| Previous changeset 0:0968856c687c (2019-03-14) Next changeset 2:328c607150ff (2019-05-08) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken2/kraken2/ commit 0f261b78ab60702ecbb81abfeb91dd27c01ecf15 |
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modified:
kraken2.xml |
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added:
test-data/cl_test2_output_1.fastq test-data/cl_test2_output_2.fastq test-data/kraken_test2_R1.fastq test-data/kraken_test2_R2.fastq test-data/kraken_test2_output.tab test-data/un_test2_output_1.fastq test-data/un_test2_output_2.fastq |
| b |
| diff -r 0968856c687c -r d4bb87ca916d kraken2.xml --- a/kraken2.xml Thu Mar 14 05:16:48 2019 -0400 +++ b/kraken2.xml Wed Apr 10 13:56:57 2019 -0400 |
| [ |
| b'@@ -12,6 +12,25 @@\n <version_command>kraken2 --version</version_command>\n <command detect_errors="exit_code">\n <![CDATA[\n+\n+ #def get_type($data)\n+ #if $data.is_of_type(\'fastq\'):\n+ #return \'fastq\'\n+ #elif $data.is_of_type(\'fasta\'):\n+ #return \'fasta\'\n+ #elif $data.is_of_type(\'fastqsanger\'):\n+ #return \'fastqsanger\'\n+ #elif $data.is_of_type(\'fasta.gz\'):\n+ #return \'fasta.gz\'\n+ #elif $data.is_of_type(\'fasta.bz2\'):\n+ #return \'fasta.bz2\'\n+ #elif $data.is_of_type(\'fastq.gz\'):\n+ #return \'fastq.gz\'\n+ #elif $data.is_of_type(\'fastq.bz2\'):\n+ #return \'fastq.bz2\'\n+ #end if\n+ #end def\n+\n kraken2\n --threads \\${GALAXY_SLOTS:-1}\n --db \'${kraken2_database.fields.path}\'\n@@ -20,21 +39,29 @@\n --quick\n #end if\n \n- #if $single_paired.single_paired_selector == \'yes\'\n- --paired\n+ #if $single_paired.single_paired_selector == "yes"\n+ --paired \n \'${single_paired.forward_input}\' \'${single_paired.reverse_input}\'\n #elif $single_paired.single_paired_selector == "collection":\n+ --paired \n \'${single_paired.input_pair.forward}\' \'${single_paired.input_pair.reverse}\'\n #else:\n \'${single_paired.input_sequences}\'\n #end if\n \n #if $split_reads:\n- --classified-out \'${classified_out}\' --unclassified-out \'${unclassified_out}\'\n+ #if $single_paired.single_paired_selector == "no":\n+ --classified-out \'${classified_out_s}\' --unclassified-out \'${unclassified_out_s}\'\n+ #elif $single_paired.single_paired_selector == "yes":\n+ #set $result = $get_type($single_paired.forward_input)\n+ --unclassified-out \'un_out#.${result}\' --classified-out \'cl_out#.${result}\'\n+ #else:\n+ #set $result = $get_type($single_paired.input_pair.forward)\n+ --unclassified-out \'un_out#.${result}\' --classified-out \'cl_out#.${result}\'\n+ #end if\n #end if\n \n --confidence \'${confidence}\'\n-\t \n --minimum-base-quality \'${min_base_quality}\'\n \n #if $use_names:\n@@ -56,7 +83,7 @@\n <inputs>\n <conditional name="single_paired">\n <param name="single_paired_selector" type="select" label="Single or paired reads" help="--paired">\n- <option value="collection">Collection</option>\n+ <option value="collection">Paired Collection</option>\n <option value="yes">Paired</option>\n <option selected="True" value="no">Single</option>\n </param>\n@@ -71,43 +98,63 @@\n <param format="@INTYPES@" label="Input sequences" name="input_sequences" type="data"/>\n </when>\n </conditional>\n-\n- <param name="use_names" type="boolean" label="Print scientific names instead of just taxids"/>\n-\n- <param name="confidence" type="float" label="Confidence" value="0.0" help="Confidence score threshold. Must be in [0, 1]">\n- <validator type="in_range" min="0.0" max="1.0" message="Confidence score threshold should be between 0 and 1" />\n- </param>\n-\n- <param name="min_base_quality" type="integer" label="Minimum Base Quality" value="0" help="Minimum base quality used in classification (only effective with FASTQ input)"/>\n-\t\n- <param name="quick" type="boolean" label="Enable quick operation" help="Quick operation (use first hit)"/>\n+ <param name="use_names" type="boolean" label="Print scientific names instead of just taxids"/>\n+ <param name="confidence" type="float" label="Confidence" value="0.0" help="Confidence score threshold. Must be in [0, 1]">\n+'..b'"tabular" label="Report: ${tool.name} on ${on_string}">\n+ <filter>(report[\'create_report\'])</filter>\n+ </data>\n+\n+ <data name="out1" format_source="forward_input" label="Unclassified forward" from_work_dir="un_out_1.*">\n+ <filter>(split_reads and ("yes" in single_paired[\'single_paired_selector\']))</filter>\t\n+ </data>\n+ <data name="out2" format_source="forward_input" label="Unclassified reverse" from_work_dir="un_out_2.*">\n+ <filter>(split_reads and ("yes" in single_paired[\'single_paired_selector\']))</filter>\n </data>\n- <data name="unclassified_out" format_source="input_sequences" label="${tool.name} on ${on_string}: Unclassified reads">\n- <filter>(split_reads)</filter>\n+ <data name="out3" format_source="forward_input" label="Classified forward" from_work_dir="cl_out_1.*">\n+ <filter>(split_reads and ("yes" in single_paired[\'single_paired_selector\']))</filter>\t\n+ </data>\n+ <data name="out4" format_source="forward_input" label="Classified reverse" from_work_dir="cl_out_2.*">\n+ <filter>(split_reads and ("yes" in single_paired[\'single_paired_selector\']))</filter>\n+ </data>\n+\n+ <data name="out1.1" format_source="input_pair[\'forward\']" label="Unclassified forward" from_work_dir="un_out_1.*">\n+ <filter>(split_reads and ("collection" in single_paired[\'single_paired_selector\']))</filter>\t\n </data>\n- <data name="report_output" format_source="text" label="Report: ${tool.name} on ${on_string}">\n- <filter>(report[\'create_report\'])</filter>\n- </data>\n+ <data name="out2.1" format_source="input_pair[\'forward\']" label="Unclassified reverse" from_work_dir="un_out_2.