Mercurial > repos > drosofff > sam_to_fastq
changeset 0:55107d4a728c draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 0651eb8c86d890e4b223fec82ab3980932710030
| author | drosofff |
|---|---|
| date | Mon, 21 Mar 2016 17:33:26 -0400 |
| parents | |
| children | 8acb72264319 |
| files | sam_to_fastq.py sam_to_fastq.xml test-data/input.sam test-data/output.fastq |
| diffstat | 4 files changed, 282 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_to_fastq.py Mon Mar 21 17:33:26 2016 -0400 @@ -0,0 +1,33 @@ +#!/usr/bin/python +# +import sys +import argparse + +def Parser(): + the_parser = argparse.ArgumentParser() + the_parser.add_argument( + '--input', action="store", type=str, help="input SAM file") + the_parser.add_argument( + '--output', action="store", type=str, help="output FASTQ file") + args = the_parser.parse_args() + return args + + +def print_fastq_sequence(samline, file): + samfields = samline[:-1].split("\t") + file.write ( '@%s\n%s\n+\n%s' % (samfields[0], samfields[9], samfields[10]) ) + +def main(input, output): + infile = open (input, "r") + outfile = open (output, "w") + with open (input, "r") as infile: + with open (output, "w") as outfile: + for line in infile: + if line[0] == "@": + continue + if line.split("\t")[1] != "4": + print_fastq_sequence (line, outfile) + +if __name__ == "__main__": + args = Parser() + main (args.input, args.output)
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sam_to_fastq.xml Mon Mar 21 17:33:26 2016 -0400 @@ -0,0 +1,28 @@ +<tool id="sam_to_fastq" name="SAM to FASTQ" version="0.1"> + <description></description> + <command interpreter="python">sam_to_fastq.py --input $input --output $output</command> + <inputs> + <param name="input" type="data" format="sam" label="SAM file for extraction of aligned reads in FASTQ format"/> + </inputs> + + <outputs> + <data format="fastqsanger" name="output" label="FASTQ extraction" /> +</outputs> + + <tests> + <test> + <param ftype="sam" name="input" value="input.sam" /> + <output file="output.fastq" name="output" /> + </test> + </tests> + + +<help> + +**What it does** + +Extract sequence and sequence quality of aligned reads in a SAM alignment file and return a FASTQ file containing those reads + +</help> + +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.sam Mon Mar 21 17:33:26 2016 -0400 @@ -0,0 +1,201 @@ +@HD VN:1.0 SO:unsorted +@SQ SN:chr1 LN:249250621 +@SQ SN:chr2 LN:243199373 +@SQ SN:chr3 LN:198022430 +@SQ SN:chr4 LN:191154276 +@SQ SN:chr5 LN:180915260 +@SQ SN:chr6 LN:171115067 +@SQ SN:chr7 LN:159138663 +@SQ SN:chr8 LN:146364022 +@SQ SN:chr9 LN:141213431 +@SQ SN:chr10 LN:135534747 +@SQ SN:chr11 LN:135006516 +@SQ SN:chr12 LN:133851895 +@SQ SN:chr13 LN:115169878 +@SQ SN:chr14 LN:107349540 +@SQ SN:chr15 LN:102531392 +@SQ SN:chr16 LN:90354753 +@SQ SN:chr17 LN:81195210 +@SQ SN:chr18 LN:78077248 +@SQ SN:chr19 LN:59128983 +@SQ SN:chr20 LN:63025520 +@SQ SN:chr21 LN:48129895 +@SQ SN:chr22 LN:51304566 +@SQ SN:chrX LN:155270560 +@SQ SN:chrY LN:59373566 +@SQ SN:chrM LN:16571 +@SQ SN:chr1_gl000191_random LN:106433 +@SQ SN:chr1_gl000192_random LN:547496 +@SQ SN:chr4_gl000193_random LN:189789 +@SQ SN:chr4_gl000194_random LN:191469 +@SQ SN:chr7_gl000195_random LN:182896 +@SQ SN:chr8_gl000196_random LN:38914 +@SQ SN:chr8_gl000197_random LN:37175 +@SQ SN:chr9_gl000198_random LN:90085 +@SQ SN:chr9_gl000199_random LN:169874 +@SQ SN:chr9_gl000200_random LN:187035 +@SQ SN:chr9_gl000201_random LN:36148 +@SQ SN:chr11_gl000202_random LN:40103 +@SQ SN:chr17_gl000203_random LN:37498 +@SQ SN:chr17_gl000204_random LN:81310 +@SQ SN:chr17_gl000205_random LN:174588 +@SQ SN:chr17_gl000206_random LN:41001 +@SQ SN:chr18_gl000207_random LN:4262 +@SQ SN:chr19_gl000208_random LN:92689 +@SQ SN:chr19_gl000209_random LN:159169 +@SQ SN:chr21_gl000210_random LN:27682 +@SQ SN:chrUn_gl000211 LN:166566 +@SQ SN:chrUn_gl000212 LN:186858 +@SQ SN:chrUn_gl000213 LN:164239 +@SQ SN:chrUn_gl000214 LN:137718 +@SQ SN:chrUn_gl000215 LN:172545 +@SQ SN:chrUn_gl000216 LN:172294 +@SQ SN:chrUn_gl000217 LN:172149 +@SQ SN:chrUn_gl000218 LN:161147 +@SQ SN:chrUn_gl000219 LN:179198 +@SQ SN:chrUn_gl000220 LN:161802 +@SQ SN:chrUn_gl000221 LN:155397 +@SQ SN:chrUn_gl000222 LN:186861 +@SQ SN:chrUn_gl000223 LN:180455 +@SQ SN:chrUn_gl000224 LN:179693 +@SQ SN:chrUn_gl000225 LN:211173 +@SQ SN:chrUn_gl000226 LN:15008 +@SQ SN:chrUn_gl000227 LN:128374 +@SQ SN:chrUn_gl000228 LN:129120 +@SQ SN:chrUn_gl000229 LN:19913 +@SQ SN:chrUn_gl000230 LN:43691 +@SQ SN:chrUn_gl000231 LN:27386 +@SQ SN:chrUn_gl000232 LN:40652 +@SQ SN:chrUn_gl000233 LN:45941 +@SQ SN:chrUn_gl000234 LN:40531 +@SQ SN:chrUn_gl000235 LN:34474 +@SQ SN:chrUn_gl000236 LN:41934 +@SQ SN:chrUn_gl000237 LN:45867 +@SQ SN:chrUn_gl000238 LN:39939 +@SQ SN:chrUn_gl000239 LN:33824 +@SQ SN:chrUn_gl000240 LN:41933 +@SQ SN:chrUn_gl000241 LN:42152 +@SQ SN:chrUn_gl000242 LN:43523 +@SQ SN:chrUn_gl000243 LN:43341 +@SQ SN:chrUn_gl000244 LN:39929 +@SQ SN:chrUn_gl000245 LN:36651 +@SQ SN:chrUn_gl000246 LN:38154 +@SQ SN:chrUn_gl000247 LN:36422 +@SQ SN:chrUn_gl000248 LN:39786 +@SQ SN:chrUn_gl000249 LN:38502 +@PG ID:bowtie2 PN:bowtie2 VN:2.2.6 CL:"/home/galaxy/tool_dependency/bowtie2/2.2.6/iuc/package_bowtie_2_2_6/0d9cd7487cc9/bin/bowtie2-align-s --wrapper basic-0 -p 8 -x /home/galaxy/galaxy-dist/tool-data/hg19/bowtie2_index/hg19.fa -k 1 --passthrough -U /home/galaxy/galaxy-dist/database/files/000/162/dataset_162397.dat" +1/1 4 * 0 0 * * 0 0 GGGTTCTTGGCATCAGTTGCTGAATGAAGCCTCTCTGATGTAGCTTGGTCTTCTTCAGGGACTCCTAACAGTGGAGTGGAGGCTGTCTATGACTCTTTTAC BBCDFFFFHHHHHJJJJJJJJJJIJIJJJJJIIIIJIHIIIIJJJJJJIIIJIJJJIIJJJJJJJJJGIGHGHJHDEHHHFFDDCAAC>@@;ACCDDDDCC YT:Z:UU +4/2 4 * 0 0 * * 0 0 CACATCAACATGATTCATTACCATCATTTCATCAATAATCACTTTATTTATCTTGTTTCAACTAAAAATTTCTTTACAATCATTTCCTCTATCACCCTCAT CCCFFFFDHHHHDIJJJJJJJJJJIJJJJJJJJJIJJJJJJJJJJJJJJJGIJJIJJJJJJJJJJJJHIIJJJJJJIIIJJJJJJHHHHHHHFFFFFDDED YT:Z:UU +1/2 4 * 0 0 * * 0 0 CTGCTGCTTCTATGATTGCCATCTCCTGGAACTCAGACCCCTTCTAGAGTCTTTCTCCATTTAAAAAAGTTGTCTCATATGTATATTACATCCCAACCACA CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJGJJJJJJJJJJJJJJJIHIIJJJJJJJJJJJIJJJJHIIHHHHHHFFFFEDEFFEEEEEEDDDDDDDD YT:Z:UU +5/1 4 * 0 0 * * 0 0 GTTTCTATCTTACTAATTTGTCTTGAGTTTTATTATTTCTTGCCATGTAAACATTTATGTGTTAGTTTTTTTGTGAGTGTGCATGTATACATGCATGTGGG CCCFFFFFHHHHHJJIJJJJJIJJJHJHJJJHIJIJJJIJJJJJJJJJJJIJEIJJIIJIIJJJIIJJJJJJJHGHEEHHFFFFFFFFFEEEEECEDACDD YT:Z:UU +5/2 4 * 0 0 * * 0 0 TGCGCAGCTCAAAAGGTACAAAAATTTGAAATAATACACTGTATCCTTTCTGACCACAATTTAAACATTAGTTCAAAATAAATATCAAAAACACCAGGAAG CCCFFFFFHHHHHJJJHIJJJJJJJJJIJJJJJJJJJJJJJHIJIIJJJJGIJJJJJJJJJJJJGHIJJJJIIJHHGHHHFFFFFFFEEEDDBD@DDDDD< YT:Z:UU +2/2 4 * 0 0 * * 0 0 GAAATATTCCCCATCTTCAGAGCCATGCAAAAAGGCCTCATTGACCAAGACACAGGCCTTGTGCTCCTGGAATCCCAGATTATCACGTCTGGCCTCATTGC @@CFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJGIJJGIJJIJIJJJIJJJJJJJHHHHHFFFFFEEECCEEDDDDDDDDDDDCEDC YT:Z:UU +6/1 4 * 0 0 * * 0 0 CCCTCCTATCTGATTCATCCACATGATGTTGACTCCAGTGGATTAACCTTGGCAGTTTATGCAGGTCACCCATTCCGGCCGCTCGTTGTAGTGGACCTCTT CCCFFFFFHGHHHJJJJJJJJJJJJJJJJJJJJJJJIJIJJJJJJIJJJJJIJJJJJJJJJJJIJJJJJJJJJJJJJHHFDDDDDDDDDDDEDDDDDDDDD YT:Z:UU +6/2 4 * 0 0 * * 0 0 CCGTGAGGCGCCGGCGGCCGGGCGCCCGGAGCGGCGGTAGCCGGCGGCCTACGGTTCTCCTCCCCCGCCGCCCTCCCACCCGAGCTGCGGCGGGGCTTGGC CCCFFFFFHHHGHJJJJBHADFDBBBDBD6@@BDBBD-70(80757B-75>?5@+88>>C:3?BDD;;B59BD9ABB9<BD0&0509?9B>59@D###### YT:Z:UU +7/1 4 * 0 0 * * 0 0 CAATTATACAAATAAGGAAATAGGTCAACATAGAATCTCACATAAATCTAATTACTGGTCAATATAAAAAGGTAACAGTTCAAGGTCATATGTTGCCTAGC CCCFFFFFHHHHHJJJJJJJJJJJHIJJJJJJJJJJJJIJJIJJJJJJJJIJJJJJJJJJIIIJJIIJJJJJ@GHHIIHIJGEHHHHGFFFFFFFECECCE YT:Z:UU +7/2 4 * 0 0 * * 0 0 ATTTTAGTGTATAGGTAATGAATACTATATGTCAGTATGCCAGCATGTTCTGGGCTAAAGAAAGCAACATTTGACAGAAGAGAAATTTTGGTTATTGTCGG ?BBFFFFDHHHHHJJEGIJJJJJJJJJJJJIIJJJIIJJJJJJJJJJJIJIIJJJJJIJJJJJJJJIJJJJJJIJGIGIIIHHHHHFFFFDCDEEEACDDB YT:Z:UU +8/1 4 * 0 0 * * 0 0 CACCTTCCTCCCGCCTTTTTCTACCGGATCAAACTGATGTTGACCCGTGAAAGGCAAATACACCGCCAGAGACGGCTGAATACCTTTCACACGACTGACTT CCCFFFFFHHHHHJJIJJJJJJJJIIJJJJJJJJJJIIJJJGIJJJJJJJJJJJJJHHHGHFECDCD@DDDDDDDDDDDDDEDDDCDDDDDCDBDDDDDDD YT:Z:UU +8/2 4 * 0 0 * * 0 0 CGAAGAGGGTGACAATCCCGTACTTGACGCGACAACCGGTGCTCTGTGATACGTTCTCAATGAGTCGAGTTGTTTGGGAATGCAGCTCTAAATGGGTGGTA @@;DDDDDFADDDHGHIEFHGIIJJGGGIIGBGGHFGBAHABEEEC?CFDDACECAB>@CCC;C;:?B?ABCDBDCDBBDDCCCDDDDDDDDDEDD?BD9C YT:Z:UU +3/2 4 * 0 0 * * 0 0 GCAAGCAGCCAGCAAAAGGAAATAGCCCAGCGACAGCCACGAAGAGGAAAATGGCAAACGTGTCGGAAAAGAAGAGAAAAAAGAAAATGTAACTCACATGG CCCFFFFFHHHHHJJJJJJJIJJJIJJJJJJJJJJJJJJJJIIJJJJJJIIHHHHHFFFFEDEEDDDBBDDBDDDDDDDDDDDDDDDDDDCDDDDDDDCDC YT:Z:UU +9/2 4 * 0 0 * * 0 0 GTTGAAGTTGCCTTTGGAAACTTTGGACAAACAGGAAGAGAAACAAACCACCCCAAGGATAATAGCCATCACTGTTGGCTTAAATCAGATTTGGTGAATTT