| Previous changeset 5:ea5bba2c569f (2017-05-30) Next changeset 7:6df84986c146 (2017-05-31) |
|
Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/repenrich commit e9282183531bacbb4bbe2d6e53258f6e0ad0bc34 |
|
modified:
edger-repenrich.xml repenrich.xml |
|
added:
test-data/Samp-paired_class_fraction_counts.tab test-data/Samp-paired_family_fraction_counts.tab test-data/Samp-paired_fraction_counts.tab test-data/Samp_L.fastq test-data/Samp_R.fastq test-data/paired-aligned_reads.tab |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 edger-repenrich.xml --- a/edger-repenrich.xml Tue May 30 20:16:05 2017 -0400 +++ b/edger-repenrich.xml Wed May 31 13:09:15 2017 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="edger-repenrich" name="edgeR-repenrich" version="1.2.0"> +<tool id="edger-repenrich" name="edgeR-repenrich" version="1.3.0"> <description>Determines differentially expressed features from RepEnrich counts</description> <requirements> <requirement type="package" version="3.16.5">bioconductor-edger</requirement> |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 repenrich.xml --- a/repenrich.xml Tue May 30 20:16:05 2017 -0400 +++ b/repenrich.xml Wed May 31 13:09:15 2017 -0400 |
| b |
| @@ -1,4 +1,4 @@ -<tool id="repenrich" name="RepEnrich" version="1.2.0"> +<tool id="repenrich" name="RepEnrich" version="1.3.0"> <description>Repeat Element Profiling</description> <requirements> <requirement type="package" version="1.2.0">bowtie</requirement> @@ -86,7 +86,18 @@ <output name="family_fraction_counts" file="Samp_family_fraction_counts.tabular" ftype="tabular"/> <output name="fraction_counts" file="Samp_fraction_counts.tabular" ftype="tabular"/> </test> - </tests> + <test> + <param name="seq_method_list" value="paired-end"/> + <param name="input_fastq" value="Samp_L.fastq" ftype="fastq"/> + <param name="input2_fastq" value="Samp_R.fastq" ftype="fastq"/> + <param name="genome" value="chrM.fa" ftype="fasta"/> + <param name="repeatmasker" value="chrM_repeatmasker.txt" ftype="txt"/> + <output name="bowtie_alignments" file="paired-aligned_reads.tab" ftype="tabular"/> + <output name="class_fraction_counts" file="Samp-paired_class_fraction_counts.tab" ftype="tabular"/> + <output name="family_fraction_counts" file="Samp-paired_family_fraction_counts.tab" ftype="tabular"/> + <output name="fraction_counts" file="Samp-paired_fraction_counts.tab" ftype="tabular"/> + </test> + </tests> <help> |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 test-data/Samp-paired_class_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Samp-paired_class_fraction_counts.tab Wed May 31 13:09:15 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Low_complexity 2.0 +rRNA 111.0 +Simple_repeat 121.0 |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 test-data/Samp-paired_family_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Samp-paired_family_fraction_counts.tab Wed May 31 13:09:15 2017 -0400 |