*">\n+ <filter>(split_reads and ("collection" in single_paired[\'single_paired_selector\']))</filter>\n+ </data>\n+ <data name="out3.1" format_source="input_pair[\'forward\']" label="Classified forward" from_work_dir="cl_out_1.*">\n+ <filter>(split_reads and ("collection" in single_paired[\'single_paired_selector\']))</filter>\t\n+ </data>\n+ <data name="out4.1" format_source="input_pair[\'forward\']" label="Classified reverse" from_work_dir="cl_out_2.*">\n+ <filter>(split_reads and ("collection" in single_paired[\'single_paired_selector\']))</filter>\n+ </data>\n+\n <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>\n <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->\n </outputs>\n-\n- <tests> \n+ <tests>\n <test>\n <param name="single_paired_selector" value="no"/>\n <param name="input_sequences" value="kraken_test1.fa" ftype="fasta"/>\n@@ -118,6 +165,21 @@\n <param name="kraken2_database" value="test_entry"/>\n <output name="output" file="kraken_test1_output.tab" ftype="tabular"/>\n </test>\n+ <test>\n+ <param name="single_paired_selector" value="yes"/>\n+ <param name="forward_input" value="kraken_test2_R1.fastq" ftype="fastq"/>\n+ <param name="reverse_input" value="kraken_test2_R2.fastq" ftype="fastq"/>\n+ <param name="split_reads" value="true"/>\n+ <param name="quick" value="no"/>\n+ <param name="confidence" value="0"/>\n+ <param name="only-classified-output" value="false"/>\n+ <param name="kraken2_database" value="test_entry"/>\n+ <output name="out1" file="un_test2_output_1.fastq" ftype="fastq"/>\n+ <output name="out2" file="un_test2_output_2.fastq" ftype="fastq"/>\n+ <output name="out3" file="cl_test2_output_1.fastq" ftype="fastq"/>\n+ <output name="out4" file="cl_test2_output_2.fastq" ftype="fastq"/>\n+ <output name="output" file="kraken_test2_output.tab" ftype="tabular"/>\n+ </test>\n </tests>\n <help>\n <![CDATA[\n' |
| b |
| diff -r 0968856c687c -r d4bb87ca916d test-data/kraken_test2_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_test2_R1.fastq Wed Apr 10 13:56:57 2019 -0400 |
| b |
| b"@@ -0,0 +1,960 @@\n+@level_3-480/1\n+TCGTAGCTAGCAGCAACTTTTACCCGTGCAAAGTGTGCGGCTAGCAATTACCAGGTTCCGGGAAACTGTTTTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGCTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCGCGGGTTTAGACTTAT\n++\n+?????BB?D<DD<DDDGGFFGFIFIHFIIFHF@IHHIHHHHEIHIHDIHHAGIIHIGIHAIIGIIIHHF@FIFAE=HFIIIIFHHIFIHHIHHFHECIHGI)IB?CDHFHH?HHHGHHFDGFGHG;3GHH8GG+HGA;GF*EFGCCEG8GGFGGEGGEEGEEEAEE:FEGGEGFE:GFGG?GC;EGG::*GEE:FGEFEG\n+@level_3-478/1\n+TCCAATTGTTCTTAACTATTGCTCGCTTGGTCCGAACTCTTTCAAACAGATCACAAGGCTGAGTTACAGACATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCAACATTGTCTGACGCATTGCACTACGGCGGTATGTTTAA\n++\n+?????BBBB@DDDDDDGCFFDFIHF+FIEHFIIICHIHIIHHHII9HHEI,GAHIGHIFIHHHHDHIIFHHII+HH5IDFIDHIIE?H?FFHHIIHHHHHFIGCI7HI(HDHHHGHHG9HHEFF@E@GHGDEFGEFGIFGGGEFEGCHEDGGFBEGEEAEGEGFHHGGGEEG:GDEEEEGG;G?CGGGEG>ECGGCGGGG\n+@level_3-476/1\n+GATGGCCCCCTGCCGTCCAATATTGTAAACAGCGTATGCTACCCGTAAGAACATAGTTCCCGGTTATTGCCAATCCAGGGAAGTTCAAATTGTTGTACTTAGTATGGGGGTGTCATACGGTGATTGCGTAACGTCAAAACCCAGAACATCATAAGTGGGTCCATATGAATGTTAACGTAAAGCGTCAGTACATTATGGAA\n++\n+?????BB=BDDDDDDDGGGGE8IHIIIHII?IHHIHFHHHIFIIIIHHHICH/IIIIIHIHHHAIHHCIFHHHEGGCIIHIIFIIDHHIEHHHIHHFFH@HFHHGICHHI:GHEFHFHFECHHHGFFHGDH:FGGGGIEEGEGGF?GG68CCG**GEFF;GE@?;*GG*C'GFGG0GEGGE?>EA?GGGEGEGGEGGEGG\n+@level_3-474/1\n+CAGAGATGATAGGCATCGTAGCTAGCAGCAACTTTTACCCGTGCAGAGTGTGCGGCTAGCAATTACCAGGTTCCGGGAAACTGTTTTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGTTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCG\n++\n+?????B@BDDBEDBEDAGFDFGHIIFFIIIIIHHHIEH>;EG9IH#HHHCHI7IHIDIHCIFIFHFIIIIIIFIIHIHCHHIFIHIHIHCIHGHHI9HHIHHHHFHF?GGG>BHHHFEGCFEGG/DG;GEHCGGG@G@C*FF;GDGEG=GGE8E@;EG@@@:EGG<;FCEFGGFE6EGGEEEGEG*F?GGCGGFGGGG;G\n+@level_3-472/1\n+ACGACGGTAAGATCGCCTACAAAGTCAGTCAAGTAAGTTCCAATTGTTCTTAACTATTGCTCGCTTGGTCCGAACTCTTTCAAACAGATCACAAGGCTGAGTTACAGACATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCA\n++\n+????ABBBBDDDDDDDF>G@GFIC;CIFIHHICIHIFIIHEFII=IHFIFGIHIIHAHII:FIDIFACIIHCEH?FFHHDHHIFHHIHDIHE7GFIHG*HFHHHHHHDBIEHH0IEHHHHGFHGGDGEFGGG:EDIIG;=GEGEEGGGGFGEHGGGGFHC:GG??A8?G?CGE+=GGGGEEEGDGGHG>GGAGGEGGE(G\n+@level_3-470/1\n+TTCCTCCCGCGATGCTCTGTGAAAATGATTGTCAGGCGTAGTCTTGTATCTTTGAATGGCTGACCTCGAAGACCCTTTGAAAATGCTGGCTGGGGGAGCTGTCAACCCGTCGTAACATTTGCTCGCGGGGGGGAGGGGTATCCTATACGCTTCTTCAGAAGAAGTCCACCCGATGGCCCCCTGCCGTCCAATATTGTAAA\n++\n+?????B?BDA?DDDDDGFGGFFFIHIIEIHHEIHHDDHHIIHIHHEIAHIIIGEHIAHIIIFIIIFIIIGHHIGIEHIFIIFICHFIHHIAHCIGIDEHIHFHFHGGHFHH-HHBCHHGGHGCHFFGFGEFAF*E1EGGGEGGDEGEEGGGFEGEGE>E;EGCGGGGCEGGGGF)?EEE2?DFEC(CG:FGEEGE:FEDG\n+@level_3-468/1\n+AGACCTCGGCACACCGTTCTCACCGTCTATTATTTCATTGGCGCGCCTATGGTGAGATGGACGCCTTTGCGGAGTCCCTCTAGACAGGCCACACAGGTTGTTCGCCGTGTTTCTAACAAACGAGTAACTTCGGATTTGAGAACATCGGACACGTAGCACCTGCGATACCAATCGGTTCCTCCTTTCCCCCGTTCCAACGT\n++\n+??A??BB??DDDDDDBGFGFGGIIFFHHIHHCIHIIIHEIFIIIF8DEHIHIHFIIHHFDIIEHDIHIFIHHHGHIGHIIEGIIHHHIIIIHH?HHI@HFH,HGFIEHGCFHF<FHGHGFGGB3GGGFG+GF0FGEE(GG?DEFEGEGFGD8EE;GGGEEG@GGFG6GGGGGCACEGFEEEEEGGEGG?'/G?GFGEFG?