CCCFFFFFHHHHHJJJJJGJJJJJJJJJJJJJJJJIIJJJIJJJJIJJJJIJJJJJJJIJJJJJJHHHHHFFFFDEEDEEEDDDEDDDDDDDDDDDDDFED YT:Z:UU +9/1 4 * 0 0 * * 0 0 GTGTAGAGTATTTATTCTACCTTAAAGGATACAGAAGTATAAATACAGCTTAGAACTTCAACTGCTCACTCAGGAAGAAACAAAGGTGACCACAACTGGGA BBCFFFFFFHHHHIJJJJJJJJJHJJJJJJJJJJJJJFHIJJJJJJJJIJJJJIJJJJJJJIIIJJJJJJJJJJJIIJJJJHHFHGBEFFFEDDDDDDDDD YT:Z:UU +10/1 4 * 0 0 * * 0 0 CCTGACCACTTCCACAAGCAAGGCCATGCAGACTGTCTTCTCCTGAATTGTCACTGAATCTATACACTAACTCAGCAACAATGGCATTTAATAATAACCAG CCCFFFFDHHHHHJJJJJJJJJJJJJIJJIJJFIIIIJJGGIIIJGIIJBGIGIHIJJJJIJJJJJJJIIJJJFJEHHHFFFFFDCEEEEEDEDDDDDCC@ YT:Z:UU +10/2 4 * 0 0 * * 0 0 ATTGGGTTTAGCCCTCTGTGGTAGGTATCTGCACTCCAAGAGACAACTGGGTTAGTAAATAATATCCGTTCTATAGGAAGAAAGAAGTCAATCATCACCGG @CCFFFDFHHHHHJJJJJHIJGHIIHHIGIJIIGIIJJJJJIGIJJJJJJHGGGIIJJJJJIJJJJIJJJHHHHHFFDEFDEEDEEDDDCADDDDDDDDD6 YT:Z:UU +11/1 4 * 0 0 * * 0 0 GGCGCGGCGCAGCATGGCGGGGGTGTGTGGTAAGCCCCACATGTCACCGGGATCGCTGCCCGGGAAACGACGTTTGGAACCTGATCAGGAGCTGCTGATAC CCCFFFFFHHGHHJJJJIJJHDD)75?8AD?CCC@CDD-7<CDCCDDDDDD5:?BBB@<BDDDD>BDCB@;;9??<BCCDDDD3::ADC>@?@C>CC:A>4 YT:Z:UU +11/2 4 * 0 0 * * 0 0 GCCTCTCATCTTCAACCTGGCAATGACACACATGTGCTGCTTCAGTCATCTATCTCAGACCCCCAGATTGTTCTTCCAGATGGGGGGGAGAGCCTAGGCCA CCCFFFFFHGHHHJJJIJJGHIJFGJGHFHIIIIGIJJIIJJIGHIGIIIHIIJJJJHIJJJJJIIHHIJHEHHFGHFF@CFFDDDDBBDDDBDD>CCCDB YT:Z:UU +12/1 4 * 0 0 * * 0 0 CTTCTGTGGGCTTCACAGGCCACAGAGTGGATCTCAAGCCAGGCACCAGGACAAGCCACAGCCTTGCTCACTGTTGGCATGAAGCATCTACCGAGGTATTC @BCFFFFFHHHHHJJJJJJJJJJJJHJGHIJJJJJJJIJJJJIJIJJJJJIJHGHIJJJJJHHHHHFFFFFFEEEEDEDDDDDDDDDDDDDDDDDD>CEED YT:Z:UU +13/1 4 * 0 0 * * 0 0 CCGGCCGTTCATGGGCTGGCAGCGGCAAGATCATGGGCCGAGCGTGCAGGGCGCGATCGAGCGGGCGGCGCACGACATCACCGGCGAGACGATAACGGTGC CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJHHFDACDDDDDBDDDBDDDDDDDDDCDDDDDDDDDBDDDDDDDDDDDDDDDDDDDDDD@BB YT:Z:UU +14/1 4 * 0 0 * * 0 0 GCCGTCAGGTAGATGGTGCCGCCGCGCACGGGGTTGCCGGCCTTGAAGTCCTGCGCACGGCGCGGATCGATCAGCCTGGCGCGCGAGGCCAGGTAGGCGTC @CCFFFFFHFHHHJJJHIJJJJJJJJIIJJJJJAHHFFFDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDDDDDDDCDDDDDDDDBBDDDDDBD>@CD>>>@ YT:Z:UU +12/2 4 * 0 0 * * 0 0 TGGGATTTGAACTCAGGACCTTCGGGAGAGCAGTCGGTGCTCTTAACTGCTGAGCCATCTTACCAGCCTGGGTCTCCCATAAGTTAATAACTGTTTACAGT BCCFFFFFHHHHHJJJJIIJJJJJJJJJIJJJIHIJJIIJJJJJJJJJJJIJJJJJJJJJHHHHHHFFFFDDCEDDDDDDCDDDDCDEDCDDDDDDCDCCA YT:Z:UU +13/2 4 * 0 0 * * 0 0 CGACGGCGTCGAGTGGCTGCGGCACGCGCCAAGCTAACCCCGCCTCCCACGTCAACGGCGCACGGCGGGTGACGATGTGGTATTCGTAATGCCGCGCCAGA CCCFFFFFHHHHHJJJJJJIJJFGHIGEEFFDCCDDC?ADDDBDDDDDDDBBDBBDBDDDDDDDDDDDD0;<@<8<@8:C3>ADCCCCD?>@C<>59B### YT:Z:UU +14/2 4 * 0 0 * * 0 0 GCGGCCACACGCTGCACGAGATCCCGCCGGGCGGGCAAGGCATTGCCGCGCAGATTGCGCTGGGCATTCTGTCCAATTTCGACCTGGCCAGCCTGCCGGTG CC@FFFFFHHHHHJJJJJJJJJJJJJJJIHIJHDDDDDDDDDDDDDDDDDBDDDDDDDDDDDDDDDDDDEEEDDDDDDDDCDDDDDDDDDDDDDDDDDDBD YT:Z:UU +15/1 4 * 0 0 * * 0 0 TGCCTCTCTCACTTCTCGCTCCCCCTTCCACGCAAGCCGGCGGGCACGCGGCGCCGGCGGCCGCAGCGCCCCGCGGGCGGGCCCCCCCCTCCCCCCCCGGC CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJIHJJJIIJFDDDDDDBB57<B@BB@B5;7557@505@D-0)5<559B05@BD&0909@DDD###### YT:Z:UU +16/1 4 * 0 0 * * 0 0 GGCCGATCTACTTGTTTGATTCTCTATCAAAGAGGCTGTTGGTCAATGAGAATAATAATAACGAAACTATGCAAGTGCCTTTTCTGTGTATTTCAATGATT CCCFFFFFHHHHHJIJJJIJJJJIIIJIJJJJJJJJJJJJJIIJJJJJIJJIIJJIGJJJJJJJJJJHHHHHHFFFCEFEEEEEEEEDDEFFFECCDDDDE YT:Z:UU +15/2 4 * 0 0 * * 0 0 CGCTTGACGATCAATCGCCCGCCCCTCCGCGGTGTGGCGCGGCTGGGAGTCTTGCTCGCAGGGCCCCTCCCCGGGGCCCTCCGTCTCCCGAAGTACAGACG CCCFFFFFGHHHHJJJJJJJJJJJJJJJJJJJ@GGIJJHHFDDDDDDDD??CDCDDDDDDDDD?BDDDDDDDDBDDBDDDDDDBDDDDDD99BDDD@CCDD YT:Z:UU +4/1 4 * 0 0 * * 0 0 GTTGAAATGAGTGAAGACGGTTACTGATTAAGCGTTCGGATGATGGAAATAGGATTGATGGGAATATAATAATGGTAATGACAATTGGTAGACCTATTACT CCCFFFFFHHHHHJIJJJJJHIIJJJIJJJIJJJJJJJJGIIIIJJJJIJIIGHIJJIJJJJIIHHHHHHHFFFFFFFEEEEECDDDDCDDDDDDCDDEDC YT:Z:UU +17/1 4 * 0 0 * * 0 0 GGGGTGTAGCCTTGTTAAAGTAGGAGTGGCTTTCTTGGAGGAAGTGTATCACTAGGGGTGGGCCTTGAGGTTTCAAATGCCTGCACCCGTGCTCCCTCAAC CCCFDFFFHHHHHJJJJIJIHIJJIJFHIJJJJIJJJJFHJIIJIIIJJJJJJJJJJJGIGFFFFEEEEE?BCDDCDDDDDDDDDDDDDDDDDDDDDDDDD YT:Z:UU +17/2 4 * 0 0 * * 0 0 TTGAACTCTAACTTTCTCTGTCGTTTCTCCCTGTAGCTTTCTTCTTCTGCACTTCCTTAGTTATGTGAGTCAGGTCCCTTTCTCACTCTGCATGAATTGGT CC@FFFFFHHHHHJJJJIJJJJJJJJGIIJIJJIIJJJJJGJJJIJIJJIIHIJJJJIJJJJJJJJJIIIJJJJIIJIJJHHHGCCHFFFEDEECEEEEC> YT:Z:UU +19/1 4 * 0 0 * * 0 0 