| b |
| @@ -0,0 +1,3 @@ +Low_complexity 2.0 +rRNA 111.0 +Simple_repeat 121.0 |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 test-data/Samp-paired_fraction_counts.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Samp-paired_fraction_counts.tab Wed May 31 13:09:15 2017 -0400 |
| b |
| @@ -0,0 +1,11 @@ +A-rich Low_complexity Low_complexity 2 +LSU-rRNA_Cel rRNA rRNA 111 +_ATA_n Simple_repeat Simple_repeat 0 +_ATTTAT_n Simple_repeat Simple_repeat 1 +_ATT_n Simple_repeat Simple_repeat 11 +_AT_n Simple_repeat Simple_repeat 0 +_CTAATT_n Simple_repeat Simple_repeat 29 +_TAT_n Simple_repeat Simple_repeat 0 +_TA_n Simple_repeat Simple_repeat 0 +_TTA_n Simple_repeat Simple_repeat 80 +_T_n Simple_repeat Simple_repeat 0 |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 test-data/Samp_L.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Samp_L.fastq Wed May 31 13:09:15 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+@ERR1044075.680 HWI-ST790:248:H0G15ADXX:1:1101:10892:2723/1\n+GCTCCTAAAATTGAAGAAATTCCTGCTAAATGTAGAGAAAAAATAGCTAAA\n++\n+CCCFFFFFHHDHHJIGGIIIGIIJJJGIJIGIAEFFHJIIIIGEEIICFHI\n+@ERR1044075.759 HWI-ST790:248:H0G15ADXX:1:1101:15792:2653/1\n+GAAAATAATCATTCACAGACTACCCAAGGATTATTTTTTACAGTTTTACTA\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJ\n+@ERR1044075.753 HWI-ST790:248:H0G15ADXX:1:1101:15644:2508/1\n+CTTATCTTACCTTAATAATAAAAGCGACGGGCGATGTGTACATATTTTAGA\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJIJIJJFHHIIJIJJJJJIHH\n+@ERR1044075.814 HWI-ST790:248:H0G15ADXX:1:1101:19529:2745/1\n+TGAGTCTGCAATAGTAAATGGAGCTTCAATATATTCATAAGCTTGAAGAAT\n++\n+?@?DDDFFHHGHHJHHIGJIEDBGGIHIJGIFCHEHI>GAEGIIGIEDHEH\n+@ERR1044075.946 HWI-ST790:248:H0G15ADXX:1:1101:8484:2908/1\n+CATACACAACATATATTTGCTCATTTAGTTCCTCAAGGAACACCCGCTATT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJIIJJJJJJJJIJJJIJJJGIIJJJ\n+@ERR1044075.818 HWI-ST790:248:H0G15ADXX:1:1101:19811:2591/1\n+ATTTTTTCCTCAACATTTTTTAGGATTGGCTGGAATACCTCGAGGTTTTTC\n++\n+@@CFFDD?FHDDDC@FHEGGG9CGDEGGGFHEI)09*?B<*7?