\n+@level_3-466/1\n+CATATGATTTGGTAATAGCACGGGCCTGTAGCTTTTGGCGAGTCTGAGACCTCGGCACACCGTTCTCACCGTCTATTATTTCATTGGCGCGCCTATGGTGAGATGGACGCCTTTGCGGAGTCCCTCTAGACAGGCCACACAGGTTGTTCGCCGTGTTTCTAACAAACGAGTAACTTCGGATTTCAGAACATCGGACACGT\n++\n+?A???B??D.DDDEDDFFFGFGHHIIIIIIHHIGCFIFHIFICIIHHIHIH/GDHIIFIIEHHIHHBHHHHIEHIIIHIHDHHHHIHHIAHCHH)3FAHIHHHHFHGIHEFHHHF=FHGFHHFDGFDHFGGHGEFGGIGGB?GGG:GCGEFFBGGGEGGGGEGCGE*GEGEFG/CG;)GGEEEEE6BGGGGF0GGG2GEE\n+@level_3-464/1\n+GGCTGATCTTCCATAATGTACTGACGCTTTACGTTAATATTCATATGGACCCACTTATGATGTTCTGGGTTTTGACGTTACGCAATCACCGTATGACACCCCCATACTAAGTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGG\n++\n+???A5B?BBD<DDDDDCFFCGFIHIHHHIHFHEHFEEHIHIIIDGGIHHHHHHHIHIFIII-GIHHIHIIIHIHH?IHHHII,HGIIFAHFIHHH,'HHHGGEEIHFHDHFHGFFHD=.EHEHFHGFGAHGFDGGBFGHGFEF1GGGGGG8G:7GGGEGGCCCEGGFEGF6EGGEEE?EEGEG.EGG(DFGEGGGGGE:G\n+@level_3-462/1\n+TAAGAACATAGTTCCCGGTTATTGCCAATCCAGGGAAGTTCAAATTGTTGTACTTAGTATGGGGGTGTCATACGGTGATTGCGTAACGTCAAAACCCAGAACATCATAAGTGGGTCCATATGAATATTAACGTAAAGCGTCAGTACATTATGGAAGA"..b"++\n+?AA??B?BDDBEDBDDGFFGFGHHIHHIII-FHIHGHHGGHHGFHIHHFIHIHHBHAHGI-GFHFHIHF5IHH5IIIHH@FHIIFIFGFHGFIHHICHHFHFHIFHHDIDEDHH5HHEEHHGBG*HG@E,FGEEGFGFGGGGGEGGEFEGFGCFFCE<EG?GEEGAGGGFFEEEGCE<GGGCGGGA:ACEGE.EGGEGG?\n+@level_3-18/1\n+AAAGTTGCTGCTAGCTACGATGCCTATCATCTCTGACAGGACCGTAACTGCACGTCTTGTTCCTCCCGCGATGCTCTGTGAAAATGATTGTCAGGCGTAGTCTTGTATCTTTGAATGGCTGACCTCGAAGACCCTATGAAAATGCTGGCTGGGGGAGCTGTCAACCCGTCGTAACATTTGCTCGCGGGGGGGAGGGGTAT\n++\n+?????BBADDDEDDDDEEGFFGIHFIHIIEHHI>FHHDIGIIGCHIHHIGIGAIHGH>GHEI?CIFHCHHHIFHAHGHBDIIHII?FGCHHFFIHI7*-GHGGHIGEFIFFHFHH?HHFHGBCGHFGHFGEH5GG'9GD2@FGEEGFAGG'?GAGGGFG?B::CGGCGFEGG/G'EEEFGEEGCGG4CEGEEGEGF:GEG\n+@level_3-16/1\n+TTAAGAGCGTGGCTCGTGTAGAGCGGGATAACATACCAGAACACGCGGTGGGAATCGTATTGGTTGCAACTTGTCTGTACGTGTTGCACCATTGAGGCCGCGCCGACATTATTCTGGCAATTTGACTGCACTCGGGTGAATGCAGATAAGTCTAAACCCGCGGTCCATGGATGGAAAAAGCAGAAATCAGATTTGAACGA\n++\n+?AA??B+BDDDDD?DDGGFFFAHIH;HHFIHHIHFEFFI=IGHGHIDIIGCFHHFIHIFIIHGH-HIFHHFHIHIFHIDHGFIHIIHGHIEHHH.HIHHHHHEFG=HH<HFFH7HGIGHHF,AHFBEFHHHEG?F?B=HCGEFFEF9EHG'EG?AEDEG<EGE8GGAG(=AGEGCG?EG?AHE<;GFE*EEEGGEGGFGG\n+@level_3-14/1\n+ACGACGGTAAGATCGCCTACAAAGTCAGTCAAGTAAGTTCCAATTGTTCTTAACTATTGCTCGCTTGGTCCGAACTCTTTCAAACAGATCACAAGGCTGAGTTACAGACATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCA\n++\n+?A??ABB@DADDDDD<GFGGGGHIIIIIICIHIIIIFHCHHIIIHHIHIIEHHHFHFICA=AHIHEIIHIGIHDIIIHFHGHDIIGGEFHFGHHGCIEIFBFCHFHHIGHHH=HGH9H@FCEGGHHGG;G6BGBG@GE=E*GG:EEHFA>GEEEGEEEAE3CFGEDGEF0FFGEG@GGGGGEC9G/E(EFEFGGE:1EEF\n+@level_3-12/1\n+GTTACTGGTCGAGTAGCAAGAGGGGCGGATCCGGAAGGGCTTCACTATTGGGAACATGGACTGCTTGGTTATCGCCACTCACCTTCTGATGATTTAGAATTACCACACTCAAATAGGTCGGTGTTCCGGTCCTGGAATATTGCGCTTTTTGGTATCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCG\n++\n+?=??<9BBDDBDDDDDFGGGFFFHHFAIAIIH9HICHIIGHDHIIHIHFIHIIHFHIFHIE8GEHEFIIEFHFIDFFCIHI*5IHFBHHHGHHHHIHIIHCCDGIFHCFEG@EGHHHHECEGGG=FGGEGFFGGGGGEGCFBDGG*GEGGFAEAGEFF?G;GEGD8E<E6EGCFGGFDCE.GEEGEGEGGCGEFGFF6GG\n+@level_3-10/1\n+TTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGCTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCGCGGGTTTAGACTTATCTGCATTCACCCGAGTGCAGTCAAATTGCCAGAATAATGTCGGCGCGGCCTCAATGGTGCAACACGTACA\n++\n+<???ABBBD+?DEDDDFGFFFFIIFIFIIIIIAEFICCIICIIAHGHIIIEHGI=HIFHHCDHEFIAGIIDIHIIAEHI>HIHHIHEIIHHIHIIIH<FHHGHGFGGGHFGEFHHEF?3=HFHFFHE@HGGGH6:CEFFEGGF*GFEAFECCG;G@GGCGFGFFGGGE:AGG>?GGF;+<ECE?EGCCGE8EEGGACEEE\n+@level_3-8/1\n+CCCGTGCAAAGTGTGCGGCTAGCAATTACCAGGTTCCGGGAAACTGTTTTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGCTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCGCGGGTTTAGACTTATCTGCATTCACCCGAGTGCAGTC\n++\n+????<?B.<DDDDDDDGEGFGGI+IIIIEFHHIAHIFIIFIGHHIFDHH:IIIIIHHIFIIIFIIIHIIHEIIIEHIGIFGIFCHEHAIIIHH,HFIIDHHFFEIGHHHHCIEF=HGHHFGG9HGFDFFE,HGE=FGGEEEFEFGEDE<GGFFGFAAGFG/FFGGGBFEFGG;E;GGECGEGEGFGGGEECF/G?GEEEG\n+@level_3-6/1\n+ACTTCGGATTTCAGAACATCGGACACGTAGCACCTGCGATACCAATCGGTTCCTCCTTTCCCCCGTTCCAACGTGTGTACGATCTAAAATTTCCAGTCTCATAGATGCGGTCACTTCTTCCACAAGAAAATCAAAACCGGATTGACGTCTGGACTCAACCGGAATCGGTATCCGTAGGTGCCGTGCCCAAGGGGTCGCCC\n++\n+?????B?BBDDDDDDDGFFFGGIHIHIIIIIHIHIEIIAIHHIIH+HGHHHFGGIFHHDGG7IGHHH-HHIDIHIHHFHAI?FDH?GIHHEIHIEIHHHD7HFIFEFHGHHEHEFFEHDHCFGGFHFHFE:FHEFDFG@GG:@FEFGFC(EEE/GGGEGEFGGFG?GEGGEEGE.CGGG1G8EC:CGGFEC<=GG26EEG\n+@level_3-4/1\n+TTGTTCCTCCCGCGATGCTCTGTGAAAATGATTGTCAGGCGTAGTCTTGTATCTTTGAATGGCTGACCTCGAAGACCCTTTGAAAATGCTGGCTGGGGGAGCTGTCAACCCGTCGTAACATTTGCTCGCGGGGGGGAGGGGTATCCTATACGCTTCTTCAGAAGAAGTCCACCCGATGGCCCCCTGCCGTCCAATATTGT\n++\n+?????BBBDDDEBDBDFG>CGGIIHHEIIHE9FHIIHCHIHIIIG=HIIIIHFHEHIGHIHIIIFHHHH-HCIFIFFHICFHHH<ICIIHHHHHHHIIFFIHGHHF.HHH.<GHGGFGGEEDHGGEFFDGG=CCGGFGGEGGEEEGGGEE*GEGF;EGFEFEFGFEFGEEC<CFEGE?EGEEFGE.GFGE(EGF*CGFAC\n+@level_3-2/1\n+AAGTCCACCCGATGGCCCCCTGCCGTCCAATATTGTAAACAGCGTATGCTACCCGTAAGAACATAGTTCCCGGTTATTGCCAATCCAGGGAAGTTCAAATTGTTGTACTTAGTATGGGGGTGTCATACGGTGATTGCGTAACGTCAAAACCCAGAACATCATAAGTGGGTCCATATGAATATTAACGTAAAGCGTCAGTA\n++\n+<??A??BBDDEDDDDEGEGF>FHIHHFFIFHIHHIIIHHFIHIIGFIAHHHHIIG@EHGIIHI5FHIIIHFI-IHGFFHHHIIFHFFHHHHHEGHHHEHHHHEHHHHHHFEFHDGGFHE*EHFF@GHHHEFFGGCED:;HEEEEFGGGFGGGGBEGGAGGE?EDGEGGFGGGGC:EGGCFG(EFAFE*GAG>D:EGFGG4\n" 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| b |
| diff -r 0968856c687c -r d4bb87ca916d test-data/kraken_test2_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_test2_R2.fastq Wed Apr 10 13:56:57 2019 -0400 |
| b |