GAAAGTAAGGCACACCCAAGAATACGGGCGTGACTCTGCCTCCAGGGCCAACCACACTAGCTAAGCCTTCTATGGAAGTTAGAATTCACTACCTTGAGACT BCCFFDFFHHHHHIJIJJJJJJJJJJJJJJGHJJJJJIJJJJJJJJJJJJHHHHFFFEEEEEEDDDDDDDDDEEDDDCCDACCDDDCDDDDDDDDDCDBDD YT:Z:UU +19/2 4 * 0 0 * * 0 0 CTGGGCTGTGTGTCTGAACGTGAGTGTGACTGGTTAGCCTGCTGTGCTTAGCCCGCTCTTATCCAAATTGTCAAGGAAGAGTGACTCCCATGTGGCAAGAT BBCFFFFFHHHHHIIJJJJJIIJJHGIJBHIIJGHIIJJIJJJJJJJJJJJJJJIJJJJJJJJJHHHHHHFFFFFFEEEDEDDCDDDDDDDDDDCDDDBDD YT:Z:UU +16/2 4 * 0 0 * * 0 0 CAGTCCAAGGTGGGCACGATGATTGCAGCTCATTGTTAGAAATTTGATGAATACAATACTTAATTCTACTCTGAGTTGAAAACCCTGCAAAACAGCATGGC ?BBFFFFFHHHHHJJJJJJJJJJJJJJJJJIIIJJIJGIJJIJJJJIJJJJIJJGIJJJJJJJJJJJJJJJJJJHHHHHHHFFFFEEDEEDDDDDDDDDDD YT:Z:UU +18/2 4 * 0 0 * * 0 0 GCCTGTCAGCATACAAGTACCACAGTGAGCAGATGAAGGTCAGAGGACAACTTATGGGTGTTGATTCCTTCCATCTACTATGTAGGCTCTAGTTTTGCAGC CCCFFFFFHHHHHJJJJIJJJJJJJHIJJIJJIJJIIJJEIIJJJJJJJJIIJGIJJJFHIJJJJJJJJJJHHHHHHFFFFFFFFEEDEEDDEEEDDDDDC YT:Z:UU +20/2 4 * 0 0 * * 0 0 CGGGTGGGTAGCCGACATCGCCGCCGACCCCGTGCGCTCGGCTTCGTCCCGCCCCCCGGGAGGAGGGAGGGACGCGTGACCGACGGCCCCCCGGGCCCGAC BCCFDFFFHHHGHJJJJJJJJJJJIJJJJJHHEFFDDDDDDDDDDDDDDDDDDDDDDDDDBDD?DDDBDDDBBDBDDDDDDDBDDDBBDDDDDDDDDDD9< YT:Z:UU +21/1 4 * 0 0 * * 0 0 TTCGTCGCGCACCCGGGCCAGGGCCCGGACCCCGCGCAGGGGGTCACCCTCGCTGTGCAGATCCACATGGGTGCGCACCGCCGTGGTGCCGCTGGCCACCA BCCFFFFFHHHHHJJJJJJIJJJIJJJIGHHFFCDDDBDDDDDBDBDDDDDDDDDDDDEDDDDDDDCDDDDCBDDDBDDDDDDDDDBBCDDDDDDDDDDDB YT:Z:UU +21/2 4 * 0 0 * * 0 0 GGGCGAAACACCGACCCGTGACACTGATCTGTATTGACGAGGTCAATATCCCGCGTCCTGGTCGAAAGCGCAAGGCACCACACCGACCCGGCCGGGGACGG CCCFFFFFHHHHHJJJJJJIJJ>GIIIJIJJIIIIIJJJJJJHJJJHHHHHHFFDBDDDCDCCDDDDDDDDDDDDBBDDDDDDDBBDBDDDDDDDDB>BBB YT:Z:UU +22/1 4 * 0 0 * * 0 0 GCGAGGCCTACGGGAGAAGGCAGCAAGTGGTGGGCGCTCACCCATCGAGGAAGAGCCTTCTTGCCACTCGGGCAAGATCCGCTTTCTTCTCGACCCCCCTT CCCFFFFFHHHHHIIIIHIJJGIIJJJHIIHIIJDFGIIGIIHHGHFEFDDEEDDDDDDDDDCDDDDDDDDDDDDDDDDDDDDDDDDDCCDDCDDDDBBDD YT:Z:UU +22/2 4 * 0 0 * * 0 0 TGGACGCGTCAGGCTCTCGATTGTCCTTACGCCGTCCGTGTCGCTCTCGTGTCCCCTTCCCCGAGCCGGGGAGGGGTGGCTGCTCTGTTGCGGTGCATACC CCCFFFFFHHHHHJJIJIJIJIHGIIIJEIIJJIGHIIHEGIHHHFFFFDDDEDDDDDDDDDDBDDDBDDD@BDDD9@DBDDBDCCDCDCCDD@B>CDCAC YT:Z:UU +23/2 4 * 0 0 * * 0 0 GGAAGGATTAACTTGGAATAAAGTTTACATCCTGTTTAGAAGACAGCACTAGCACTCTCTGAAATACCAGTTATGACAGACAGATGCTGCCTGGGAGCCCT BCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJIJJJJGIJJJJJJIJJJJJJJJJJJJJJJJJJIIJJHIJJJJIJHHHHFDFFFFDEEEEDDDDDDDC YT:Z:UU +24/1 4 * 0 0 * * 0 0 GCGATGGAGATCCTGAAGACTCAAGTGGTGCCCGCGCTGGGGGCTCGCGAGGGGGTGGGCGACGCGAAAATTGCCAAGGTGTCTATCGTTGGCATCGGCAT @@@DDDFDFDAFHHIGJIEHGGGIGEFHAFCHIGGEGEFIJJJEE?<9A8=B'5<07BD?B@7;5>;BDD:>:@CCCBD4>4:A@CC@<A?B:>@ABB### YT:Z:UU +23/1 4 * 0 0 * * 0 0 CGGAAACTCTTCCCCCAAAGTTCTACTGTTTAAATGTGTGGAAAAATTAAAACCGGGATCAGAGTCTAGAAGTCTTGATCCAGTCTGACCAAGTTTTCATT CCCFFFFFHHHHHJJJJJJJJJIJGIJGJJJJJJJJIGHIJJJJJIJJJJJJJHGIJJJJHHHHHHFFFFFFCDDCECEDDDDDDDDDDCDDDDDDDDDEE YT:Z:UU +24/2 4 * 0 0 * * 0 0 CTCTCGGTCACGTCTCCAGCAACAGCAAGCATTCTAGCTCAGAAATTCAAGCCCTCTGCCTGTTGTGCTCAAAACAACAGATCAGGCCTTGGCCTCATCCA @CCFFFFFHHHHHJJJJJJJIJJJIJJJJIJJJJJJJJJJJJJJGIJJJIJJJJJJJJJJJJJJJJHHHHHHFFFFDDDEDDDDDDDDDDDDDDDDCDDDC YT:Z:UU +25/1 4 * 0 0 * * 0 0 ATGGCAAGCTTCTCTGAAGTCATCCAGAGTTTCTTGGATCATGTTCTGAATGAAGCGGATCTGGACTGAGGTAAGTGGCGCACTTGGCCGACTGTTCCCAA BCCFFFFFHHHHHJJJJJJJJJJJJJIIIHIIIJJIJIJJJJJJJJJJJIJJJIJJJJHIJJJJJJJJHHHHFEFFFFDDDDDDDDDDDDDDDDDDDDDDC YT:Z:UU +26/1 4 * 0 0 * * 0 0 AGCTTTGGGTGGCCCTCTCTCTAAAACAAAACCTACTGGCCTTGTAATGTGCTGTGAGCCCGTTTTTTTCTGTTATAAAGAACTCTCCTCCACATGCTCAT @CCFFFFFHHHHHJJJJJJJJJJJJJIJJIJJJJJJJJJJJJJJIJJJJIJJJJJJJJJIJIHHHHFDDDDDEDDCDEEDDDDDDDDDDDCDDDDDDDDDD YT:Z:UU +27/1 4 * 0 0 * * 0 0 GAGGGAATGCAATTAATTCATGTTGTTCTGGTTCCTGTCTCCATTTAAGCTTCCTCAGTCCCCACTAATTCCCATCAAGTGCCTTAATTAAACAAAGCTTA CBCFFFFFHHHHHJJJJJJJJJIIJJJJJJJIJJJJJJIJJJJJJJJJJJJJJJJJFIIJIJJJJJGIJJJIIIIHIIHHHHHHFFFFFFEEEDDCDCDDD YT:Z:UU +2/1 4 * 0 0 * * 0 0 GTCCAGATTAATACAGTTCTCACTAGGGGGGAAACTGAAACCTCCAGTTGCCAGGTGAATTTCTAAGACTTTTAATCCAAGTCTCTCACTGATTATTTTCT CCCFFFFFHHHHHJJJJHHJIIJJIJJJJJDBDDDDDDDDDDDDDDDDDDDDDDDCCCCDEDDEDEDDCCDDDDDCDCDCCCDEDDDDDDDDDDDDEEEEC YT:Z:UU +27/2 4 * 0 0 * * 0 0 TTTTTTTCTTTTTTTGATTGGGTCTTCCTGTTTTGGAGTCTAGGCTGTCCCGGATTCTGTAGATCAGGCTAGCCCCCAAATTCAGAGAGATCCTCTTACCT BBBFFFFFHHHHHJJJIJJJJJGIIJIIIIJIJJJJGJIIJJJJJJIJJHHHFEDDEEEEEDEEDDDDDDDDDDDDDDD@CCDCDDDDDDDDDDDDDACDC YT:Z:UU +25/2 4 * 0 0 * * 0 0 GGTGCTGCACTCCAGCCCTCTTAACGTCCTCATGGGGTCTCCAGGGAAAGAAGAAAATGAAAGCCATGAGCTGTCAGCCGAGACTAAGAGAGCATACCTAG