ -@4@@=6=@@<4:@@681@@@.24. -@1378_157_1580/2 -GGGATTGAAGGGATGTATGCTAGG -+ -#%$&%#$$'%$%#$##*#%$$$$# -@1378_161_317/2 -AATCCATACCCACAAAAGCAGGCC -+ -.&%','(@''?7//+&)+2.+)0) -@1378_177_735/2 -CGAGCCCTAAACCATGAGATCGGA -+ -@@B>@AC9@A<B8@=9>7@5)>,0 -@1378_181_1684/2 -TTTCTGTTGTGGTTTTGTTGGGGT -+ -$##'$%'##%##$%$#$$####$* -@1378_187_1407/2 -TTGGGTGAAATCTTGTCGAGTGGA -+ -####&##$$###$#####%##%%) -@1378_203_721/2 -CCTTTACGATCATAAACCATGACC -+ -9<&./1&@;12')?<1',?/)&/. -@1378_206_2039/2 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -?=>>?=:;<>>4::<=56199(05 +@081017-and-081020:1:1:1715:1759/1 +GGACTCAGATAGTAATCC ++/1 +II#IIIIIII$5+.(9II diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_in4.fastq --- a/test-data/bwa_wrapper_in4.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,192 +0,0 @@ -@1378_11_329/1 -AGACCGGGCGGGGTGGCGTTCGGT -+ -%##+'#######%###$#$##$(# -@1378_17_1788/1 -TGCCGTGTCTTGCTAACGCCGATT -+ -#'#$$#$###%%##$$$$###### -@1378_25_2035/1 -CTGCGTGTTGGTGTCTACTGGGGT -+ -#%#'##$#$##&%#%$$$%#%#'# -@1378_28_770/1 -CTGCTATGCCGGCCGCCTGCCCCT -+ -%##(#$$#%$#$%###$%%$##$# -@1378_33_1945/1 -GGGGGGGGGGGGGGGGGGGGGGGG -+ -+9;64287788752796/576352 -@1378_34_789/1 -ATGGTGGCTGACGCGTTTGACTGT -+ -#$##%#$##$&$#%##$##$###$ -@1378_35_263/1 -GGGCGGGGGGCGGCGGGGGGGGGG -+ -),,#%'$)'-(%&%'%',%%&&(& -@1378_43_186/1 -ATACTAGTTGGGACGCGTTGTGCT -+ -#$(4%$########$#$###$$$# -@1378_51_1671/1 -TGGGTAGGTGCGGCTCTTGCGGTC -+ -##$#$%###%%#%#$##$$##### -@1378_56_324/1 -AGGCTTGGATTGTTGCGCTGACCT -+ -/+#**###%%##%#####$$$#$# -@1378_56_773/1 -TGTCGTGAGGTCACTTATCCCCAT -+ -&%#%##%%#####&#$%##$%##$ -@1378_62_2027/1 -CTTCCACGATCTGCTCGCTGTGGT -+ -(#&&$##$$#$%#%$$$#$###'# -@1378_62_2029/1 -TCTGGGCTGTCTTCGGGTCGGTGT -+ -$%$$####$##$$#)##%%#$### -@1378_67_1795/1 -TAGTGGGCTAGTCCGGGATCTACC -+ -B@C2@@?;-@@1>'A@@91@.@1' -@1378_68_466/1 -GTGATCGTCGGTGCCAGTCCCTGT -+ -#(%)+##$#$#%#+$%##$##### -@1378_68_1692/1 -GGTCTTCTGGGCACGGGCCAAGTT -+ -###)%'&%##$###%#######$# -@1378_80_664/1 -CTGCTTTGATCCCCGGTGGAGCAC -+ -7#%###$$6#######$##$$$## -@1378_85_1786/1 -ATACTATGTCGATCTGTAAAAAAA -+ -)&.)#3%@$&%-,2#&+.-%0&./ -@1378_86_1011/1 -CTACGTTATTGCTCTGTTTGTCCT -+ -######$%##$$$%###%#$#### -@1378_86_1789/1 -CGAATATCCCCTGGTTTAGAAGTA -+ -61?1;@/>@<=/(.7'(<5@=%$= -@1378_91_1596/1 -TTAGCGGTTGACTATCTGCTGACA -+ -*&+'#9'(%*'#//,&<),/)'*# -@1378_94_1595/1 -CGTGCGACAGCCCATGTTTTCAGA -+ --=..5,3826&*+.+#+#%%6;%# -@1378_95_1039/1 -CGGCGTCCATCTTCGCCTTGAGAT -+ -$##.#$##$$#%$#$%%$###$)$ -@1378_95_1767/1 -ACACGCACCATCTGGCGGCTAACC -+ -86<65<4<C27/$5+#;-$+#2%$ -@1378_96_1037/1 -ATCCCCCAAGATGCCTGTTGATTG -+ -$#$'##$$$#%$$#%###+##$#$ -@1378_96_1764/1 -TACACCGGAACCTTGCACTAAAGC -+ -6-9'<#+81?+*<8-=69&6;*3) -@1378_98_1574/1 -GTTCTGCCGGTGTCTGTGGCGGGC -+ -$$#+&$$####%$$$###$%#%%# -@1378_107_1647/1 -AGGCCTACTACGCGTCATTGATAG -+ -&#$$#$(.