| b"@@ -0,0 +1,960 @@\n+@level_3-480/2\n+GGGGATTCTCTACGCCGACGAATATCTTCTGACATGGGAGGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTGTTCGACACAGGATGGTCTTGGCGACTTGCAAAGCATTCGCTACATTACACAGTACAGTTGGCCTCGGTTAAAAGTCCA\n++\n+???=?B?B?@@B5DBD>8FC>CHHF@FIHHHIIIDHHHEHHG-HIFDIGHCH-H7EIF=H-HHIHHHFFI=)F@HEHIEIHGHHEH@B-DH5IF,HCH5GHCG>EDFHDHHIDFHF+HG3=F=8H@G*HHFF0+GEC@@EH.E@ECGE@EEDGGEFGBFG=@EAAAFEEG:E(FGE(E'?GEEG?7E=E?4FEE(G(EEE\n+@level_3-478/2\n+TTGACGTTACGCAATCACCGTATGACACCCCCATACTAAGTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGGGGGCCATCGGGTGGACTTCTTCTGAAGAAGCGTATAGGATACCCCTCCCCCCCGCGAGCAAATGTTACGAC\n++\n+?=???BB?<DDD5DDBFFGGF?FHICIHIIHE.IHIHEAHD5GDHFHCIH@FHF=HH.DHIHIIHGHAHIHIIDAHHHHGDIIIFIFI+HHIFGHIIH,HHHGH8HBHEH=GHIFDHHCHFHHHCGG=EGGHFDEGIFDCFEGEEDGE?(EFGBE**B<D.GCF?GC?EGE>@EGGGE<.EEGCGCC(FECGEGEGEG:?\n+@level_3-476/2\n+GTGTTCCGGTCCTGGAATATTGCGCTTTTTGGTATCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCGTCTCAAAGAATAACGGCTCTAGCTAAAGAAGAGCGAGTAGAGATTCTTTGTAACCTATGATAAATCAAACGAACCTGGTGGCGCACGGGTGGGCGTGCACGTGAAGGGGGCGGATGTTGC\n++\n+???,?B7@--BD@DDBFGGACFH>HI/FEHDIF,IHHI7HIFDAH9GEIGFA>IDHHDI-I@ICAHIHHIGHFHH5HDFHHHHHH.FGFFHDGFGH.FFHFHEHH+HED=)IHHHGHC.BFFF.HHGHD9FF)HDFI1GA@GA;G*GFAGGGDCGA?E?EFG?GGECGF?/G<B*(CGEEEEE*GCA/(EEGEGECDG:8\n+@level_3-474/2\n+GATTCTCTACGCCGACGAATATCTTCTGACATGGGACGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTGTTCGACACAGGATGGTCTTGGCGACTTGCAAAGCATTCGCTACATTACACAGTACTCTTGGCCTCGGTTAAAAGTCCAGCG\n++\n+=??9=B=BDD+DBDDDG*>GGFHFIH/HHBGHHIIIIIGGIHF=FH/EHAIGGHIF?IIH?FFIECH@CDH-HI@-HCEHFE+IIIE-ICH+H+IHDHIFHGFHFHH4HHG9DGH?GBBFEHFHHEG9.GFH?#EEF8FD/AECGEEEEFG(EEGEGFEGD/GE/E:FEG*E*E#GGECE6BEEGE/F;EEEFE?G.CEE\n+@level_3-472/2\n+CCGTATGACACCCCCATACTAAGTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGGGGGCCATCGGGTGGACTTCTTCTGAAGAAGCGTATAGGTTACCCCTCGCCCCCGCGAGCAAATGTTACGACGGGTTGACAGCTCCCCC\n++\n+?=?A?BB3DBDDDAEDGG/GGGBIHHHHIHHFI=C9II@E,HIHIIIHI-HIIHHGDF9.IHFIHHIGE,HEHHIFHI=HIHHHHDEHHFHHIBFHHFIIFHDIF=F+IGHHDAGHFHG*BFF:F*GDEFBGEEGGF8GEFEEGE(G(GE*/GE=EFGG(E*GGEEF8EEF@G6?D8.E)EE3C4AGG;EGGFEF?.CCF\n+@level_3-470/2\n+TGTCTACATTAGCGTGTACGCCGGGGCAGGACGGGATAGTGCCTTCTTGAAGCGGCGGTATTAGTCTGCTACCCGCAAGCCCGAAAGTAGTCACCATAGCAGATGCATATGATTCTCGCACTCCATAATCCAGTCTTTTCAGTAGAGCGGCTCCGGCCTTGGGGCAGATGATTGGCTGAACCATATGATTTGGTAATAGC\n++\n+?<?A?B<B6DE@DDD-FGFGFFCIFHIIICIEFHDIEFIFIIHHHDH=BFHHHIG3HFIHHHHIDIIGEII@HFHEHFFHHBFG@IHHEGDICIHFIHIDHHFE5=HHGHFE;HHDHEH)H?H1<GF2EED(;FDAGGGDGBFG,E>GG8GGBFGEECEGGGGGE?:@6*EGACGCG6:G?GEEEE(0GE*FA'EG:G8A\n+@level_3-468/2\n+GCAGACATCAGATTTGAACGACCTTGCGCGTTCGCGAAAAAGCGGCGAATATAGGACAGATTACTCAGGGGGGGTATCCTGGAGATGTATTATGAAAACAGTTTCCCGGAACCTGGTAATTGCTAGCCGCACACTTTGCACGGGTAAAAGTTGCTGCTAGCTACGATGCCTATCATCTCTGACAGGACCGTAACTGCACG\n++\n+??A??<>ADDD,D-DDFFFFFFHHFIBIHIIACIIHI99HHHHHHEEEHHI+@EGFEHDIFB*HIIEIIFGG?-,IFFC++5+BFHHHBHHHIHCIGGIFHFH(FHHHD=HDCHFGE+EFHH2HFDHHGGEF9CFE?FCEG8GGG;EA?GG0GGG@3G=GEEEFG?<*GEEEF<EEC.GEGEFFEE(ED:E)G/FEAGE:\n+@level_3-466/2\n+TTTGAACGACCTTGCGCGTTCGCGAAAAAGCGGCGAATATAGGACCGATTACTCAGGGGGGGTATCCTGGGGATGTATTATGAAAACAGTTTCCCGGAACATGGTAATTGCTAGCCGCACACTTTGCACGGGTAAAAGTTGCTGCTGGCTTCGATGCCTATCATCTCTGACAGGACCGTAACTGCACGTCTTGTTCCTCC\n++\n+??A??==B?-DDDDDD-;FGGFHI-EH8/IHHHG?DHEIHEHCHH.GH?>GIGIIGDGHEF0IIG,A*E=HHHICAIHH-HB-EBIHFFFHHGHHIHIII+HGHGHHFFGFCHGFHFDDHG'G;GF*EEHDEFG83EGEGE0,;FE(7GB)EBGFG@FAFFE6?C?BG;GFEHGGEAGG;8GGDEECG;FEGAE6FGEE0\n+@level_3-464/2\n+CATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCAACATTGTCTGACGCATTGCACTACGGCGGTATGTTTAACGCGCCTGATGTCTCACGGTCGTCGGAACAGCTAAATACCCTTGGTGGCGTTGGCTCAATGTATTATGAT\n++\n+A<A????>DDDDDDDBFFCFGGAHI-CHGEFGGFAAHFF/IIGHEIIHCCE+AFG0FHHIICEFGFG=HHAHHHFIGEHHGIHHFDHHIHHIHIDCFHE=GFHB+6=GFHBHHHF+2=HHGFHDF8FHGG)DBGECGFG?DG,,GE4GFGGBEGE*G8GFGG*:FEEE:?GE;GE)CFG.FGC;E(?E8?:0;=?'GGE(\n+@level_3-462/2\n+ATTTAGAATTACCACACTCAAATAGGTCGGTGTTCCGGTCCTGGAATATTGCGCTTTTTGGTATCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCGTCTCAAAGACTAACGGCTCTAGCTAAAGAAGAGCGAGTAGAGATTCTT"..b'++\n+=<????B-BDD7DBEDF8GGFG8HIIFHF;HHEAFIFCIHIHHHIHFEHE#DI5HII=FEC.IFCCEHFBDDH+IHHFIHHIHHIHHHHI-H-IDDAHHHH#HF*HHH=HFHGBEFHHDEHD@HCEBEHHHFHG*#EHGEG;DDDGG/F3EFDEFF(G*GG(EGFEG<EEGCG:F:GE?FEFA*?(FAGGAGGGEEEEG:\n+@level_3-18/2\n+GTGCCTTCTTGAAGCGGCGGTATTAGTCTGCTACCCGCAAGCCCGAAAGTAGTCACCATAGCAGATCCATATGATTCTCGCACTCCATAATCCAGTCTTTTCAGTAGAGCGGCTCCGGCCTTGGGGCAGATGAGTGGATGAACCATATGATTTGGTAATAGCACGGGCCTGTAGCTTTTGGCGAGTCTGAGACCTCGGCA\n++\n+?<????B>D@-DD-@BGCF?/GHIFDHG>I8G>FHIHH@EHCDFCFHIHD=HAHHGI=II++F>F?5IHB?EFFHGHEGEHHIHDHD?HC:HDGHHHHFCIGFEH3HGFDHHHHH;DHDH=EFEG@HEHDFHG(@F0#AEB4E:G4A:*E(;GEEEFE(FGEEEEGAFGE8/EE=EFEFF(FGG:DEGGEEE68?F(ECG\n+@level_3-16/2\n+AACTTCGGATTTCAGAACATCGGACACGTAGCACCTGCGATACCAATCGGTTCCTCCTTTCCCCCGTTCCAATGTGTGTACGATCTAAAATTTCCAGTCTCATAGATGCGGTCACTTCTTCCACAAGAAAATCAAAACCGGATTGACGTCTGGACTCAACTGGAATCGGTAGCCGTAGGTGCCGTGCCCAAGGGGTCGCC\n++\n+???,?BBBDDD5DB@DGGAGGFFIFHHIEHHIF9IIHHHHFHH=HHIHG/HFHIFIH@IIHHIIHHIEFHIH)GIHEHGHICDGCHFIHEHFHHFFFEHHHHHH=GHFE@DCEFHF=-EHD@E=HGFC*D4GHGG/CEEFEGGG@EECEGAG(E/GCF0C(;@GG*)<EEG*?FGE@CGG>6G=FG0/E;EECGEAGEE?\n+@level_3-14/2\n+GTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGGGGGCCATCGGGTGGACTTCTTCTGAAGAAGCGTATAGGATACCCCTCCCCCCCGCGAGCAAATGTTACCACGGGTTGACAGCTCCCCCAGCCAGCATTTTCAACGGGTCT\n++\n+??<5?B??BD@-@D<DFFGG>EHI>IIBCEHHCIHHHIHIHIIIF0HIHHHH.DH@>GEEH-HIIFHHDEGICFHHGHF5ECHFGEHHHHIHHHHH5,EEEHCGBI6HFFHHHF@@HGHFFG=DDG+EGDF(.GEBGFGC4F:G<CGGGGEECFGFCG).8F0<EEEC=CFB*G8?86<6GGE;DAGG:GGAE*E;E(EG\n+@level_3-12/2\n+TAAGTGGGTCCATATGAATATTAACGTAAAGCGTCAGTACATTATGGAAGATCAGCCTTTCTTCGCCTTGGGTGGTGAAGCACGCTCCCTCTTCTAGACGGGCGACCCCTTGGGCACGGCACCTACGGATACCGATTCCGGTTGAGTCCAGACGTCAATCCGGTTTTGATTTTCTTGTGGAAGAAGTGACCGCATCTATG\n++\n+5AA??B?BDDBD?D@DCGF6FF-IAHFHI>HI/HEHDHH9III-H?IHIFIFIIC8HHHFHHEHCHDFIHGIHFIAHIIFDHHCH+EDH=HFHI=HFFDF5HDH>BHH3H;EFHF.HHDFHHHFG*E=EFFEDG+EIG9*EADG;GG2F?FE0E8GEEGG9EEEAEGA?0CFCFEEEEEAGAGGG*FEEEEF;G<EC:GE\n+@level_3-10/2\n+CAACCATTGCCATCGTGCCTAACTCGCTATACAAGTCCGGCTCACCCAATATGGTGGGGATTCTCTACGCCGACGAATATCTTCTGACATGGGAGGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTATTCGACACAGGATGGTCTTGGCG\n++\n+?5<?=BBB-DDDDADAAGFGEFFHAEHFIEHHFIFHHIFHHDBHFHIHGEHHHIFIC=E+FIGHHHAFHFAFHE--+IHHA>FI2HIEHCE@AHHHHIEEEFHIHHIHHGDHHGHHDG+7HECH;IGGH5HAEG?