CC@FFFFFHHHHHIJJJJIJJJJJJJJJIIJJJJJJJDGIJJJJJJGIIIGGGIIJJIIJJJJJHHHHHFFFFFEEEEDBDDBDDDDC@CDDDDDCDDCCD YT:Z:UU +26/2 4 * 0 0 * * 0 0 CTGGATTTTAGTTGAAAGTTGTCAAGGAATGTATTTTGGAACTGTTTTGACCATGAGACCATCTTGTATAAAGGTTGTTTTAGTCACCTACTGACTAAGCT CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJHIIJJJJJIJJJJIJJJIIDHIJJJJJJJJJJJJJIJJJIJJJCDHAHHHHFFFFFFEEEEDEDDCDDDD YT:Z:UU +28/2 4 * 0 0 * * 0 0 GTTCTATACATAACACTGGCCACAATCTGAAAGGACTTTCAAATTTGCATTTTACTCTTGTACCTTTGGGTAAGATGATCTTTTGAGTCCTGTTCATTTTC CBBFFFFFHHHHFJJJJIJJJGJJJJIJJIJIJJJJJJJJJJJJJJJIIJIJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHHHFFDFEEEEEEEEEEED YT:Z:UU +3/1 4 * 0 0 * * 0 0 GCCATCTGCCAAAATAATTTTATCATTCAACAAAACAAAGCACCACCTAAAAGTGGTTCTTTTTTTAAGCTGAACATTTTCTCCAGAAGGAGAAATTTTTT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIJJJIIGIJIGIJIJJJJJJJJJDGIHIJJJJJJJHHFFFFFFEECEEFEEDDDDDDDDDDDBDCDDDDDD YT:Z:UU +29/1 4 * 0 0 * * 0 0 GTGGGGCCAGATGTAGAACTTTTCCAGTACCATGCCTGCCTGTGTACCACCATGTTCTCAGCCATGATAATTGACTAAATCTCTAAAACTTTAAGCAATTT B@CFFFFFHHHHHIIJJJJIJJJJJJJJIJGGGFJIIIJJFIHIHGIJGIGGIIJJGGEHIIIIHI@GIGHIGHHEHHEDDFFDFFEEDEEECCA@CCCDA YT:Z:UU +29/2 4 * 0 0 * * 0 0 CCTTGGTCAAGTTACCTAGGTTTGTTGTTCCTGTATTAAATTTTCACACAAAAATAATTGGGTAAAAGCAGGGAAGAAAGAGACAAGACCATCACAGCACC CCCFFFFFHHHHHJJJJJJJHIIJJJJIJJJJIFHIIJIJJJJIJJJJJIIHIJJJJJJJJJGGIEHIJGIJJEHHFFFFFEEEEDDDDCCDCDCCDDDDB YT:Z:UU +28/1 4 * 0 0 * * 0 0 CTCAGATATTAACAGATGTTTACACAGGGTAAGGCAATCCATTCAAAGGAACAGGGTATTTGGGGGCTGGATAAATTTTGCAAAGCTGGTTTACAAGGTTT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJFFHIJJJJJJJJJJJJJJJIJJJIJJJFGHIJJJIJJHFFDEEEEE@CDDDDEDDDDDDDDDDCDDDDDDDD YT:Z:UU +30/1 4 * 0 0 * * 0 0 GCCAAGTGTGGATGTAAACTGAGAAGGGAGATAGGAACACATATAGTCCATTACAGTTCCCTAAGAGCTTTGATCGCATTCTCCTAAGTTCATGCATGTGT CCCFFFFFHHHHHJIJIJJJJHIJJJJJFHHIJJIJJJJJJJJJIJIIIGIIJJJJJJJAHHJJJJJJJJIIJJJHHHFFFFFEEEEEEDEEEDDDEDDDE YT:Z:UU +31/2 4 * 0 0 * * 0 0 TGTGCCTTGTGAACTGCTTGCTTGTGGCACGGAAATTTCCTTCCCGGCACCTGTAGAAACTGAGCAAGCAAGATGCTTGTTCCAATCAAAGGAAGTGGAAG BCCFFFFFHHHHHJJJJJJJJJJJHIJJJJJJJJJJJJJJJJJJJJJJJJHIIHGIJJJJJFHHHGFFFF@CDEEEDDDDDDDEDDDDDDDDDDDCCDDD> YT:Z:UU +32/1 4 * 0 0 * * 0 0 GTTGTGTTTAAGTTCTAACAATGAATTTTTACATATTAGTTGAATTTTAATTCTATTAATGTATGTTCAATTAACACGTTTTACGCCGAGAATAATTAATT CCCFFFFFHHHHHJJJIJJJJJJIJJJJJJEIIJIIJJIJIGIIIJJJJHIJIJIJJJIJJIJJJJJJJJJJJJJFHIIJJJJJGEHFDDDDDDDEFECED YT:Z:UU +32/2 4 * 0 0 * * 0 0 CCTGGCCTTATAATTAATTGGAGGTAAGATTACACATGCAAACATCCATAAACCGGTGTAGAATCCCTTAAAGAACTATTAAAATTTAAGGAGAGGGTATC @CCDDFFFHHHHHJJJJJJJJJJJFFHIIIJIJJJJJJJJIJJJJJJJJJIJJJJJIIIHIJHJJIIJJHHHHFFFFFFFEFEEEEEDEDDDDDDDD?AC@ YT:Z:UU +33/2 4 * 0 0 * * 0 0 CGGCATTCACAGCATGCCAGCAGTTGTCTCTGAAACTGTAATTTCTGTTTGCCAGTGTTTGTTATTTATCCTATAGTTCTCTGTCTGGACTGCAGTTTAAT @BCFFFFFHHHHGJJJJJGJJJJJJJJJJJJJIGIJJJIGHJJJJJJJJJIJJJJHIIJIJHIGIJJJJJJJIJJJJJJJJICHHHGHFFFFFEEEEEEDD YT:Z:UU +30/2 4 * 0 0 * * 0 0 CCCAGATCAACCACAAGCTTGAGGTGAGCCTCGGGGCTGGCCGCAATGGCATTCAAACCCCGGGCTGTCCGAGGGCGTTAGATCCCATTTAAACGCCCTAG CCCFFFFFHGHHHJJJJJJJJIJJHIIJJJJJJJJJJIIJIJJJGHHHHCDEDFFFEEDDDDDDDDDDDDDBBBDDDBB>BDDDDDDDDCCDACB>BDBCD YT:Z:UU +33/1 4 * 0 0 * * 0 0 AGTGGCTTCACGTGGGTCTCCGTTGGTATTTGAGTGCATAATTCTTGATTCTTCCATCTTCCAAACTGTAAGTTTTAAGATATATTCTCCTGGCTTTCAGA @CCFFFFFHHHHHJJJFHIJJJIJJJGEIIIDFDBGHIJIIJJFIJIGIJDHHHDHHGIJGIJGGIIJEHEEHHHEFHFFFFFFFFEEEEEEDDDDDDDDD YT:Z:UU +31/1 4 * 0 0 * * 0 0 TTCAAGTTTAGGATTATTGTCTCCCGAACAGTTTACTAGTGAAATGCTAAGTTCTTCACCCAAAGGCTCCAGATGGCTCTCACTGGCTGCAGCTGCTTTTG CCCFFFFFHHHHHJJJJJIJJIJJJJJJIJJJJJIIIJIHIJJJJJIJJIJJJJJJJJJIJJJJJJJJJJJJHHHHHFFFFFEEEEDDDDADDDDDDDDDC YT:Z:UU +34/2 4 * 0 0 * * 0 0 GTCAGGGGCTCGTCCGAAAGCCGCCGTGGCGCAATGAAGGTGAAGGGCCCCGTCCGGGGGCCTGAGGTGGGATCCCGAGGCCTCTCCAGTCCGCCGAGGGC BBCFFFFFHHHHHIJIIJJGGIEGIJGIJGHGHHHHBDFF;BCDDEDDDDBD@DDBDDDDBDDDD(<9?BDBDDDDDBDD@BCDDDDDDCCDBDDBBBBD9 YT:Z:UU +35/1 4 * 0 0 * * 0 0 TGGCTGTCTAATAAGAAAATGAAACATGAAGTCTCCAAGTACCACCTGCACAGAAATGCTCTAGCAATTTTGCTCAAGTATTGTTGGCTTACTTCTTCCAT CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJHIJHIJJJIJJJJJJJJJJJJJJJJIJJIIIIJJIIHIJFHHHHHHFFFFEEEEEEEDDDDE YT:Z:UU +36/1 4 * 0 0 * * 0 0 GCCCTCCTACTCGTCGCGGCGTAGCGTCCGCGGGGCCCGACGCCGCGGGGGCGAGACCCGGCGCGCGGGGGAGGGCGGCCGGAACCGACACCCCCCCCGAC CCCFFFFFHHHHHIJJJJJJJJJJJIJIJJGFDDDDDDD6BBBDDBBDDDDDDBD<BD?7@<BBBDDDDDDBDDDBB@9@>B@BB?B3905@BDDDDD### YT:Z:UU +37/1 4 * 0 0 * * 0 0 