#%#$$####&$%##($ -@1378_111_829/1 -TGCGGCACTTGCTTCTTCGTATTT -+ -%#%##%#$%#$#%###$$##&#$$ -@1378_111_1900/1 -TCCCCTCGCTCGGCTCTGTGCTGT -+ -$&%*$#(#)##$#'##%(##$#$% -@1378_112_1483/1 -TGTCCAGCTATGCGGCTTCCTCCT -+ -%#$+#%#&#$#####%####%$## -@1378_125_1287/1 -TGTCTCTGGGGGGCCTGGTTAGGT -+ -$##13$'%#$###$$###$$$#&# -@1378_126_468/1 -TCTCCTGATTAGACATATCTCCGT -+ -7>@318?=,=8@49579?..7,7) -@1378_127_664/1 -AGAGGTTGGTGTCTTGTCGCAGCT -+ -##'#$######$$%######$$$# -@1378_129_463/1 -CCTGTGGGCCAAGCCCAATGAAAG -+ -8),,<6(--)<()5&.&/8+;.2+ -@1378_129_875/1 -TTTCTATGGCTTACGCTGTCTGCC -+ -#$($##%####%$#$#####$### -@1378_140_1251/1 -ATCCTAGCGCGGTGTCTTGGGGAC -+ -#$%1#$$$##$##$#$#$##$%$$ -@1378_141_809/1 -TGTCCTCCAGTGTCTGTTGGGTGT -+ -%&,-##$$#(%###$#$$'###'# -@1378_144_983/1 -AGCGCCCGGTTGGTGCGGCTCGTC -+ --$(&%*$#*#))#$$$#%%$#$## -@1378_153_270/1 -AGTCCTTGTCCCCTGGGTTTTCCC -+ -+''$#&%$%#$##&$$($#&#$$# -@1378_155_1689/1 -TTGGGAGGGAGAGAGACTAGACCG -+ -?4@@4<<??<?-@4@=4<5<?:/> -@1378_157_1580/1 -TGGGCCTCGGTGCCCTTGGTCTGT -+ -#%)$##'#$$$&#####%#$#$## -@1378_161_317/1 -TTGGCCGGCAACCCCGGTACCTAA -+ -7<,<'@)@>.)2@/')'&(?/-<( -@1378_177_735/1 -AGTACGCCATGTATTTGCGACCAG -+ -=?@?C<88@=>:7>@55/.,416, -@1378_181_1684/1 -CGACTCCCGCATTCACGGTCAAGT -+ -&*#,##$#&$*$$#$#$$$#%$## -@1378_187_1407/1 -TGGCGTCCACTCGTGGGTCTATCG -+ -$#$'%#$%$%&$%#####$#$#%# -@1378_203_721/1 -CCTAAATAACCCAGGGTAAAAGAT -+ -9<1+2+1@=259@+;2.71&@+2& -@1378_206_2039/1 -CCCCCCCCCCCCCCCCCCCCCCCC -+ -9@?8>;>>><<994;=895895-8 diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_in5.fastq --- a/test-data/bwa_wrapper_in5.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@081017-and-081020:1:1:1715:1759/2 -ACGCTCCTTTAAAATATC -+/2 -IIIII$%*$G$A31I&&B diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_in6.fastq --- a/test-data/bwa_wrapper_in6.fastq Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -@081017-and-081020:1:1:1715:1759/1 -GGACTCAGATAGTAATCC -+/1 -II#IIIIIII$5+.(9II diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_out0.sam --- a/test-data/bwa_wrapper_out0.sam Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -081017-and-081020:1:1:1715:1759 16 PHIX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_out0b.sam --- a/test-data/bwa_wrapper_out0b.sam Fri Jan 22 08:47:05 2010 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,144 +0,0 @@ -1831_573_1004 0 phiX 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -1831_573_1219 16 phiX 2202 37 1S33M * 0 0 TACGTCACCTTATCAGTCCAATTTAAATTACACT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1242 0 phiX 648 37 33M1S * 0 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATCC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) -1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -1831_573_1448 16 phiX 2563 25 1S33M * 0 0 CGAAGTAACGTAAGTCTACCTATGTAGACAGTTG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1490 0 phiX 1767 25 33M1S * 0 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%�'%#*,2' -1831_573_1578 4 * 0 0 * * 0 0 CGAGTAGCAAACAAGACGCCAATCCAGGCGACCC ?