@E<G,G?GEGE?1:@=GEEGFEGCBGCEC0FEEGEEFFE6E#BE6EG/8<(GEG?(EEE(GAEA?\n+@level_3-8/2\n+GGCTCACCCAATATGGTGGGGATTCTCTACGCCGACGAATATCTTCTGACATGGGAGGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTGTTCGACACAGGATGGTCTTGGCGACTTGCAAAGCATTCGCTACATTACACAGTACACTTGG\n++\n+???A?@B?D<5DDBDDBGAFCFCEAFAHHHAHIGHHHGHFHIEHA.IEH9IIF@CHFE0AICHHHEAEHIHEHIHHIH5HH+HDBIIHDIH78GHHHIIGHHHFFFDFCE=)EHDFG;=H*HH9EGG=GGFEBDGGG;7*EA,G*CCFEEEEDEEGCCG(*EEAGC(GE8G*CGGC><6FFF:/AGGE9GE;E:ECEE:8\n+@level_3-6/2\n+TAAACTCTTAAGAGCGTGGCTCGTGTAGAGCGGGATAACATACCAGAACACGCGGTGGGAATCGTATTGGTCGCAACTTGTCTGTACGTGTTGCACCATTGAGGCCGCGCCGACATTATTCTGGCAATTTGACTGCACTCGGGTGAATGCAGATAAGTCTAAACCCGCGGCCCATGGATGGAAAAAGCAGAAATCAGATT\n++\n+=??<<B?BB--?<BB@FCACGFEIFIIFEFFH9HHC9ICFIDH.HIDC>FFIHHH-GHFHIHC+FHCFHFHHHDHA>IFDDH5IEH-HFFHE7HEFHGHDHGHFHGHHFH?HGCHHHHGE;CFBHHFFEEGCGFGF2CFE?G>GGGFGEDAFEGGEGE4;GGEGC:EEE6(EG<EG/:GEE+C:G?GFGGGFGCE:E*F*\n+@level_3-4/2\n+CGATCCTAGCGAGCGTCGGAGAGCATGTCTACATTAGCGTGTACGCCGGGGCAGGACGGGATAGTGCCTTCTTGAAGCGGCGGTATTAGTCTGCTACCCGCAAGCCCGAAAGTAGTCACCATAGCAGATCCATATGAATCTCGCACTCCATAATCTAGTCTTTTCAGTAGAGCGGCTCCGGCCTTGGCGCAGATGATTGG\n++\n+A??=,BBBDBB@DD-EGGFGFFBC8CH+HHEH@HI@FHHA-IFHHFHHFCFHHGIHHFHF58?CH+EIHI=HHFGFIAIAFDI=HIIFDHHEIIGHIHGHHHHD+-HHCF)GHHHFHGHHEGDCGGGFFDE?GHEG#*G?EGGBFEGE/FEEDFF/EEF0G6AE.FE.GC@B6,EGEC?E.F/EDGE(A?06CCGE6CEG\n+@level_3-2/2\n+TCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCGTCTCAAAGAATAACGGCTCTAGCTAAAGAAGAGCGAGTAGAGATTCTTTGTAACCTATGATAAATCAAACGAACCTGGTGGCGCACGGGTGGGCGAGCACGTGCAGGGGGCGGATGTTGCCATGCCGATCCTAGCGAGCTTCGGAGAGCATGTC\n++\n+????AB-BDABDBD@DEFFGGC>>FH8IFII7HIHHHHHHII@AHEHIIIHHBIIGFIFHIEIH5H=HCHE5GFD-HHIHHHGIHFFIEHH=(HH5AHHEECFHHHHEFH+3EFHHHEH1+G@+EG:FFHGG>CFGGE5B2:DEFCEEEEEF;FFEEG1*GGG(?EG8GGD**GEF/G6FCECEA/4GG<GG;GGECEEC\n' |
| b |
| diff -r 0968856c687c -r d4bb87ca916d test-data/kraken_test2_output.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kraken_test2_output.tab Wed Apr 10 13:56:57 2019 -0400 |
| b |
| b'@@ -0,0 +1,240 @@\n+U\tlevel_3-480\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-478\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-476\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-474\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-472\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-470\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-468\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-466\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-464\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-462\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-460\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-458\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-456\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-454\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-452\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-450\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-448\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-446\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-444\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-442\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-440\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-438\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-436\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-434\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-432\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-430\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-428\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-426\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-424\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-422\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-420\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-418\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-416\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-414\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-412\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-410\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-408\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-406\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-404\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-402\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-400\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-398\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-396\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-394\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-392\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-390\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-388\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-386\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-384\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-382\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-380\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-378\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-376\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-374\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-372\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-370\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-368\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-366\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-364\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-362\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