########\n+@ERR1044075.978 HWI-ST790:248:H0G15ADXX:1:1101:10873:2966/1\n+CTCATCAGTAAATTGTGATATATAAAAATAATCAAACTACATCGACAAAAT\n++\n+CCCFFFFFHHHHHJJHIJJJJJJJJJJJJJJJJJJJJIJJJIJJJJJJJJJ\n+@ERR1044075.998 HWI-ST790:248:H0G15ADXX:1:1101:12703:2936/1\n+TTTTCATTTAGTGGATTATAGTCCATGACCATTAACAGGAGCTATCGGAGC\n++\n+BCCFDFFFHHHDHIIIJJJIJGHJJJJFJIFIIJIJJJIGGHJIIGIIIJI\n+@ERR1044075.1137 HWI-ST790:248:H0G15ADXX:1:1101:1525:3138/1\n+TTGGAAGATTAGTAATATTAGCTGCTATAACTAAAAGAGCTCAGATTCCTT\n++\n+BB@DDDEBFHHHDGIJJJJIJIJIJHHIJGGJJJJIGDFGGHEGCGHJGIJ\n+@ERR1044075.1446 HWI-ST790:248:H0G15ADXX:1:1101:1567:3357/1\n+TAATCCAGCTATAAATATTGTTAATCCAGATAATAATAATATTAATTGTCC\n++\n+@@CFFDFFHHGHHIBFGHIFC>HHHIHCFGHC>FH@HG<DFHGHEGHC?CG\n+@ERR1044075.1652 HWI-ST790:248:H0G15ADXX:1:1101:16002:3269/1\n+CTTGAGCCCACCATAGACTTATAGAAAATAATCATTCACAGACTACTCAAG\n++\n+BCCFFFFFHHHHHJIJIJJJJJJIJJJJGIJGIJHIIJIJHGGIIJEGIII\n+@ERR1044075.2019 HWI-ST790:248:H0G15ADXX:1:1101:20598:3595/1\n+CTAAAATTGAAGAAATTCCTGCTAAATGTAGAGAAAAAATAGCTAAATCAA\n++\n+@@@DDDE>DHBHHJJJIIJJGIJGIGHGGHHGCHGGIIGFGHIEGHGHIEC\n+@ERR1044075.2025 HWI-ST790:248:H0G15ADXX:1:1101:1366:3788/1\n+CTACCTTTGCACAGTCAAAATACTGCGGCCATTTAAAATTTTCAGTGGGCA\n++\n+@@CDDDFFHHBF<GG<FHGIJFIJJJIGJFIGHIJJJGIIIEDDBDHIIC?\n+@ERR1044075.2112 HWI-ST790:248:H0G15ADXX:1:1101:7863:3843/1\n+CCGTGGGAATGCTATATCAGGAGCACCTAATATTAAAGGCACTAATCAATT\n++\n+CCCFFFFFHHHHHJJIJIIIHIIIIJIJJIJJJJJJJJJHIIIGHHIIHJJ\n+@ERR1044075.2117 HWI-ST790:248:H0G15ADXX:1:1101:8122:3811/1\n+TAAGATTTTGACTTCTACCTCCTGCTCTTTCTTTACTATTAGTAAGTAGAA\n++\n+BBBFDFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJFIGIGIEFFGIBGEGG\n+@ERR1044075.2555 HWI-ST790:248:H0G15ADXX:1:1101:1876:4399/1\n+CTGTTACTAAAATTCGAATTTGTGAGTTTATGGGTAAAACTACTCGGTTAT\n++\n+CCCFFFFFHHHHHJJJJJJJJJIJHIJIJHHJJICHIIIIHIGIGHGJIGI\n+@ERR1044075.3073 HWI-ST790:248:H0G15ADXX:1:1101:1378:4822/1\n+TTTATTTGTTTGATCAGTAGTTATTACTGCTTTATTATTATTATTATCACT\n++\n+BB@ADDEFFHHHHIGIIJGIIIJJJIIIGGIJGHGIAHG@FI<EF?D?FGH\n+@ERR1044075.3103 HWI-ST790:248:H0G15ADXX:1:1101:3753:4970/1\n+TAGATACTCGAGCTTATTTTACCTCAGCTACTATAATTATTGCAGTTCCTA\n++\n+@BCFFFFFHHFHHJJIJJJJJJIJIJJHIIIIGIJJJIGIIHIHGIJJDCA\n+@ERR1044075.3115 HWI-ST790:248:H0G15ADXX:1:1101:4946:4934/1\n+GCTGAGGTAAAATAAGCTCGAGTATCTACATCTATTCCAACGGTAAATATA\n++\n+CCCFFFFDFHHHHJJJJIJJJJHFHIJJJJJIJIJJJIIIGHJFHIJIHGH\n+@ERR1044075.3167 HWI-ST790:248:H0G15ADXX:1:1101:8133:4808/1\n+CTGGGTCAAAAAATGATGTATTTAAATTTCGATCTGTTAATAATATAGTAA\n++\n+CCCFFDFFHHHHHJJIJJIJJJJJJJJJJJJJJJJJJJJIJJJJIJIIFGI\n+@ERR1044075.3206 HWI-ST790:248:H0G15ADXX:1:1101:9789:4942/1\n+TCATCATATATTTACCGTTGGAATAGATGTAGATACTCGAGCTTATTTTAC\n++\n+8?