=@<@C@?@@??=>@;7<<8<694)3511(+1<. -1831_573_1647 16 phiX 1118 37 1S33M * 0 0 ACTGAGGAAGCTCTACCTGCGGCAACCGCGAGAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1684 16 phiX 3696 37 1S33M * 0 0 ATCACGACTCCAACTGAATCAAGTAGTCGTTTGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1769 4 * 0 0 * * 0 0 TGGACGTATAGTGGCGATGAGCATGTAGGTTCTC 54749&&767%/7;3$-7;3#,3//#,45/#&06 -1831_573_1853 4 * 0 0 * * 0 0 CAAAACGCCCGGGGCCTCACATGCGCGGCAGTTC 4./B@@72B+/4?@?7?+@9/+99.')2<2&)2& -1831_573_1943 4 * 0 0 * * 0 0 ATAACGTATGGCAGTGAACGGGCGGAACCTGCCC >/*1,),@-)'0*>5'$/?6@/.&?8/(')A43, -1831_573_1977 4 * 0 0 * * 0 0 GGCGTAGGGCTCATTGTGCAAGTATCCGACCTCC @?6@8@@9A@=4633A7?9?<3:+7>'@%@?%32 -1831_574_109 0 phiX 3729 37 33M1S * 0 0 CAGAATCAGCGGTATGGCTCTTCTCATATTGGCT VTO/2URQ]]]TZWU[UTQP\]XY]VS[WLN]] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_148 16 phiX 2369 37 1S33M * 0 0 GATCCAAAAGACGAATCCTCAAATTAGTACAAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_185 4 * 0 0 * * 0 0 CCGTTTTGCCTAGTAATGCTCGGCGCAGCGTCGC <4;%%@7>#*>97%6;+8$#<07%1372$%<54# -1831_574_243 0 phiX 2129 37 33M1S * 0 0 TCTGGTGATTTGCAAGAACGCGTACTTATTCGCA ]]]W]]]]RQ]YRBI]]Y0<]]]CI]]]FM]]Y XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_257 4 * 0 0 * * 0 0 ATACCTTCCAAAGCAATAGAATAAAAAACAGTAC >>B>)@?>B@B?@1%*%,#+00.'(+&5&%#$3& -1831_574_293 4 * 0 0 * * 0 0 TGCTGCAAATAAACATACAGCCTTCTAATGACTA ')7'.*%#&$'/.$##$.$&*)+*$#8%&%#&&% -1831_574_389 4 * 0 0 * * 0 0 CATGGCTATGCACCGGTTTGTAGCGTACTCGAGA )$>/>8):2@:213;;.1)@3%64%+)<7)+$92 -1831_574_575 16 phiX 4006 37 1S33M * 0 0 CTTACAGTGCGACTAATAAAACTGAAACTCGCAT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_592 16 phiX 2950 37 1S33M * 0 0 TCGCCATAACGAAGACGAGAACGACCACCGCGGT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_617 4 * 0 0 * * 0 0 AAGCATCGGCGGGAGCGCAAGCTGGGAAGGTGCC >@?;>?=@==@>@=5?@+@:@40@><:0)')64- -1831_574_725 4 * 0 0 * * 0 0 GACAAGATGGCTATTATTTACAATCCGATCTGCA '>?52+5=;4$6;<8.1<47*9+?7(+5;-).)4 -1831_574_734 16 phiX 5263 25 1S33M * 0 0 CCTCTCTACTCTAACTCCGACCCTTTTCAATGAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_574_824 16 phiX 3997 37 1S33M * 0 0 ATGGGAAGACTTACAGTGCGACTAATAAAACTGA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_959 4 * 0 0 * * 0 0 CGCGCTAGGACTCGGCCCCAAGAGACGTTCCGCC A=;+?@9;/<@;<8#&&/*%(%.0$0$2)+1$-1 -1831_574_1062 4 * 0 0 * * 0 0 ACCGGTAATATAAGGCAACATGATTACGGCCACG @821<//:136/8<1/5.427.;>288/0<1$)/ -1831_574_1092 4 * 0 0 * * 0 0 GACTGGCGAAATCATCGCGGAAAAACCCCTATCA 8?.,98)03%#,,,(,++$'69'#9'7#';6.%2 -1831_574_1103 4 * 0 0 * * 0 0 ATCTCCTGATTAGACATATCTCCGTAGCTCACGC ??>?@=>@@A<>?=@==<:?<;58'&&):+35'1 -1831_574_1116 4 * 0 0 * * 0 0 CACCTCACGTGAGTATAGCAGCCCGAGCGTCACC @++,)/)?./)%<)2>.==:8?