GCGGCGACGGGTATCAGGCTTCCTCGGCCCCGGGATTCGGCGAACGCTGCTGCCGGGGGGCTGTAACACTCGGGGCGGGGTGGGTCGGCCCCACGGGGGAC @C@FFFFFHHF??DGIGFCGHIJIGGGHGIIGHFCDCC?ABDD19BDDB8CCCD<888<<B@7AC@CCCDCDD>55<<09&5@################## YT:Z:UU +38/1 4 * 0 0 * * 0 0 CATTCACTCACCAGTACATACTGGGAACTGGCTAGGTGCCGGGCCTAAAGATACAATGTTGAATAGACATATTTGTGGAACTTATGAAACCAGACTGACTA CCCFFFFFHHHHHJIJJJJJJJJJJJJJJJJJJJJJDHIJJJJJJJJIJJJJJJJJJJJJJJHHHHHHFFFFFFFFEDEEDDDDDDDEDDDDD?BDDDDDD YT:Z:UU +35/2 4 * 0 0 * * 0 0 CTCAAAGTAAACTTCATTTTCTGCCAATGATAAGAAAAAAAAGAAAAACATGATAATCAGTTGTATGCATCAGTGATGAAATTTGGCAGTATGAGTTCAAG CCCFFFFEHHHHHJJJJJJJJJJJJIJJJJJJJJJJJIIIJJJJJJJJJJHIJJJJJJJJHHHHHHHFFFFFFEEEFEECDDDDDDDDDDDEEDDDEDEED YT:Z:UU +38/2 4 * 0 0 * * 0 0 ATGCGGTTCACCCTAAGGCCAGGCCCAACCCATCTCTTACCTATCCCAGCAGGTCACCCAGGTCACTCCCAAGCACTCTGGCCACTACACAGGTAATCTCA @BCFFFFFHHHHHJJJJJJJJJJGHIJJJJIJJJJJJJJJJJJJJJJJJJHIJIJJJJJHHHHFFFFFFDEEDDDDDDDDDDDDDDDDDDDDDCDDEECDD YT:Z:UU +39/1 4 * 0 0 * * 0 0 AGCTTAAAGAACCACCACAGATGCCTTCTTTAGGAAACACTTAATGGAAGATAACAAGTTTTCCAGGGGAGGAAGGTAGAAGTGACTTCTATTTTTTCAAT C@CFFFFFHHHHFIJIGHGIIGGIIJJIJGGGIIGEIJGGIGHFHGFEEGGHIGHCIJCFHHJFFHHIJBHFDFD@>>@ACC;AAACCCCCCCDDDDDCDC YT:Z:UU +20/1 4 * 0 0 * * 0 0 GGCGCCGAACCACCCCGCCCCGAGTGTTACAGCCCCCCGGCAGCAGCGTTCGCCGAATCCCGGGGCCGAGGAAGCCTGATACCCGTCGCCGCGCTCTCCCC CCCFFFFFHHHHHJJJJJJJJJJJFHIIJIJIJJJHHDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDBDDDCDDDDDDDDDDBDDDDDDDD YT:Z:UU +39/2 4 * 0 0 * * 0 0 GGAAACCCCCACAGGCGCGCTCGCGGGGCGGCCTCCGCGGGGCGAGTCCACCGCGCGGCCGGCCTGGTCCTCAACTCCCGCCTGCCGAGCGCCCGCGGCGC B@?DFFFFHHHHHGGHIJJJJJJIJGIDDB@BD1AD@BDBDDDD8B@CCCCBBBDDDBBBDD@B@BDCCCAACCDCACBBBDBAAB<5<BDDBD@<>BDDD YT:Z:UU +40/2 4 * 0 0 * * 0 0 GTCATCCAAGAAGAGAAACCACTCTTGACATGATGCCACCAGAAGATTGGCCTATCGGAAGCCGGAGTGGCATTTCCTTAATTAGTGATTGATGTGTGATG CCCFFFFFHHHHHJJJJJJJJJJJJJGJJJJIJJJJJJJJJJIJJHHIIJHIJJJJJJJJJJJJHFF;ACDEDDDEEDDDDEEED>ACDECCDDDDDBCDC YT:Z:UU +34/1 16 chrUn_gl000220 158989 255 32M3D11M4D58M * 0 0 GTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATCTCAAC DBDBDDDDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD?FFHHHJJJJJJIHJJJJIJJJJIJJJJJJIIJIIJJJHJJIJJJJIJHHHHHFFFFFCCC AS:i:-56 XN:i:0 XM:i:5 XO:i:2 XG:i:7 NM:i:12 MD:Z:32^CCC3G1A0C0C0C2^GCCA58 YT:Z:UU +37/2 0 chrUn_gl000220 113795 255 31M2I22M1I45M * 0 0 GCGCAGTCCGCCCGGAGGATTCAACCCGGCGGCGCGCGTCCGGCCGTGCCGGTGGTCCCGGCGGATCTTTCCCGCTCCCCGTTCCTCCCGCCCCCTTCACC @@CFFFFFHHHHGGJHIJHIJGHHJJJAFEBEE?@BBDDBD6BDD5:B8B<88@@5@C?@B7<B87;CAAAADD<&&&8590<CCCDCBD&&0590<?CCC AS:i:-40 XN:i:0 XM:i:6 XO:i:2 XG:i:3 NM:i:9 MD:Z:34G11T3C21C14A5C4 YT:Z:UU +41/1 4 * 0 0 * * 0 0 GTGTGTTTCCAAAACCTAGGTAATACCAGACATTTGGGGGAAAAGAAAGTGGAGGGTATGGTAAGTCTTTGTTTTGGCCACATCCTATTTACTTAGAAGAT CCCFFFFFHHHHHJJJJJJJHIIJIJJJJIJJJJJJJJJJHIJJIIJIJFGIGIJJ?EHHFFFFFFFEEEEEEDDDDDDDDDDDDDDDDEEEDDEDDDDC> YT:Z:UU +42/2 4 * 0 0 * * 0 0 GCCGGACGATATTTTATCGGACGACACGATCGTGGATCTTTTGAAGGGCCAGGGCGTTGAGATTGCACGGCGTACGGTTGCCAAGTACCGCGAGGCGATGA @CCFFFFFGHHHHJJJJIJJJJJIJGGGIIJIDGIEHFHHHHFDEFFDDDDBDDDD@BD?C?CCDCDDDBDDBDDBDCDBBDDDDDDDDDDD>BBDD3@BC YT:Z:UU +42/1 4 * 0 0 * * 0 0 CCCAGATACACGCAGACTCATGATACCTCACCTTCATTGTGACTTTTCATTGCCCGAGCCAATCTACACTGTTGTTGAGAGACGAGCAAAGACATCCCGCA CCCFFFFFHHHHHJJJJJJIJIJJJJJJJJJJJJJIJJJHIJIIJJJJIJJJIIIJGJJJJJIHHHHFFFFFFFEAEEEDDDDDDDDDDDDDDDDD>ABBB YT:Z:UU +44/1 4 * 0 0 * * 0 0 GGTTTTGCATTTCTCTGTGACCCAATGGGAAGCACAGCTTCTCTCCAGAGTTTGGAGAATTCAGGGTATTCATCTTGCTGCTGCAAAGTTAGTAGTTGGAA CCBFFFFFHHHHHJJJJJJJJJJJJJJJJIJJJJJJJJJJIJJJJJJJHIIIJJJJJJJJJJIJIJFHHJJJJHHHHHHHFFFFFECECEEDDEEEDDDDC YT:Z:UU +41/2 4 * 0 0 * * 0 0 TGATTGCAAAATAAGAATCCGGTTTAGTCTGATTGTATACAGGTTGCCAAATTCAATGTTCACCTTCTATGATGACAACCGTTTGTCTATACTTTTCATAA CCCFFFFFHHHHHJJJJJJJJJIJJIJHGIIHJJJHGIJJJJJHHIJJJJJIJJJJIIJJJIJJJJJJJJJJJJJJHHHHFFDEDEEDFEDDEDEDDDEEC YT:Z:UU +18/1 4 * 0 0 * * 0 0 CTTGTCTAACATATAAGGGCCCTGGGTTCGATCCCCAGTACTGAAAGAAAAAAAAAAAAAAAAAAGCAAACAAGAAATACAAAACTGATAATACTAGAAAC CCCFFFFFHHHHHJJJJJJJJJJJJJHIJJJJJJJJJJHIJJJJJJJJJJJJJJHFBDDDDDDDD>8ACDADD<CAC>C>CDCBBC:A>CC:>>>>:ACD9 YT:Z:UU +43/1 16 chrUn_gl000220 158975 255 46M3D5M1I5M5D44M * 0 0 TGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCC BDBBDDDDDDDDDDDDDDDDDDDEDDDDDBBDDDDDDDDDDFFFFFHHGHHJIHGJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC AS:i:-57 XN:i:0 XM:i:3 XO:i:3 XG:i:9 NM:i:12 MD:Z:46^CCC3G2C0C2^CGCCA44 YT:Z:UU +43/2 4 * 0 0 * * 0 0 