<:DDBD<D?A:A<A)CC7B9AFEFE<A2+22@9:CE7D?DDB*99?D##\n+@ERR1044075.3251 HWI-ST790:248:H0G15ADXX:1:1101:12710:4758/1\n+TTTAGCTAATTCATCAGTAGATATTATTTTACATGATACTTATTATGTAGT\n++\n+BCCFFFFFHHHHHJJJJGHJIJJJJJJJJJIIGJJGIIIIJGHIIJJFHEH\n+@ERR1044075.3552 HWI-ST790:248:H0G15ADXX:1:1101:10536:5030/1\n+CTCTTTCTTTACTATTAGTAAGTAGAATAGTTGAAAATGGAGCTGGGACAG\n++\n+CCCFFFFFHHHHHIJJJJHIJJIHJIJJJJJJJJJJJIIIIJIIJJIIJJJ\n+@ERR1044075.3658 HWI-ST790:248:H0G15ADXX:1:1101:18523:5017/1\n+TCT'..b'JIJGG\n+@ERR1044075.659985 HWI-ST790:248:H0G15ADXX:1:1106:11631:62123/1\n+AAAGAATCGGCCATCAATGATATTGAAGTTACGAATATTCAGATTTTAATA\n++\n+<<@DDDDDBF1CDC:C?,C9AAC42?C@H@AGG1?DFGEFF@HGGGCEHE?\n+@ERR1044075.660170 HWI-ST790:248:H0G15ADXX:1:1106:7215:62363/1\n+TGGAAGTGATAATAATAATAATAAAGCAGTAATAACTACTGATCAAACAAA\n++\n+BBCDDFDDHHHHHIJJJIIJJIIJJJIJJIJJJJJIIIJJIIJGIJJGJJJ\n+@ERR1044075.660255 HWI-ST790:248:H0G15ADXX:1:1106:12160:62309/1\n+CAGCTGTTACTAAAATTCGAATTTGTGAGTTTATGGGTAAAACTACTCGGT\n++\n+CCCFFF=DFHFGHJIGHGIGEHIHFCEFGGHJHIJJJ:DGGIIGGEHGCHD\n+@ERR1044075.660247 HWI-ST790:248:H0G15ADXX:1:1106:11554:62387/1\n+CTTGAGCCCACCATAGACTTATAGAAAATAATCATTCACAGACTACTCAAG\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJIIJJJIIJIJJJJJJJJJIJJJJ\n+@ERR1044075.660686 HWI-ST790:248:H0G15ADXX:1:1106:8134:62985/1\n+TATCATTCAATTGATGAATTTAGTTGAATTGGGTAAATTACTTGTCGTTGT\n++\n+CCBFFFFFHHHHHJJJJJJJJIIJJJJJJJIJJCFGHJJIIJJJHIGHIGG\n+@ERR1044075.661147 HWI-ST790:248:H0G15ADXX:1:1106:8314:63385/1\n+AATTGGAAGATTAGTAATATTAGCTGCTATAACTAAAAGAGCTCAGATTCC\n++\n+@@CFFDEDHHFFHIACGIJGIJIGIIGGHGGGHGIIJGHHGIJJIIJIJHH\n+@ERR1044075.661472 HWI-ST790:248:H0G15ADXX:1:1106:13982:63648/1\n+TACAAATCATAAAGATATCGGAACTTTATATTTTATTTTTGGAGCTTGAGC\n++\n+CCCFFFFFHHHHHJIJJJJJJJJJJJJJIIJJJJIJJJJJIIJJIJJGIJI\n+@ERR1044075.661879 HWI-ST790:248:H0G15ADXX:1:1106:7696:64091/1\n+TTCATGTAAAGTAGCTAATCAACTAAAAATTTTAATTCCAGTAGGAACTGC\n++\n+@BBDFEBDFHHHHIIIJJIHIJIJGIJJJJIJIJGIIIIJIEFHHIJJIII\n+@ERR1044075.662140 HWI-ST790:248:H0G15ADXX:1:1106:8516:64305/1\n+CAGCAATTATATTAGCAGTTAATCGAACAGCTAATGTTCCAGGTCGAATAA\n++\n+@@CFFFFFFHFHHJJBEHGCGHGCHIJEHG>FGIGHEDHHJHI??F@BDHH\n+@ERR1044075.662813 HWI-ST790:248:H0G15ADXX:1:1106:21170:64761/1\n+CCAAGACGTTCATAAGATACATTAGCTAAACAAAATAACCCAGAAGAACAT\n++\n+?@BF?DEAFFDDFIJJJIJIGJIIIJIHHJGHHIJJJIJJIIGIJCHDFDD\n+@ERR1044075.663073 HWI-ST790:248:H0G15ADXX:1:1106:5648:65498/1\n+GATAAACTTCTGTGAAAAAAAGCTCAAAAAAATCTCACAAAAAATAAAAAT\n++\n+?@<DDD>DF4CFACFBEEGH:G)@:?DGGGG<F9B?F4C>=@C@CCEGH##\n+@ERR1044075.663162 HWI-ST790:248:H0G15ADXX:1:1106:11759:65389/1\n+CAGAATATCTATGTTCAGCTGGTGGAGTATTTTGGTATCATTCAATTGATG\n++\n+CCCFFFFFHHHHHIJJJJJJJJHHIHJFGHIJJJJFHIIJIJIJIIJJIJJ\n+@ERR1044075.663390 HWI-ST790:248:H0G15ADXX:1:1106:10400:65584/1\n+CAACCATTCATTCCAGCCTTCAATTAAAAGACTAATGATTATGCTACCTTT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJJJIJJJIJJJJIJGIJJ\n+@ERR1044075.663400 HWI-ST790:248:H0G15ADXX:1:1106:11192:65654/1\n+ATTGAAGCTCCATTTACTATTGCAGACTCAATTTATGGATCAACATTTTTT\n++\n+@CCFFFFBHHHHGJJJJJJIIIIIEGIIIFHIIHFIIJGHGIIIJIJJJJJ\n+@ERR1044075.664278 