&;44&/&,)/*4 -1831_574_1194 0 phiX 1136 37 33M1S * 0 0 GCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTG \]PT]]]]]]]ZZ]]]\Y]]]]\]]]V\]UMDK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1204 16 phiX 1445 25 1S33M * 0 0 TGGATTACTCGAATTAGTTCTACTACGAGCAATA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1306 4 * 0 0 * * 0 0 ATTGCTTAGATCCAGTGGCGCTCAATACAACGGA 2.7&%''.$&#'%##$#'#%')')$'$%$,)'.1 -1831_574_1387 4 * 0 0 * * 0 0 GTACTTCTCAATGCTGCACTACTATGTACGCCCC ?A??:@?@@9?@@?9C;:>&).,,);&'<&7(/' -1831_574_1431 4 * 0 0 * * 0 0 GACCAGTTTCAGGGCTAACCGTCCCTACTCGACC 7?>9BA897;+8*=6#6.+5&-#26$0.,5&'$1 -1831_574_1560 4 * 0 0 * * 0 0 GGCGTCTTAGGATTGAAGAGGGCCTCCCACCCCC ))&65<4=>99@:597(1&;+&(%&4#,#&&&*$ -1831_574_1591 16 phiX 5118 37 1S33M * 0 0 CTTCGACAAGTCTTAGTCTTACTCGGCGTTGAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1624 16 phiX 4058 37 1S33M * 0 0 CATAACTCCGAACACCGTAAAGATGAGAAAGAGT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1826 4 * 0 0 * * 0 0 TACGTCGCGACCGAGCGTTATATAGTCTGACCCC @<<,))459<?.+57'-'&6?1)(;1;0&%4,#$ -1831_574_1903 0 phiX 5209 37 33M1S * 0 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGAC WT]]]][]]]][]]]]]]]]]]][X]QYYTYZ- XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_574_1961 0 phiX 3555 25 33M1S * 0 0 CGCGTTGCGTCTATTATGGAAAACACCAATCTTA TFPMV]OCBP]H<OS]<1CN]]M=K]52KO]WT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_54 16 phiX 3587 37 1S33M * 0 0 TAAGGTTCGTTGTCGTCCAAAGGCTCTAATACGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_80 4 * 0 0 * * 0 0 TCTTTGGGTTTGGGGCAATTTGGTATGTTCGTCT ?5><@?/=5%(&.5)+#/0'/'>#$/'37#()6& -1831_575_192 4 * 0 0 * * 0 0 AACTACGCCCCTTAATTACACAGCGCGTTAGACC :8<,9(.=/)#%8$,4'<,:)3/.'.5<,>-;7' -1831_575_197 16 phiX 4861 37 1S33M * 0 0 CCGAACGTTTTATGCACCGGAATACCAATGTCAT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_223 4 * 0 0 * * 0 0 ACGCACAAAGGAGCTCGGCGCATAGCAACGCAGA ?>?8?@:?;>+$'%&,+#$.--#%$1'&#-7$&' -1831_575_420 4 * 0 0 * * 0 0 CCCACATGGAAAACACTCACCGCCGAACAGAGCG 2?.>?(-''2+..@),$%1@;')1)?+)7.').. -1831_575_434 4 * 0 0 * * 0 0 ATCGCTGCGAGGTCACCCTGGTTACGCCCCTTCC @@><@B@>=@@?>><@?;)@?;6.?=4,'';/3) -1831_575_444 16 phiX 5098 37 1S33M * 0 0 TTCGACAGCGATGAAGGGTTCTTCGACAAGTCTT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_459 4 * 0 0 * * 0 0 CTTATCAGCACACGGTTTACCAGTCCGACTCCAA @@C@?A@@A@??A@@'6@@B'=;C@'4<=9,@1. -1831_575_506 4 * 0 0 * * 0 0 CGCAGAACCCGCACGCTTGTGCTCACCACTGTAC ?)2*5@3+.7=?A:8@,/&):@37/<89'+4*)* -1831_575_569 0 phiX 5043 25 33M1S * 0 0 GACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAAT IOBU[TMHTYG4M]7$?Q]]]57]SKXQC;:FE XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_622 0 phiX 2485 37 33M1S * 0 0 GTTTTACAGACACCTAAAGCTACATCGTCAACGC ]]]]]]]]]]]]]]]X[YVYINYLTLJWHO[$! XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_644 4 * 0 0 * * 0 0 CTTGAATGGCGATCTCGTCGAGGAAATACCACTA <8>.>&,+)8.10':5(/-62&*.=/%(.<&&18 -1831_575_663 16 phiX 1554 25 1S33M * 0 0 TGCTGAAGATGGTGTAGATAACTGTAATACCCAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_681 4 * 0 0 * * 0 0 TCTCCTGATTAGACATATCACTGTTGAACACAGC 72?.)25;96-14'*.03'#4#++$)/8+%/((& -1831_575_711 4 * 0 0 * * 0 0 TATGTTCGTCCACGTCAGACGCGCAAAGTTGCGC %+:2(#'1+.)