-360\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-358\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-356\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-354\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-352\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-350\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-348\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-346\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-344\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-342\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-340\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-338\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-336\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-334\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-332\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-330\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-328\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-326\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-324\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-322\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-320\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-318\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-316\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-314\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-312\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-310\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-308\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-306\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-304\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-302\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-300\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-298\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-296\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-294\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-292\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-290\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-288\t0\t200|200\t0:166 |:| 0:166\n+U\tl'..b'l_3-198\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-196\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-194\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-192\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-190\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-188\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-186\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-184\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-182\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-180\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-178\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-176\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-174\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-172\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-170\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-168\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-166\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-164\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-162\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-160\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-158\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-156\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-154\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-152\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-150\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-148\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-146\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-144\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-142\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-140\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-138\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-136\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-134\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-132\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-130\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-128\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-126\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-124\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-122\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-120\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-118\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-116\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-114\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-112\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-110\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-108\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-106\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-104\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-102\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-100\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-98\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-96\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-94\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-92\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-90\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-88\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-86\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-84\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-82\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-80\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-78\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-76\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-74\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-72\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-70\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-68\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-66\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-64\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-62\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-60\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-58\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-56\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-54\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-52\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-50\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-48\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-46\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-44\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-42\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-40\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-38\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-36\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-34\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-32\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-30\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-28\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-26\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-24\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-22\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-20\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-18\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-16\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-14\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-12\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-10\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-8\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-6\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-4\t0\t200|200\t0:166 |:| 0:166\n+U\tlevel_3-2\t0\t200|200\t0:166 |:| 0:166\n' |
| b |
| diff -r 0968856c687c -r d4bb87ca916d test-data/un_test2_output_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/un_test2_output_1.fastq Wed Apr 10 13:56:57 2019 -0400 |
| b |
| b"@@ -0,0 +1,960 @@\n+@level_3-480/1\n+TCGTAGCTAGCAGCAACTTTTACCCGTGCAAAGTGTGCGGCTAGCAATTACCAGGTTCCGGGAAACTGTTTTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGCTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCGCGGGTTTAGACTTAT\n++\n+?????BB?D<DD<DDDGGFFGFIFIHFIIFHF@IHHIHHHHEIHIHDIHHAGIIHIGIHAIIGIIIHHF@FIFAE=HFIIIIFHHIFIHHIHHFHECIHGI)IB?CDHFHH?HHHGHHFDGFGHG;3GHH8GG+HGA;GF*EFGCCEG8GGFGGEGGEEGEEEAEE:FEGGEGFE:GFGG?GC;EGG::*GEE:FGEFEG\n+@level_3-478/1\n+TCCAATTGTTCTTAACTATTGCTCGCTTGGTCCGAACTCTTTCAAACAGATCACAAGGCTGAGTTACAGACATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCAACATTGTCTGACGCATTGCACTACGGCGGTATGTTTAA\n++\n+?????BBBB@DDDDDDGCFFDFIHF+FIEHFIIICHIHIIHHHII9HHEI,GAHIGHIFIHHHHDHIIFHHII+HH5IDFIDHIIE?H?FFHHIIHHHHHFIGCI7HI(HDHHHGHHG9HHEFF@E@GHGDEFGEFGIFGGGEFEGCHEDGGFBEGEEAEGEGFHHGGGEEG:GDEEEEGG;G?CGGGEG>ECGGCGGGG\n+@level_3-476/1\n+GATGGCCCCCTGCCGTCCAATATTGTAAACAGCGTATGCTACCCGTAAGAACATAGTTCCCGGTTATTGCCAATCCAGGGAAGTTCAAATTGTTGTACTTAGTATGGGGGTGTCATACGGTGATTGCGTAACGTCAAAACCCAGAACATCATAAGTGGGTCCATATGAATGTTAACGTAAAGCGTCAGTACATTATGGAA\n++\n+?????BB=BDDDDDDDGGGGE8IHIIIHII?IHHIHFHHHIFIIIIHHHICH/IIIIIHIHHHAIHHCIFHHHEGGCIIHIIFIIDHHIEHHHIHHFFH@HFHHGICHHI:GHEFHFHFECHHHGFFHGDH:FGGGGIEEGEGGF?GG68CCG**GEFF;GE@?;*GG*C'GFGG0GEGGE?>EA?GGGEGEGGEGGEGG\n+@level_3-474/1\n+CAGAGATGATAGGCATCGTAGCTAGCAGCAACTTTTACCCGTGCAGAGTGTGCGGCTAGCAATTACCAGGTTCCGGGAAACTGTTTTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGTTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCG\n++\n+?????B@BDDBEDBEDAGFDFGHIIFFIIIIIHHHIEH>;EG9IH#HHHCHI7IHIDIHCIFIFHFIIIIIIFIIHIHCHHIFIHIHIHCIHGHHI9HHIHHHHFHF?GGG>BHHHFEGCFEGG/DG;GEHCGGG@G@C*FF;GDGEG=GGE8E@;EG@@@:EGG<;FCEFGGFE6EGGEEEGEG*F?GGCGGFGGGG;G\n+@level_3-472/1\n+ACGACGGTAAGATCGCCTACAAAGTCAGTCAAGTAAGTTCCAATTGTTCTTAACTATTGCTCGCTTGGTCCGAACTCTTTCAAACAGATCACAAGGCTGAGTTACAGACATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCA\n++\n+????ABBBBDDDDDDDF>G@GFIC;CIFIHHICIHIFIIHEFII=IHFIFGIHIIHAHII:FIDIFACIIHCEH?FFHHDHHIFHHIHDIHE7GFIHG*HFHHHHHHDBIEHH0IEHHHHGFHGGDGEFGGG:EDIIG;=GEGEEGGGGFGEHGGGGFHC:GG??A8?G?CGE+=GGGGEEEGDGGHG>GGAGGEGGE(G\n+@level_3-470/1\n+TTCCTCCCGCGATGCTCTGTGAAAATGATTGTCAGGCGTAGTCTTGTATCTTTGAATGGCTGACCTCGAAGACCCTTTGAAAATGCTGGCTGGGGGAGCTGTCAACCCGTCGTAACATTTGCTCGCGGGGGGGAGGGGTATCCTATACGCTTCTTCAGAAGAAGTCCACCCGATGGCCCCCTGCCGTCCAATATTGTAAA\n++\n+?????B?BDA?DDDDDGFGGFFFIHIIEIHHEIHHDDHHIIHIHHEIAHIIIGEHIAHIIIFIIIFIIIGHHIGIEHIFIIFICHFIHHIAHCIGIDEHIHFHFHGGHFHH-HHBCHHGGHGCHFFGFGEFAF*E1EGGGEGGDEGEEGGGFEGEGE>E;EGCGGGGCEGGGGF)?EEE2?DFEC(CG:FGEEGE:FEDG\n+@level_3-468/1\n+AGACCTCGGCACACCGTTCTCACCGTCTATTATTTCATTGGCGCGCCTATGGTGAGATGGACGCCTTTGCGGAGTCCCTCTAGACAGGCCACACAGGTTGTTCGCCGTGTTTCTAACAAACGAGTAACTTCGGATTTGAGAACATCGGACACGTAGCACCTGCGATACCAATCGGTTCCTCCTTTCCCCCGTTCCAACGT\n++\n+??A??BB??DDDDDDBGFGFGGIIFFHHIHHCIHIIIHEIFIIIF8DEHIHIHFIIHHFDIIEHDIHIFIHHHGHIGHIIEGIIHHHIIIIHH?HHI@HFH,HGFIEHGCFHF<FHGHGFGGB3GGGFG+GF0FGEE(GG?DEFEGEGFGD8EE;GGGEEG@GGFG6GGGGGCACEGFEEEEEGGEGG?'/G?GFGEFG?