HWI-ST790:248:H0G15ADXX:1:1106:20222:66346/1\n+CTAAAATTCGAATTTGTGAGTTTATGGGTAAAACTACTCGGTTATCAACAT\n++\n+@@@FFFFFHGDHHIGIIIIGHHGIGIJJAFGHEGHIIEIJJEHIIJIJIJJ\n+@ERR1044075.664837 HWI-ST790:248:H0G15ADXX:1:1106:12794:67053/1\n+CATATATTTGCTCATTTAGTTCCTCAAGGAACACCCGCTATTCTTATACCT\n++\n+@@CFFDEFHHHHHJJJJJJIIJJJJJJJJJJJJJJJJJJJJJIJJIIIJII\n+@ERR1044075.665607 HWI-ST790:248:H0G15ADXX:1:1106:15165:67769/1\n+CTCGTGATACATCTCGTCATCATTGATATACAGTTAAAATAGTAATAATAT\n++\n+@?@DFDFDHHHFHIJIDEFEHCHIEHIIHIHIJIGGGGGDHIGHGGII@GG\n+@ERR1044075.665680 HWI-ST790:248:H0G15ADXX:1:1106:19772:67837/1\n+GTTAAATAATAAATGATTAAAAAGTCATTTCATTATTATATTTATTGGAGT\n++\n+@?@DDFFFHHDHHGFFGIJECF>BBHEIJJJIIGAHHIIJIGGIGIHGAFG\n+@ERR1044075.665714 HWI-ST790:248:H0G15ADXX:1:1106:6180:68224/1\n+ATTTCCTAAAAGAGTTAATAATAAATGTCCAGCAATTATATTAGCAGTTAA\n++\n+4114422=:CBFCEEFEAHH@4FFHCH<CAEF+A@E9C9:C?C<:?BFD@4\n+@ERR1044075.665736 HWI-ST790:248:H0G15ADXX:1:1106:7267:68163/1\n+AGAGAACCAAAAGTTTCCTTTTTTCCTGATTCTTGTCTAATAATATGAGAA\n++\n+?@BDDFFFHHHHHJIJJJJJJJJJJGJEHIJGIJGHIGGECHHHGGADDHI\n+@ERR1044075.665878 HWI-ST790:248:H0G15ADXX:1:1106:16309:68134/1\n+CATGACCATTAACAGGAGCTATCGGAGCTATAACAACTGTATCAGGTATAG\n++\n+CCCFFFFFHHGHHJJIGHJJJJJJJJIJJJIJJJIHIJIFHGEGIJ9BGII\n+@ERR1044075.666310 HWI-ST790:248:H0G15ADXX:1:1106:13497:68695/1\n+TAAAAAAACAAATCCTAAAGCTCATAAAATAGCTGGAGAATAAGAAAGTTG\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJIJJJJJIIJJIJJJJJJJHII\n+@ERR1044075.666724 HWI-ST790:248:H0G15ADXX:1:1106:8127:69208/1\n+GCTCAAGTTACAGTAACTCCTGAAGCTAATAAAATAGCTGTATTTAATAAA\n++\n+CCCFFFFFHHGHHIIJHJJJJJJJJIJJJJJJJJIJJJJJHHIJJJIGIJI\n' |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 test-data/Samp_R.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Samp_R.fastq Wed May 31 13:09:15 2017 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+@ERR1044075.680 HWI-ST790:248:H0G15ADXX:1:1101:10892:2723/2\n+ATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGAAATTGATTA\n++\n+@<??DDADFFFFFDG@<G<F@GE??C:CG>FE*??0?DGFI<B>FDE<FFB\n+@ERR1044075.759 HWI-ST790:248:H0G15ADXX:1:1101:15792:2653/2\n+TGCTGCTTCAAAACCAAAATGATGATTTTTTGAGAAGTGATTATTTAAATG\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJIJJJJJJJGIIIJFGHIJGIJJJJIII\n+@ERR1044075.753 HWI-ST790:248:H0G15ADXX:1:1101:15644:2508/2\n+GGAACCTGTTTTTTAATCGATAATCCACGATGGACCTTACTTAAATTTGTA\n++\n+@@CFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJIJJJJJJJJIHI\n+@ERR1044075.814 HWI-ST790:248:H0G15ADXX:1:1101:19529:2745/2\n+ATTTAATCCATTTCAAATTCCTTTATTAAATACAGCTATTTTATTAGCTTC\n++\n+;@<DDFFFHHHFDHIIJIGHIHEGHIIIJJIJIJICHJIJIGIGJIE@GGE\n+@ERR1044075.946 