&*45-#,<A-%4;>+))<;##*& -1831_575_730 4 * 0 0 * * 0 0 CACACAGGAACCATAGCGTATGTTATTCACCCCC %8<%-')5,*1&=#)(1*1)->7$.,4'4'&'*& -1831_575_904 4 * 0 0 * * 0 0 ACCCGCTTAAAGACGTGAATTTTGCCTCCGCGCC <><.689@@7@<54:4=@>69=:+6-=42;8<:# -1831_575_938 16 phiX 1133 37 1S33M * 0 0 TCTGCGGCAACCGCGAGAGGCAGAAAGAGGTAAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_970 16 phiX 232 37 1S33M * 0 0 GCTCCTCTTCACCGAATTATACGAACCGTGCAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_991 4 * 0 0 * * 0 0 TTCGGCGATCCCCCCCACGGCGCGATGCCGCGCA >>;7???/4<:::,#&*%'$--5-#(7)&&,-)% -1831_575_1138 0 phiX 1913 37 33M1S * 0 0 GCTAAAGGTGCTTTGACTTATACCGATATTGCTC VT7-SURJS]X]TT]Z]UY]]]]]]X[UN[NMT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1157 16 phiX 3736 25 1S33M * 0 0 GTCGCCATACCGAGAAGAGTATAACCGCGATGAC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1180 0 phiX 4169 37 33M1S * 0 0 GGGCGTTGAGTTCGATAATGGTGATATGTATGTA ]]\]OJROX]]UUYSX\[Y]]]]VZ]\VRWLT] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1283 4 * 0 0 * * 0 0 GGTGGAATACTAAGGACTAATGTGCTGTCTCTTT C@A54><?A78@<?2>:#>=?@2>80:'?69.'7 -1831_575_1302 16 phiX 5202 37 1S33M * 0 0 GGAATGGTTCGACCCAATGCTGCGCTGCGGCAAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1310 16 phiX 1612 37 1S33M * 0 0 AATGACTGGTTCTTGCACTAATGAAGTACGTCGC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1321 0 phiX 2664 37 33M1S * 0 0 TTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACG ]]]]]]]]]]]]]]]]]]]\ND]]]7/]]]WPZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1373 16 phiX 4221 37 1S33M * 0 0 TAGACTGCAAGCACTACTCAAACATAGACAATGA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1419 4 * 0 0 * * 0 0 TGGGGAATATAACAGCGTAGCGTTGAACACTAGA //3->&-.->%11/@&/&7:<,-1=,+2<6'%&< -1831_575_1436 0 phiX 3460 37 33M1S * 0 0 CTGGCATTCAGTCGGCGACTTCACGCCAGAATAC []]WULFXOGY]]\PY]]IGZ]]M@V]XAAMR[ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1442 0 phiX 3317 37 33M1S * 0 0 TGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCG \V]]]]RE\]LEQ]]]X]]]]TZ]]QUPW]LIX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1454 4 * 0 0 * * 0 0 CCTCCTAACCACGAGCCGAGGGGTCTCTGCCCCT 4=?8=6589=0:A=:?>6<;@/,4+-6+/'.,(, -1831_575_1500 16 phiX 4269 37 1S33M * 0 0 GCTTAACCGTGTTACGATGTTACACGAGGGGGTT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1535 16 phiX 1225 37 1S33M * 0 0 GAGTGCAAATACCACTTGTCACCTAATTCAAGTA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_575_1724 4 * 0 0 * * 0 0 TCGTAAGTGTTAAGGAGCTGTGTACAAAACAACA <B.+@),2*.%)))4%2@;7#%(%+$8))85%&5 -1831_575_1829 4 * 0 0 * * 0 0 CATTTGCTGACCCTGCGTAGTTTAGTCTCACAGC 2(*'%.3$+7)@&%$'3*+*#/#/*+0.=&#)+0 -1831_575_1898 4 * 0 0 * * 0 0 CTTACCATATCATCTCAACCCATAACAGCACTTA B>@@&1/))'40)%#8/.%#8$((#;4'$'63,, -1831_575_1964 4 * 0 0 * * 0 0 GACAGACCATGAGGCTGAAGACTACTAAGTGCGT >39)@2<2/@+9?2=&)>>@*62=5&2<42.'