GAGTCTAACGCGTGCGCGAGTCAGGGGCTCGTCCGAAAGCCGCCGTGGCGCAATGAAGGGGAAGGGCCCCGTCCGGGGGCCCGAGGGGGGATCCCGAGGCC CCCFFFFFHHHHHJJJJJJJJJJJJJJJJIG@DHEEHFDDEDDD@?BDBBBBDDDD:@C&057@DBBDD@>9@9<BDDD@B<<)9>9@BD&0?CA<09>B< YT:Z:UU +45/1 4 * 0 0 * * 0 0 CGGTGCGGCTACCTTGTTACGACTTAGTCCCAATCGCCAATCCCACCTTAGACGGCTCCCTCCCAAAAGGGTTAGGCCACCGGCTTTGGGTGTTACCAACT CCCDFFFFHHHHHJJIJJJJJJJJJJIJJJJJJIJGIJJJIJJJGJJJJIJJJHHFFFDDEEDDDDDBDDDDDDDCDDDDDDDDD>CDDD8<>BDDDDDBC YT:Z:UU +44/2 4 * 0 0 * * 0 0 TAGTGGTACTAACATCCCTCCTACCATCAATGTCCAAGTGATTTTAATTTATAGTCTCTTAGTTTAACACTGTTCTTAGAAAAAAATTGGCAAACTCAAGC BCCDFFFFHHHHHJJJJJIJJIJJJJJJJJJJIIIJJJGHIJJJJJJJJJJIJJJJJJJJJJIJJJJIJJJIIJJJJJJIJIGHFDEEEDDDDDBDDD>CA YT:Z:UU +46/1 4 * 0 0 * * 0 0 ACCACCACTGCCCAACAGCAAATTCTTAAAATAAAGTTAGTTATATTCAGTCATTAGCCAGAAACTTAGTATATCTGACTCCTTCCTATTTATGATCAAGC CCCFFFFFHHHHHJJIJIJJJJJJJJJJJJJJJJJJGHIJJJJJJJJIIJHIJJJIJIJGIGGIJJJJIGIIJJJGHGHGHHHHFFFFFFFFEEDEEDCDC YT:Z:UU +46/2 4 * 0 0 * * 0 0 GCAAAACTGGTTTTAGTTTCTTATAATGAATTGGACAATGTTTTTGAACGTCAGAAGAGGCAAGTGTCAAACTTTTCTCCCTTTAAAAAAAGCCCTAAGTG CCCFFFFFHHHHHJIJHJJJJJIJJJJJJJJJIJJJJJJJHJJJJJJJJJJIIJJJJJJJJJIJJIJJJJHHHHHHFFFFFFEEEEEEDBBDBDDDDDDDD YT:Z:UU +47/2 4 * 0 0 * * 0 0 CGCTTTGCCATCGATGCCGGTGCCCTGCACATTTTCGACAAGGCGACCGGTAGGCGGCTCTAGCCTTCCAGCAGATAGTCCGGCATGTCCTTCAGCCGGGC CCCFFFFFHHHHHJJJJJJJGIJJJIJJJJIJJJJIJIJJJJJIJJIJFFDDDDCBDDDDDDDDDDDDDDDDDDDDDCDECDDDDDDDDECCCDDDCB>B5 YT:Z:UU +48/2 4 * 0 0 * * 0 0 CACCTGATGGCTTTGCTCATGTCCTTCACTGGAAGAACTTGTGATGTCCCCTTTTGTCCTGATTCCTTTACTGAATCACTCTGTCACTGCCCTTTTCTGCT CCCFFFFFHHHHGJJJJJJJJJJJJJJJJIJJJJJJJJJJFHIJJJJJJJHIIJIJJJJJJJJJJJJJJJJJJJJJJIJHHHHHHC@DDFFDEEEEEDDDC YT:Z:UU +36/2 0 chrUn_gl000220 115012 255 37M3D11M4D53M * 0 0 CCGAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATC BCCFFFFFHFFHFJJIJIJJIJJJJJIIGHGIJIIHIIDIJJHIIIJIIJBHDBDFFEEEEDDDBBDDDD@BDDDDEDDCCBACACCCDDDDDDBBDDBDD AS:i:-60 XN:i:0 XM:i:5 XO:i:2 XG:i:7 NM:i:12 MD:Z:37^CCC3G1A0C0C0C2^GCCA53 YT:Z:UU +45/2 4 * 0 0 * * 0 0 GTTAAGTCCCGCAACGAGCGCAACCCTCGTTCTATGTTGCCAGCACGTTATGGTGGGGACTCATAGGAGACTGCCGGGGTCAACTCGGAGGAAGGTGGGGA CCCFFFFFHHHHHJJJJJIJJJJJJJJJJJJJJJJJIJJJJGIJJHHHGFBEFDEDDDBDDDDDDDDDDDDDDDDBDDD9@DDCDDDDDDDDBBD9@BDD? YT:Z:UU +47/1 4 * 0 0 * * 0 0 GCCGAAGGACATTTCCATGCTGGCGCCGCTGACCGAGCGTGAATTGCTCTACCGGCTCCTGACGGGCGAACAGTCCGGCCGCCTGCGCCAGATCGCCCAGT CCCFFFFFHHHHHJIJJJJJJIJJJJJJJJJJJJIFIJJHHHHHFFFFFFEEEDDDDDDDDADDDDDDBDDDCAC@?B@BBBD9??55<<91>?8?BD084 YT:Z:UU +50/1 4 * 0 0 * * 0 0 TTCCTCTCGCCGGGAGGCGCGTCCCGGGGTGTCCTCGTCGCGCGCGTGCGCGCCCGGTGCGCACCAGCGTCGGCGTCCGGAGTCGTGGAAGGAGGGGGTCG BBBDFFFFHHHHHJJIIJJJJJJJJJJJF<ACDDDDDDDBDDCDDD@BDDDDDDDDD7@BDDDDDDDDDDD>BDDDDDDDDDBCDDDDBCDD<BDDDD55< YT:Z:UU +49/1 4 * 0 0 * * 0 0 CTGGTATGTGGTTGCTGGAACTGTACCCCAGTCCTGCAGAAGAGCAGCCAGTGCTCTTAACCACTGAACCATCTGGCCCTTTAATTCATTTTGAGCTGGTT CCCFFFFFHHHHHJJJJJJJJJJJGJJJJJJJJJJJJJJJJJJJJJJIJJJIIJJJJJJJJJJJJJIIJJHHHHHFFFFDEEEEEEEDEEEEDDDDDDDDD YT:Z:UU +51/2 4 * 0 0 * * 0 0 AGAGAAAGCAAGAGTCACAGGCTGGGAGAACCCCATCTTGGACCCTCTTTCCTGAGAACATCCACATTCCACCCAGGTTGCCACTCCCGTGGGACCCAGGT @CCFFFFFHHHHHJIJIJJJIIJJJJIE:C?CGGIIIIIGJIIJJJIIIJJJJJJJJ=8=@CHIGHHHEHFDFFDDD@CCBDDDDDDDDDDDDDDDDBDD> YT:Z:UU +52/1 4 * 0 0 * * 0 0 GCCTTGACATTTGTAACTCTTGTATCAAGTTTGAAGAAGAGGACTTTATAAGTTATTCTTTCTCTGAGATGGATGCTTTTCCAAATTATCACAGCTAATGA CCCFFFFFHHHHHIJJGIIIJJIIJIJJJIJJJIJJIJJIJJGIJJJIJJIIIJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJHHHGHHFFEFFECEEDC YT:Z:UU +53/1 4 * 0 0 * * 0 0 GTCGCGCCGTGGGAGGGGCGGCCCGGCCCCCCCCGCCCCGGTTTGACCCGGGGGAAGGGGGGGGGGGCGCGGCGACGGGGATCAGGCTTCCTCGGCCCCGG CCCFFFFFHFHHHJJJJJJJHFDDDDDDDDDDDD69BDD05)07<>CCD58BDD-5?BBDDDD&5&0)0&5>-5&&09>&&)8<@C38CCC@>@52<<@99 YT:Z:UU +50/2 4 * 0 0 * * 0 0 GGGAGCGGCGACGACGGCGGGAGCGGCCTCAAGAGTCTGAGGAGAGCCAGGAGGCTCCCCTACGGGCCCCACCGCCCCCCGACCCCGGGGGCGGAGGGGCG CCCFFFFFHHHHHJJJIIJDD@8@BBBB3?CC>><3>A>ACDCBA<ADDDAB<@<BBBDDCB?7BB@B@DBBDDDBDDDD99B@BD9<@BD-9@5<@@D## YT:Z:UU +48/1 4 * 0 0 * * 0 0 CCAGCCTGTTGTGATAGGTTTTGAGGGGGTTATGGGTAAGAAGTTAACTGCTTGTTCAATTTTATGTATGACTTACACTGAAGTGAAGGAATGCTGGATAA CCCFFFFFHHHHHHJJJJDHIJIGHIJJJDHFHIJJBGEGHGGHIJIJJCHIJJGHHHFHFFFFFFFFEEEEEEDCDDDDDDDCDDEDCDDDDDDDDDDDC YT:Z:UU +52/2 4 * 0 0 * * 0 0 CTTAAATGAACATAAATATATAAAGTCTTTTTGTTTGTTTTGTATTTAGTAGAGTTTAAAATCTTGGCTCTTACTGTGGTACAAGCCCAAAATAAGAACAA @CCDDFFFGHHHHIJIJIJJJJJJJJJIJJJJJIJJJJJJJIGGIJJJJIFGGIHIJJHIJJIJIGIJJJJJJIJJHIIIJHHGHHFFDFECDEEEDDDD; YT:Z:UU +51/1 4 * 0 0 * * 0 0 TGGGCATCGAGGCTTGGCACTCAGATAGGAGGAGGAGGAATGGCTTTCTCCTGTTTTCTCTGGCATCACCCCTGCTGCCAGTCTCCTTTGATCCTGCTGCT CCCFFFFFHHHHHJJJJJJJJJJJIJIIJGIJGHJDFHGIIIIJJJJJIJJJIIJJJHHHHHHFFFFFEEEDDDDDDDDDDDDDDDDDDDCDDDDDDDDDD YT:Z:UU +49/2 4 * 0 0 * * 0 0 GCATGGTCATGGTATCTCTTCACAGCAATAAAAACCCTACTAATAACTAAGACAATCCAATCTCTTATCTGTCATAAAACCAGCTCAAAATGAATTAAAGG @C@FFFEEHHHHHFIJJJJJJJJJJJJJJIJJJIJIJJJJJJJJIJJJJJJJJJHJJJJJJJJJJJJJJJIJJJJJIHHHHHFFFFEDEEEEDDEEDCCDD YT:Z:UU +53/2 4 * 0 0 * * 0 0 CCGGAGGATTCAACCCGGCGGCGCGCGTCCGGCCGTGCCGGTGGTCCCGGCGGATCTTTCCCGCTCCCCGTTCCTCCCGACCCCTTCACCCGCGCGTCGTT @BCFFFFFHHHGGJJJJJJJJJJHFDDDDDDDDDDDDDDDD@BDBDDDDDBBD@DDDDDDDDDDDDDDDD@BDDDDDDDBDDDD?BD:ACDBBBDDDDDD< YT:Z:UU +55/1 4 * 0 0 * * 0 0 GATCCTCTTGCCTCTGGTGCTGCCAGCACCACCACCCAGCAAGAAAACTTTTAAAGACAGTCTCATTAGCTGAGCATGGTCTTGAACTTAACATATAGCTA CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJIJJJJIJJJJJJJJJJJJJJJJJJJJJIIJJJJJEIHHHHHFCEFFCCEEEEDDDDDDDDDDEEDCCE YT:Z:UU +56/1 4 * 0 0 * * 0 0 CTGCGGTTATGAGTACGACCAGGCGTGAGACTAATGCGTTCCGTGGGATTTTCAAGGACTGTCAGGGACGCACCGGACACAACACAAGTGTTGTGCTCTAC @CCFFFFFHHHHHIHJJJJJIJJJJIJIIHJJJIJJIJIJJIJFHIJJJHHHHHHFFFFFDEEEEEDDDDDBDDBDBBDDCDBDDDD?>ACDBCDDDDDDC YT:Z:UU +56/2 4 * 0 0 * * 0 0 CGCTCAAGCGTGTTACCCATACCTCACCGTTGATGTTAAAGTGATGCATCAACGAGTAGGCAGGCGTGGAGGTTGTGAAGAAGCCTTGGCAGTGATGCCGG CCCFFFFFHHHHHJJJJJIJIJJJJJJJJJJJJJJIIEIIIGGGIJIIJIHGIIIJGHIJJJJHHHBDDACD@BD@BDEDDDDDDDCCDDDD<CCCDDDDD YT:Z:UU +40/1 4 * 0 0 * * 0 0 CCTCTCTCTCTCTCCCTCTCTCTCTCTCTGCCCTTCTGTGCCTCTACTACCCTCTTAACTCCCCTCTCCGTGCCCTGAATAAACTCTATTCTATACTGTAC BBBFFFFFHHHHHJJJJJJJJJJJJJJJIIJIGGHIJJGHGIJJIEIJGIGIJIIJHFHIJIIIJJJJJIAHHFFEDDCEECCEEDDDDEEEEEEDECDDD YT:Z:UU +57/2 4 * 0 0 * * 0 0 TGCACCGGCGGCGGGGTGAGGTGTAGGGGGATGGGCGGGACGCTGGGAGGAGCCAATGACCCGTGCGAACGTTCAGGTCGATGGCAGCTGCGACGTGCGTC ##################################################################################################### YT:Z:UU +58/1 4 * 0 0 * * 0 0 AGCAGGAAGTAGCCCAAGAGATACGACGCCCTCATTCCCTTTTCATCATCGGCTTCCCCTTCCCTTTTTCTTTCCTTCTCTTTATAATATAAAAAAGGGAG ??@DADDDDHHHAGHIBB;FACDB@DHIF@??G>DBBEBFG?C=@=F4==F4ADGHCHH;;3@DC>;;>CCCCC(-(5:A>3:;>>;BCDDE;@><<BBBB YT:Z:UU +59/1 4 * 0 0 * * 0 0 GCCCAAGGTACACGCCCCTCAGCTCTGCCCTACATAGAAATGGGGCTTGGACAGGAGGTACTGTCCAGTCTAGGTGCTGGCCAGCGGAAAAAATCCTCAGT BCCFFFFFFFHHHJJJJJJJJJJJJIJJJJJJJJJIIJJJJJJJJJJJJJIIIJJIIHAEHFFFFFFECCECCECACDDD?ACB?=B9BDCA<8>CCCA>: YT:Z:UU +59/2 4 * 0 0 * * 0 0 GTGTTTATGAATCAAGGCAGGCTAGGTGGAACCTGTTCAAGGCCGCTGGATGCTGAAGGATGGGATGGTCGAGTCACGTGTTCATCGCCTCCCTTTTCTCC BBBDFFFFHHHHHJHIJJJJJJJJJJCFHIJJJJIGHGGIJJJJJJJIJHHHIJJJJJJHHHHFFFFDDEDDDDDDDDBB?BDDEEDDDDDDDDDDDDDDC YT:Z:UU +55/2 4 * 0 0 * * 0 0 TCTGACCTGTTATTCTCCATATATTTATATTTATATTTCTCCATATATTTATGAATATTATATGAGGTATATAGTGTGGAAGTAAAGGCCTATAATTCCAG CCCFFFFFHHHHHJJJJJJJJJJJJJIJIJJJIIGIJJJJJIIJJJJJJJJIJIJJJJJJJJJJIJJFHIJJJJIJIIJJJJJJJIIIJJHHHHFGFFFFB YT:Z:UU +54/1 16 chrUn_gl000220 158967 255 54M3D11M4D36M * 0 0 CTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTC DDDDDDDDDDDDBDBDDDDDDDDDDDDDDDDEDDDDDDDDDDDDFFHHJJJJJJJJJIHGIHGJJJJJJJJJJJJJJJJJJJJJJJJJHHHHGFFFFFCCC AS:i:-58 XN:i:0 XM:i:5 XO:i:2 XG:i:7 NM:i:12 MD:Z:54^CCC3G1A0C0C0C2^GCCA36 YT:Z:UU
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.fastq Mon Mar 21 17:33:26 2016 -0400 @@ -0,0 +1,20 @@ +@34/1 +GTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATCTCAAC ++ +DBDBDDDDDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDD?FFHHHJJJJJJIHJJJJIJJJJIJJJJJJIIJIIJJJHJJIJJJJIJHHHHHFFFFFCCC +@37/2 +GCGCAGTCCGCCCGGAGGATTCAACCCGGCGGCGCGCGTCCGGCCGTGCCGGTGGTCCCGGCGGATCTTTCCCGCTCCCCGTTCCTCCCGCCCCCTTCACC ++ +@@CFFFFFHHHHGGJHIJHIJGHHJJJAFEBEE?@BBDDBD6BDD5:B8B<88@@5@C?@B7<B87;CAAAADD<&&&8590<CCCDCBD&&0590<?CCC +@43/1 +TGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCC ++ +BDBBDDDDDDDDDDDDDDDDDDDEDDDDDBBDDDDDDDDDDFFFFFHHGHHJIHGJJJIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHHHHHFFFFFCCC +@36/2 +CCGAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTCTTGGGGCCGAAACGATC ++ +BCCFFFFFHFFHFJJIJIJJIJJJJJIIGHGIJIIHIIDIJJHIIIJIIJBHDBDFFEEEEDDDBBDDDD@BDDDDEDDCCBACACCCDDDDDDBBDDBDD +@54/1 +CTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGCGCTCTCGCAGAGACTCGAAACCCGCAGTTTTATCCGGTAAAGCGAATGATTAGAGGTC ++ +DDDDDDDDDDDDBDBDDDDDDDDDDDDDDDDEDDDDDDDDDDDDFFHHJJJJJJJJJIHGIHGJJJJJJJJJJJJJJJJJJJJJJJJJHHHHGFFFFFCCC