HWI-ST790:248:H0G15ADXX:1:1101:8484:2908/2\n+ATTATATTAGCAGTTAATCGAACAGCTAATGTTCCAGGTCGAATAATATTT\n++\n+CCCFFFFFHHGHHJJJJJJJJJJJJJJJJJJIJJJJIJGII?BBFHGGIIJ\n+@ERR1044075.818 HWI-ST790:248:H0G15ADXX:1:1101:19811:2591/2\n+GAGTATTTTGGTATCATTCAATTGATGAATTTAGTTGAATTGGGTAAATTA\n++\n+@@BDDFFFHHGGHJJJIJIJIJIGIIJIGIJJDEHEHEGHJGGG:CGDHIE\n+@ERR1044075.978 HWI-ST790:248:H0G15ADXX:1:1101:10873:2966/2\n+AATTCATGTATTAATCGGAACAACTTTTTTATTAGTATGGTTACTACGACA\n++\n+CCCFFFFFHHHHHJJJJJIJIJJIJJJJJJJJJIIHIJJIJJJIIFJJJJI\n+@ERR1044075.998 HWI-ST790:248:H0G15ADXX:1:1101:12703:2936/2\n+ATGTTCCTTCTCGTGATACATCTCGTCATCATTGATATACAGTTAAAATAG\n++\n+CCCFFFFFHHHGHJJJJJJJJJJJJIJJJIJJJIGIIJJJJJJJIJJIJII\n+@ERR1044075.1137 HWI-ST790:248:H0G15ADXX:1:1101:1525:3138/2\n+GATAATAATAATATTAATTGTCCTAACCAAGAAGTTCTTAAGATAATATTA\n++\n+@BCFFFFFHHFHHHJJJIIGHHHIJJFIHHHGGGGGGIDHGGI@GFC>DDI\n+@ERR1044075.1446 HWI-ST790:248:H0G15ADXX:1:1101:1567:3357/2\n+TGCAGCTATAGCTGCTCCTACACCTGTTTCTGCTTTAGTTCATTCTTCTAC\n++\n+@@CDDDDDFHHHFHIIIJJJGGGCGJCHIIAHGIIEHIEE@FIIBHGHEHC\n+@ERR1044075.1652 HWI-ST790:248:H0G15ADXX:1:1101:16002:3269/2\n+CCGATTAATACATGAATTCCGTGAAATCCTGTTGCTATAAAAAATGTTGAT\n++\n+@@BDDFFFHHHHHIIIIIJJIGHGIIEIGIIHIIIJGIIJJJIJIIGIEHI\n+@ERR1044075.2019 HWI-ST790:248:H0G15ADXX:1:1101:20598:3595/2\n+CTGCTCTTTCTTTACTATTAGTAAGTAGAATAGTTGAAAATGGGGCTGGGA\n++\n+:41A:ADBFFDFFFBE4A<,<<CFCAF>,3<<FE4+9A?:<?E):?:?A=F\n+@ERR1044075.2025 HWI-ST790:248:H0G15ADXX:1:1101:1366:3788/2\n+AATTTATATGAAAAGTTTAAATAAAGAATTCGGCAAAAATAATATTCGCCT\n++\n+CCCFFFFDHFBHFGIHIIHGGHIGGGAAFHHHGHIGGGGGGEGEDH4?FEI\n+@ERR1044075.2112 HWI-ST790:248:H0G15ADXX:1:1101:7863:3843/2\n+TGGAGATGATCAAATTTATAATGTAATTGTAACTGCACATGCTTTTATTAT\n++\n+?@BBDBDFHHHHGIJJIJJJHJGJJIJJJFIIIIJIGIIGIGGIJIEIIII\n+@ERR1044075.2117 HWI-ST790:248:H0G15ADXX:1:1101:8122:3811/2\n+CTAAAATTGAAGAAATTCCTGCTAAATGTAGAGAAAAAATAGCTAAATCAA\n++\n+CCCFFFFFHHGHHJJJJJJJJJJJJJJJHIJIIJJJJJJJJJJJJJJGIIJ\n+@ERR1044075.2555 HWI-ST790:248:H0G15ADXX:1:1101:1876:4399/2\n+GTAACTTTAAAAAGAATCGGCCATCAATGATATTGAAGTTACGAATATTCA\n++\n+BB@FFFFFHHHHHJJJJJJJJJJJJJJJIIIIIIBHIIHIIJIIIDHIJII\n+@ERR1044075.3073 HWI-ST790:248:H0G15ADXX:1:1101:1378:4822/2\n+CTCCCGCTGGGTCAAAAAATGATGTATTTAAATTTCGATCTGTTAATAATA\n++\n+CC@FFFFFHHHFHIJJJJIJJIIJGHIIIJJGJJJHIHJGIGIJJIIJIIG\n+@ERR1044075.3103 HWI-ST790:248:H0G15ADXX:1:1101:3753:4970/2\n+CTCCTGTTAATCCTCCTACTGTAAATAAAAAAACAAATCCTAAAGCTCATA\n++\n+CCCFFFFFHHHHHJJJJIIJIHIJIIJJJJJJIGIJIIJJIJJJJGGGGHI\n+@ERR1044075.3115 HWI-ST790:248:H0G15ADXX:1:1101:4946:4934/2\n+AAAAAAGGAAACTTTTGGTTCTCTAGGAATAATTTATGCTATATTAGCTAT\n++\n+CCCFFFFFHHHHHJJJJJHJJJJIJJJIIIJJJJJJJJJIIGGIIIIIIJI\n+@ERR1044075.3167 