?+ -1831_576_32 16 phiX 988 25 1S33M * 0 0 TAACTCCTATTTAATACAGATTATAAGTTTGACC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_576_74 4 * 0 0 * * 0 0 ACATTCTGCAGTGGGACAGAGCGGTACGCCGCAA =@@?@>(??<B5?@@@9<@><+><;@';>6961? -1831_576_86 16 phiX 2981 37 1S33M * 0 0 TGTACAGATTTAACAAACCTCCGCCAGTTTTTCG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_89 4 * 0 0 * * 0 0 GCTGTTTGATTTGAGAAGAGGAATTAAGCGCCGA )69+,'.4=-,>/>(*$#)3030*'(,%)2##$, -1831_576_266 16 phiX 280 37 1S33M * 0 0 ATCTATACTCAGTGTAAAACAAGTACCATCTCTA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_327 16 phiX 4517 25 1S33M * 0 0 TATGATAAGTCGCAAACTACTTACGTTACGCTGT XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:1G31 -1831_576_331 4 * 0 0 * * 0 0 GACGCTTTACTCCGGTAGTACCGTGCCGTTTATA -2)+(*.*1/;5%.-9&#/1'+($*$##()%/$. -1831_576_387 4 * 0 0 * * 0 0 ACACGCCATGATCCGATAAGAAGGGAACGTAAGG 8).$5#1#*%.$##.*#$%##-%,+,1#&%.%)) -1831_576_406 4 * 0 0 * * 0 0 AGGTCTTACAGCACGGGGCTGAGCGCATCTGACC 4<>%%14:*4656)&<251&2+3#&19,6&4>5( -1831_576_449 4 * 0 0 * * 0 0 CTCGAACCGCGGGGTCCAAAGACTGCTGCAAGGA +'&'.,,$/+.)$$8&%#+?&,#)-&###7,+#* -1831_576_519 16 phiX 1625 25 1S33M * 0 0 GGCACTAATGAAGTACGTCGCAATGGCACTACAA XT:A:U CM:i:1 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:25A7 -1831_576_603 16 phiX 1576 37 1S33M * 0 0 GGTAATACCCAGACGTTCGACGAATACGATTAAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_655 16 phiX 3292 37 1S33M * 0 0 CAACGACGACGTAAAGGACTCGAATTACGAACCC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_677 4 * 0 0 * * 0 0 TTTACTCAGTTGATACATCACTGTAGCACATAGG 290&/*0#&'&,.2'#&*$&('#-%($*#%$)#% -1831_576_718 4 * 0 0 * * 0 0 CGTGCCTTTCAGGGTCTTTTCTGGTCTGGTCGCT 4###$0###%(#########,####%####$### -1831_576_722 4 * 0 0 * * 0 0 CGTATGATGGCGAGTCTTTATAATCCAATCTGAA *,-,##.)*&(*1%*(%(-2#+)-#.&-#%%$') -1831_576_754 4 * 0 0 * * 0 0 AGGCGTCCTGCATCGACCGTTCTATCCGCTTAGA 4//#(.$)'',>(
$<,##%((,#5?#0*%1* -1831_576_815 0 phiX 5186 37 33M1S * 0 0 GGAGTGCTTAATCCAACTTACCAAGCTGGGTTAC Z]]]]]]]]]]]]]]]]]]]UP[ZKIP]][ZUN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_882 0 phiX 5053 37 33M1S * 0 0 CTAAAGGTCTAGGAGCTAAAGAATGGAACAACTG Q]]]]]W[]]]X]]]]][EAV]]ZUS\]]]VX] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_898 0 phiX 518 37 33M1S * 0 0 GATTGCTACTGACCGCTCTCGTGCTCGTCGCTGT ]]]Z]]]]]]]YW]]]]VV]]X]]]]]VO]]]T XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_923 0 phiX 1050 37 33M1S * 0 0 ATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCG MLOW]RMX[]]X]]]XV]]]UKU]]]W\\]\ST XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_930 4 * 0 0 * * 0 0 CTGGCATGTACGTCCATGTCAGACGAGCAGAACT #*0.2&.:((#'14'##-)#%$$2%#$/1&#%/# -1831_576_1019 4 * 0 0 * * 0 0 GATGCGCGCTGTCATGGCATCGAACCATCGGTCG <$>$,1,&++&@,.)'