# HG changeset patch
# User drosofff
# Date 1458596006 14400
# Node ID 55107d4a728c72d1ef3974a634872c6658b59c13

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sam_to_fastq commit 0651eb8c86d890e4b223fec82ab3980932710030

diff -r 000000000000 -r 55107d4a728c sam_to_fastq.py
--- /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)
diff -r 000000000000 -r 55107d4a728c sam_to_fastq.xml
--- /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>
diff -r 000000000000 -r 55107d4a728c test-data/input.sam
--- /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
diff -r 000000000000 -r 55107d4a728c test-data/output.fastq
--- /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