HWI-ST790:248:H0G15ADXX:1:1101:8133:4808/2\n+TGGAGCTTCAGTTGATTTAGCTATTTTTTCTCTACATTTAGCAGGAATTTC\n++\n+CCCFFFFFHHHFHIFIJJJJJJJJJJJJJJJJJJJIIJJJIJJJJJJJJJI\n+@ERR1044075.3206 HWI-ST790:248:H0G15ADXX:1:1101:9789:4942/2\n+CTGTAAATAAAAAAACAAATCCTAAAGCTCATAAAATAGCTGGAGAATAAG\n++\n+@@<;DDDDFHDFFDG<BEHFFF@E?FF:?FEC>BBFBB9?BBGH8?;*=F4\n+@ERR1044075.3251 HWI-ST790:248:H0G15ADXX:1:1101:12710:4758/2\n+GAATAAAACCTGCTATAATAGCAAATACAGCTCCTATAGATAAAACATAAT\n++\n+CCCFFFFFHHHHHJJJJJJJIJJJJJJJJJJIJJJJJJGIIJJJJIJIJJJ\n+@ERR1044075.3552 HWI-ST790:248:H0G15ADXX:1:1101:10536:5030/2\n+CTGCTAAATGTAGAGAAAAAATAGCTAAATCAACTGAAGCTCCACCATGAG\n++\n+B@CFFFFFHHFHHJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJIJIIJ\n+@ERR1044075.3658 HWI-ST790:248:H0G15ADXX:1:1101:18523:5017/2\n+CTC'..b'IIJJH\n+@ERR1044075.659985 HWI-ST790:248:H0G15ADXX:1:1106:11631:62123/2\n+CCACAGATTTATGAACATTGACCATAAAATAAACCCGGTCGATTAATAAAA\n++\n+:1++2<A+<7,C?A>=ACA7<7@AAA7C?A<BACBAA@A<A0=B<?B77=>\n+@ERR1044075.660170 HWI-ST790:248:H0G15ADXX:1:1106:7215:62363/2\n+TGAAAATGGAGCTGGGACAGGATGAACTGTTTATCCACCTCTATCCGCTGG\n++\n+@CCFFFFFHHHHHJJJIJJJJGGJIJJJIIJJJJJJJJJJIJGJJJJJJII\n+@ERR1044075.660255 HWI-ST790:248:H0G15ADXX:1:1106:12160:62309/2\n+AAAGAATCGGCCATCAATGATATTGAAGTTACGAATATTCAGATTTTAATA\n++\n+@@@FDDDDDAHFHGGIEIEF@HGIJJIIGJIIGHEHIBG:??BHGGGEBDI\n+@ERR1044075.660247 HWI-ST790:248:H0G15ADXX:1:1106:11554:62387/2\n+TGTTGCTATAAAAAATGTTGATCCATAAATTGAGTCTGCAATAGTAAATGG\n++\n+@CBFFFFFHHHHHJJJJIIJJJJJJJJJIJJJGGHIJJIJJGEGGIJJIIJ\n+@ERR1044075.660686 HWI-ST790:248:H0G15ADXX:1:1106:8134:62985/2\n+CTGGAATACCTCGACGTTATTCAGATTACCCAGATGCTTACACAACATGAA\n++\n+@CCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJJIJJJJJJJJJJJIJJJJJ\n+@ERR1044075.661147 HWI-ST790:248:H0G15ADXX:1:1106:8314:63385/2\n+AGAAGAATGAACTAAAGCAGAAACAGGTGTAGGAGCAGCTATAGCTGCAGG\n++\n+@@@FFFFDHHGHGJIJJIIIJIIIJGI<AFEGHHHIIHGDGEGII@GEHIJ\n+@ERR1044075.661472 HWI-ST790:248:H0G15ADXX:1:1106:13982:63648/2\n+CTCCAATTAATGCTCCAGGATGTCCTAATTCAGCTCGAATTAAAATTCTTA\n++\n+BCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJJJJJJJJJJJJJJIJJIJJJ\n+@ERR1044075.661879 HWI-ST790:248:H0G15ADXX:1:1106:7696:64091/2\n+GATTTATTGTATGAGCTCATCATATATTTACCGTTGGAATAGATGTAGATA\n++\n+CCCFFFFFHHHHHJJJJJJIIJIJHJJJJHJIJIIJJGHJIG@DHDDHDGH\n+@ERR1044075.662140 HWI-ST790:248:H0G15ADXX:1:1106:8516:64305/2\n+TATGATTATGTTTTATATTATATGGATGAATTAATCATACACAACATATAT\n++\n+@@@FDDFFHGDHHJJIEIJGHEIIJIJIJIJGHEHGIFHIACGIGAGGFDI\n+@ERR1044075.662813 HWI-ST790:248:H0G15ADXX:1:1106:21170:64761/2\n+CTTTAATTCCTTATTCATCTTTTGCTCATATAGGAATTTTTCTGTCAGGAC\n++\n+@@@FFFFD,2AC?GHBFIEGIE<3:<FEHGEGC+?E3C*@CE**:?DC??D\n+@ERR1044075.663073 