+/+#9'69/6'2(+-'9- -1831_576_1068 4 * 0 0 * * 0 0 AAGAGTGACTCACTTACCGGGATGCGATGGAGCC >><=4?;@7=??9?;9>5@9?:8@:=5';7;'#4 -1831_576_1131 16 phiX 4061 37 1S33M * 0 0 TACTCCGAACACCGTAAAGATGAGAAAGAGTTAG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1168 4 * 0 0 * * 0 0 CACTTAACTCCGCTGTCGGAAGCCTTACAAGACA @CC6@@2?9=>7?;76<;467@;9,0%26'',4$ -1831_576_1207 4 * 0 0 * * 0 0 CAACCTGACTAAACGGGGATACGCTGGCGCTACA $>2,(&?4?(,@:<&,@>?$&:8A%%=0.%,597 -1831_576_1289 16 phiX 1899 37 1S33M * 0 0 AAAGTCATGGAATTGCGATTTCCACGAAACTGAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1329 4 * 0 0 * * 0 0 CCAATAGCAGAGACCTAATAGGAAACGAAAGCAA >&0,870/A@@/5.;=;:'&@3'&$$%,+#($&2 -1831_576_1367 0 phiX 1839 37 33M1S * 0 0 AGCATGGCACTATGTTTACTCTTGCGCTTGTTCT ]]]]]]]]]]]]]]]]]]\]]]]]]]\YW]]XX XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1416 0 phiX 4522 37 33M1S * 0 0 TTCAGCGTTTGATGAATGCAATGCGACAGGCTCC K]VEHHS]P>TQJML]]\UFU][L6K]\TMPZ] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1461 4 * 0 0 * * 0 0 GAGGGGCGGCCCGGTTCAAGCAGGTAAGCAACAA 1&74#(#(&##$#,'###%#%%#*#&%%##%%%' -1831_576_1605 0 phiX 5209 37 33M1S * 0 0 AGCTGGGTTACGACGCGACGCCGTTCAACCAGAC ]]]]]XU]]]]]]]]]]]]]]X[]KHLWZUXW, XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1664 4 * 0 0 * * 0 0 CGCGCACAACTCGCCATGATACGACAAGACCCGA @?>?@=A:@@>@='=<>=).>=9*8)(7#/++;) -1831_576_1671 4 * 0 0 * * 0 0 GTCTTTGTAAGCCTGGCCTGGTCAGGTCTGGTCT @?@5>@@8&8?25#&)&5&&)15&&,&4%&,&6% -1831_576_1729 16 phiX 5194 37 1S33M * 0 0 TATTAGGTTGAATGGTTCGACCCAATGCTGCGCT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1880 4 * 0 0 * * 0 0 TATGCGCTGTTGAGCTTACAACTCACTAGCGAAT 515/792,:,7/%/05,%$):+#8%2(1754))3 -1831_576_1982 16 phiX 5024 37 1S33M * 0 0 TATTGTTTTTCAGTCTATACCTGGAACGACGATT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_576_1987 4 * 0 0 * * 0 0 AAGGTCTTCTGTCGGCGCTGGACTGAACACCTGA ##()(#&##)%)/-#%$11#%3>'##&$,#$$'+ -1831_576_2014 4 * 0 0 * * 0 0 CCGTGACACACAATGCCGGCCCCAGCCTAGCAAT @@9,B29-5>'?,+?79+/A';'2@'5&/9,6&1 -1831_576_2028 4 * 0 0 * * 0 0 ACTCGCCGCATCCCCGAGTGACGCTCGAGACCAA <>9>5'2(&707.8#&&39,0%7/#(#,*%&5*+ -1831_577_40 0 phiX 2772 25 33M1S * 0 0 TGTGACTATTGACGTCCTTCCCCGTACGCCGGGT JLE8>>9:MOR=!&74KQDKU]M?IG@P]]]PK XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_119 4 * 0 0 * * 0 0 TCCCACAAGCCATTGACATGCTCGCTCTAAACAG >?C11)-1/)#;#/,850*+.+$$5550+%-.40 -1831_577_133 16 phiX 1714 37 1S33M * 0 0 CGTACGCGAGATTAGAGACCCGTAGACCGATACT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_255 4 * 0 0 * * 0 0 ATTGAGGCCAAGATAATTGAGGAGAGAGAAGGTG <=87@>69%**#&#-+$.#&&#+$-+%&%.,%5# -1831_577_281 16 phiX 4577 37 1S33M * 0 0 TAAAACTGTGAGAGTGCAACCGACTGCTGGCTAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_288 0 phiX 3201 25 33M1S * 0 0 GGCACTTCTGCCGTTTCTGATAAGTTGCTTGATA SOY]]NL]]]UTZKIMNOCH/-LFLLK]VN5%F XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_322 16 phiX 458 37 1S33M * 0 0 CAAGACGGCAAAACCTAAATTGGCTTCTACTAAA XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_362 0 phiX 2153 37 33M1S * 0 0 CTTATTCGCCACCATGATTATGACCAGTGTTTCA ]]]]]]]]]WV]RHVONRSI6=O[NK[ZL?%(J XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_382 16 phiX 4686 37 1S33M * 0 0 TCCAGCGTTCCGATTACTAAGTGTGCGGCTGACG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_464 0 phiX 2126 25 33M1S * 0 0 CCTTCTGGTGATTTGCAAGAACGCGTACTTATTG ]\OT]SQHP<,>6COKMHI3-HMNHNJLS@FUT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_488 16 phiX 4948 37 1S33M * 0 0 GCCGGACAACTACGATTTCCACTCGGCGAATTTC XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_511 4 * 0 0 * * 0 0 GGTGCTTATCAGTTCTTTCTCGGGACTTGTATTT 7/+&$:<7%6,$$%'%/+)#$7((&*3>16'0/+ -1831_577_545 0 phiX 1711 37 33M1S * 0 0 TGTCATGCGCTCTAATCTCTGGGCATCTGGCTAT ]]]]]]]]]YURZ]]]]]]]VNNPV]WLLWZYN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_577_559 0 phiX 3840 25 33M1S * 0 0 GCTGTTGCCGATACTTGGAACAATTTCTGGAAAG ]]]]]]]]WJWSWZW]XLX\P#-]]V=A(/TD9 XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_577_562 4 * 0 0 * * 0 0 GTTCCACTACGTTCCACGCAAAGGAATCCGAATC ((&*&0%)1%)#($2-,***%/-,,))&,-.1'* -1831_577_637 0 phiX 4247 37 33M1S * 0 0 TGTTACTGAGAAGTTAATGGATGAATTGGCACAA BI2<]PLJN[M;7FYWYVW]]\WG@IQH6O]XI XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_577_641 4 * 0 0 * * 0 0 TATCTACCACCGCGGTGGCGCGAGAATGCTCCCT 47;/':A;;5?:72,(=),#*?+.#&7$8#%7/' -1831_577_692 0 phiX 3905 37 33M1S * 0 0 GTCTAGGAAATAACCGTCAGGATTGACACCCTCA WU]]]SQ]]]TT]]]TS]]]PM]]]]]]]]]UZ XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 diff -r ea652508497a -r 4cd66d01aaf0 test-data/bwa_wrapper_out1.sam --- a/test-data/bwa_wrapper_out1.sam Fri Jan 22 08:47:05 2010 -0500 +++ b/test-data/bwa_wrapper_out1.sam Fri Jan 22 10:49:38 2010 -0500 @@ -1,144 +1,1 @@ -1831_573_1004 0 PHIX174 278 25 33M1S * 0 0 TTAGATATGAGTCACATTTTGTTCATGGTAGAGG ]]>!4[WPFW]\ZSV]\YNRZOWWTTU]MJQEM XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1050 4 * 0 0 * * 0 0 TTTATGGGTATGGCCGCTCACAGGCCAGCGGCCT ;@@17?@=>7??@A8?==@4A?A4)&+.'&+'1, -1831_573_1067 4 * 0 0 * * 0 0 AAGTATGAGTCATTTACCGGGATGCGAAGAAAAG ++#%(',%/$,+&1#&),)&+'*'*%#$&#%('$ -1831_573_1219 16 PHIX174 2202 37 1S33M * 0 0 TACGTCACCTTATCAGTCCAATTTAAATTACACT XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1242 0 PHIX174 648 37 33M1S * 0 0 CATCCCGTCAACATTCAAACGGCCTGTCTCATCC ]]]]XQ]]]]]]]][]]]VIMOW]SW]]]T*1] XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1333 4 * 0 0 * * 0 0 AGAATCGTTACCACACACTGCGTCTGGGTATCCG ='@#%3=.>)/34*117,,/6-4+.9742456<) -1831_573_1362 4 * 0 0 * * 0 0 CGATCTCAACCAGGTCCGCGCCCACCCCTGCCTC B@@?@@?@C@BA?@>@<@8A@?@'.8'?17:,+? -1831_573_1448 16 PHIX174 2563 25 1S33M * 0 0 CGAAGTAACGTAAGTCTACCTATGTAGACAGTTG XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1490 0 PHIX174 1767 25 33M1S * 0 0 CGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACC ]]]TU]]]=;]]]R9=BQQDF>QZQ1,LBIGEN XT:A:U CM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:33 -1831_573_1523 4 * 0 0 * * 0 0 ATGGAACGGAACGGGTGAGGAGGGGAACGTAGGG ,//*,#8''.6''6'2&27/80)%�'%#*,2'