HWI-ST790:248:H0G15ADXX:1:1106:5648:65498/2\n+TTTGTATTAGGTAATATTATTACTATTTTAACTGTATATCAATGATGACGA\n++\n+@@BFFFFFHHHCFHIJJJJJJJJIJJJJJJJIJJHIJIJJJIJIEHDIIJI\n+@ERR1044075.663162 HWI-ST790:248:H0G15ADXX:1:1106:11759:65389/2\n+ATTGGAGTTAATTTAACATTTTTTCCTCAACATTTTTTAGGATTGGCTGGA\n++\n+CCCFFFFEHHHHHJJJJJJJJJJJJJJJJJJIJJJJJJJJJGIJJIIJJJA\n+@ERR1044075.663390 HWI-ST790:248:H0G15ADXX:1:1106:10400:65584/2\n+ATTCGCCTGTTTAACAAAAACATGTCTTTTTGAATTATATATAAAGTCTAA\n++\n+CCCFFFFFHHGHHJJJJJJJIJJJJJJJJJJJJIJIJJIJIIJJJHIHHIJ\n+@ERR1044075.663400 HWI-ST790:248:H0G15ADXX:1:1106:11192:65654/2\n+CCTCATCAGTAAATTGTGATATATAAAAATAATCAAACTACATCGACAAAA\n++\n+C@CFFFDEHFFHHIIJFHHHIIIJJGJHGGHHIFHGIGEGFEDDGCFGIHF\n+@ERR1044075.664278 HWI-ST790:248:H0G15ADXX:1:1106:20222:66346/2\n+AATTATTTTACTATTTATTGCTCTTCCTTCTTTACGTTTACTTTATTTATT\n++\n+<@@FFFFFHGFGFGHIJEHHEGEHECHGHEHGIGEHHHIDHIHIGIIJHIG\n+@ERR1044075.664837 HWI-ST790:248:H0G15ADXX:1:1106:12794:67053/2\n+ATTTCCTAAAAGAGTTAATAATAAATGTCCAGCAATTATATTAGCAGTTAA\n++\n+CCCFFFFFHHHHGJJIJJJJIIJIJJJHGGGJIJIJJJIGJJJJJIIIIHI\n+@ERR1044075.665607 HWI-ST790:248:H0G15ADXX:1:1106:15165:67769/2\n+TTTTCATTTAGTGGATTATAGTCCATGACCATTAACAGGAGCTATCGGAGC\n++\n+@@CFFFFFHHHCFHHIIIJJJJIJJIJJJJIJJJIIJJIIIIJIJGIJIJJ\n+@ERR1044075.665680 HWI-ST790:248:H0G15ADXX:1:1106:19772:67837/2\n+CATCTGGGTAATCTGAATAACGTCGAGGTATTCCAGCCAATCCTAAAAAAT\n++\n+@C@FFFFFDHHHFIIHGFHIIIFHIHJJ:EGIJIGHFHIHJIICGIGHIIJ\n+@ERR1044075.665714 HWI-ST790:248:H0G15ADXX:1:1106:6180:68224/2\n+GGAACACCCGCTATTCTTATACCTTTTATAGTATGTATTGAAACTATTAGA\n++\n+CCCFFFFFHHHHHJJJJJIIJIJJJJJJJJJIIIIFHIIDHHHIIIJIJJJ\n+@ERR1044075.665736 HWI-ST790:248:H0G15ADXX:1:1106:7267:68163/2\n+ATTTTATACCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTTTATATT\n++\n+CCCFFFFFHHHHHJJJIJJJJJJJJJJJJJJJGHIIJIJIJIJJJIHGAGI\n+@ERR1044075.665878 HWI-ST790:248:H0G15ADXX:1:1106:16309:68134/2\n+CGTGATACATCTCGTCATCATTGATATACAGTTAAAATAGTAATAATATTA\n++\n+B@@DFFFFHHHGHJGIIIJJHHIJIIJJJIIIIJJJIIJIDEHGIJJIGJJ\n+@ERR1044075.666310 HWI-ST790:248:H0G15ADXX:1:1106:13497:68695/2\n+CTCATATTATTAGACAAGAATCAGGAAAAAAGGAAACTTTTGGTTCTCTAG\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJIJJJJJJJJJJJIIIIJJJ\n+@ERR1044075.666724 HWI-ST790:248:H0G15ADXX:1:1106:8127:69208/2\n+CATACTTATGCAGTAACTATTGGTTTACGATGAGGAATAATTCTATTTATT\n++\n+CCCFFFFFHHHHHJJJJJJJJJJHJJJJJIJIHIJIJIJIIJ<FFIIIGIJ\n' |
| b |
| diff -r ea5bba2c569f -r 77807fc5d609 test-data/paired-aligned_reads.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired-aligned_reads.tab Wed May 31 13:09:15 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +2082 |