\n+@level_3-466/1\n+CATATGATTTGGTAATAGCACGGGCCTGTAGCTTTTGGCGAGTCTGAGACCTCGGCACACCGTTCTCACCGTCTATTATTTCATTGGCGCGCCTATGGTGAGATGGACGCCTTTGCGGAGTCCCTCTAGACAGGCCACACAGGTTGTTCGCCGTGTTTCTAACAAACGAGTAACTTCGGATTTCAGAACATCGGACACGT\n++\n+?A???B??D.DDDEDDFFFGFGHHIIIIIIHHIGCFIFHIFICIIHHIHIH/GDHIIFIIEHHIHHBHHHHIEHIIIHIHDHHHHIHHIAHCHH)3FAHIHHHHFHGIHEFHHHF=FHGFHHFDGFDHFGGHGEFGGIGGB?GGG:GCGEFFBGGGEGGGGEGCGE*GEGEFG/CG;)GGEEEEE6BGGGGF0GGG2GEE\n+@level_3-464/1\n+GGCTGATCTTCCATAATGTACTGACGCTTTACGTTAATATTCATATGGACCCACTTATGATGTTCTGGGTTTTGACGTTACGCAATCACCGTATGACACCCCCATACTAAGTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGG\n++\n+???A5B?BBD<DDDDDCFFCGFIHIHHHIHFHEHFEEHIHIIIDGGIHHHHHHHIHIFIII-GIHHIHIIIHIHH?IHHHII,HGIIFAHFIHHH,'HHHGGEEIHFHDHFHGFFHD=.EHEHFHGFGAHGFDGGBFGHGFEF1GGGGGG8G:7GGGEGGCCCEGGFEGF6EGGEEE?EEGEG.EGG(DFGEGGGGGE:G\n+@level_3-462/1\n+TAAGAACATAGTTCCCGGTTATTGCCAATCCAGGGAAGTTCAAATTGTTGTACTTAGTATGGGGGTGTCATACGGTGATTGCGTAACGTCAAAACCCAGAACATCATAAGTGGGTCCATATGAATATTAACGTAAAGCGTCAGTACATTATGGAAGA"..b"++\n+?AA??B?BDDBEDBDDGFFGFGHHIHHIII-FHIHGHHGGHHGFHIHHFIHIHHBHAHGI-GFHFHIHF5IHH5IIIHH@FHIIFIFGFHGFIHHICHHFHFHIFHHDIDEDHH5HHEEHHGBG*HG@E,FGEEGFGFGGGGGEGGEFEGFGCFFCE<EG?GEEGAGGGFFEEEGCE<GGGCGGGA:ACEGE.EGGEGG?\n+@level_3-18/1\n+AAAGTTGCTGCTAGCTACGATGCCTATCATCTCTGACAGGACCGTAACTGCACGTCTTGTTCCTCCCGCGATGCTCTGTGAAAATGATTGTCAGGCGTAGTCTTGTATCTTTGAATGGCTGACCTCGAAGACCCTATGAAAATGCTGGCTGGGGGAGCTGTCAACCCGTCGTAACATTTGCTCGCGGGGGGGAGGGGTAT\n++\n+?????BBADDDEDDDDEEGFFGIHFIHIIEHHI>FHHDIGIIGCHIHHIGIGAIHGH>GHEI?CIFHCHHHIFHAHGHBDIIHII?FGCHHFFIHI7*-GHGGHIGEFIFFHFHH?HHFHGBCGHFGHFGEH5GG'9GD2@FGEEGFAGG'?GAGGGFG?B::CGGCGFEGG/G'EEEFGEEGCGG4CEGEEGEGF:GEG\n+@level_3-16/1\n+TTAAGAGCGTGGCTCGTGTAGAGCGGGATAACATACCAGAACACGCGGTGGGAATCGTATTGGTTGCAACTTGTCTGTACGTGTTGCACCATTGAGGCCGCGCCGACATTATTCTGGCAATTTGACTGCACTCGGGTGAATGCAGATAAGTCTAAACCCGCGGTCCATGGATGGAAAAAGCAGAAATCAGATTTGAACGA\n++\n+?AA??B+BDDDDD?DDGGFFFAHIH;HHFIHHIHFEFFI=IGHGHIDIIGCFHHFIHIFIIHGH-HIFHHFHIHIFHIDHGFIHIIHGHIEHHH.HIHHHHHEFG=HH<HFFH7HGIGHHF,AHFBEFHHHEG?F?B=HCGEFFEF9EHG'EG?AEDEG<EGE8GGAG(=AGEGCG?EG?AHE<;GFE*EEEGGEGGFGG\n+@level_3-14/1\n+ACGACGGTAAGATCGCCTACAAAGTCAGTCAAGTAAGTTCCAATTGTTCTTAACTATTGCTCGCTTGGTCCGAACTCTTTCAAACAGATCACAAGGCTGAGTTACAGACATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCA\n++\n+?A??ABB@DADDDDD<GFGGGGHIIIIIICIHIIIIFHCHHIIIHHIHIIEHHHFHFICA=AHIHEIIHIGIHDIIIHFHGHDIIGGEFHFGHHGCIEIFBFCHFHHIGHHH=HGH9H@FCEGGHHGG;G6BGBG@GE=E*GG:EEHFA>GEEEGEEEAE3CFGEDGEF0FFGEG@GGGGGEC9G/E(EFEFGGE:1EEF\n+@level_3-12/1\n+GTTACTGGTCGAGTAGCAAGAGGGGCGGATCCGGAAGGGCTTCACTATTGGGAACATGGACTGCTTGGTTATCGCCACTCACCTTCTGATGATTTAGAATTACCACACTCAAATAGGTCGGTGTTCCGGTCCTGGAATATTGCGCTTTTTGGTATCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCG\n++\n+?=??<9BBDDBDDDDDFGGGFFFHHFAIAIIH9HICHIIGHDHIIHIHFIHIIHFHIFHIE8GEHEFIIEFHFIDFFCIHI*5IHFBHHHGHHHHIHIIHCCDGIFHCFEG@EGHHHHECEGGG=FGGEGFFGGGGGEGCFBDGG*GEGGFAEAGEFF?G;GEGD8E<E6EGCFGGFDCE.GEEGEGEGGCGEFGFF6GG\n+@level_3-10/1\n+TTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGCTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCGCGGGTTTAGACTTATCTGCATTCACCCGAGTGCAGTCAAATTGCCAGAATAATGTCGGCGCGGCCTCAATGGTGCAACACGTACA\n++\n+<???ABBBD+?DEDDDFGFFFFIIFIFIIIIIAEFICCIICIIAHGHIIIEHGI=HIFHHCDHEFIAGIIDIHIIAEHI>HIHHIHEIIHHIHIIIH<FHHGHGFGGGHFGEFHHEF?3=HFHFFHE@HGGGH6:CEFFEGGF*GFEAFECCG;G@GGCGFGFFGGGE:AGG>?GGF;+<ECE?EGCCGE8EEGGACEEE\n+@level_3-8/1\n+CCCGTGCAAAGTGTGCGGCTAGCAATTACCAGGTTCCGGGAAACTGTTTTCATAATACATCCCCAGGATACCCCCCCTGAGTAATCTGTCCTATATTCGCCGCTTTTTCGCGAACGCGCAAGGTCGTTCAAATCTGATTTCTGCTTTTTCCATCCATGGACCGCGGGTTTAGACTTATCTGCATTCACCCGAGTGCAGTC\n++\n+????<?B.<DDDDDDDGEGFGGI+IIIIEFHHIAHIFIIFIGHHIFDHH:IIIIIHHIFIIIFIIIHIIHEIIIEHIGIFGIFCHEHAIIIHH,HFIIDHHFFEIGHHHHCIEF=HGHHFGG9HGFDFFE,HGE=FGGEEEFEFGEDE<GGFFGFAAGFG/FFGGGBFEFGG;E;GGECGEGEGFGGGEECF/G?GEEEG\n+@level_3-6/1\n+ACTTCGGATTTCAGAACATCGGACACGTAGCACCTGCGATACCAATCGGTTCCTCCTTTCCCCCGTTCCAACGTGTGTACGATCTAAAATTTCCAGTCTCATAGATGCGGTCACTTCTTCCACAAGAAAATCAAAACCGGATTGACGTCTGGACTCAACCGGAATCGGTATCCGTAGGTGCCGTGCCCAAGGGGTCGCCC\n++\n+?????B?BBDDDDDDDGFFFGGIHIHIIIIIHIHIEIIAIHHIIH+HGHHHFGGIFHHDGG7IGHHH-HHIDIHIHHFHAI?FDH?GIHHEIHIEIHHHD7HFIFEFHGHHEHEFFEHDHCFGGFHFHFE:FHEFDFG@GG:@FEFGFC(EEE/GGGEGEFGGFG?GEGGEEGE.CGGG1G8EC:CGGFEC<=GG26EEG\n+@level_3-4/1\n+TTGTTCCTCCCGCGATGCTCTGTGAAAATGATTGTCAGGCGTAGTCTTGTATCTTTGAATGGCTGACCTCGAAGACCCTTTGAAAATGCTGGCTGGGGGAGCTGTCAACCCGTCGTAACATTTGCTCGCGGGGGGGAGGGGTATCCTATACGCTTCTTCAGAAGAAGTCCACCCGATGGCCCCCTGCCGTCCAATATTGT\n++\n+?????BBBDDDEBDBDFG>CGGIIHHEIIHE9FHIIHCHIHIIIG=HIIIIHFHEHIGHIHIIIFHHHH-HCIFIFFHICFHHH<ICIIHHHHHHHIIFFIHGHHF.HHH.<GHGGFGGEEDHGGEFFDGG=CCGGFGGEGGEEEGGGEE*GEGF;EGFEFEFGFEFGEEC<CFEGE?EGEEFGE.GFGE(EGF*CGFAC\n+@level_3-2/1\n+AAGTCCACCCGATGGCCCCCTGCCGTCCAATATTGTAAACAGCGTATGCTACCCGTAAGAACATAGTTCCCGGTTATTGCCAATCCAGGGAAGTTCAAATTGTTGTACTTAGTATGGGGGTGTCATACGGTGATTGCGTAACGTCAAAACCCAGAACATCATAAGTGGGTCCATATGAATATTAACGTAAAGCGTCAGTA\n++\n+<??A??BBDDEDDDDEGEGF>FHIHHFFIFHIHHIIIHHFIHIIGFIAHHHHIIG@EHGIIHI5FHIIIHFI-IHGFFHHHIIFHFFHHHHHEGHHHEHHHHEHHHHHHFEFHDGGFHE*EHFF@GHHHEFFGGCED:;HEEEEFGGGFGGGGBEGGAGGE?EDGEGGFGGGGC:EGGCFG(EFAFE*GAG>D:EGFGG4\n" |
| b |
| diff -r 0968856c687c -r d4bb87ca916d test-data/un_test2_output_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/un_test2_output_2.fastq Wed Apr 10 13:56:57 2019 -0400 |
| b |
| b"@@ -0,0 +1,960 @@\n+@level_3-480/2\n+GGGGATTCTCTACGCCGACGAATATCTTCTGACATGGGAGGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTGTTCGACACAGGATGGTCTTGGCGACTTGCAAAGCATTCGCTACATTACACAGTACAGTTGGCCTCGGTTAAAAGTCCA\n++\n+???=?B?B?@@B5DBD>8FC>CHHF@FIHHHIIIDHHHEHHG-HIFDIGHCH-H7EIF=H-HHIHHHFFI=)F@HEHIEIHGHHEH@B-DH5IF,HCH5GHCG>EDFHDHHIDFHF+HG3=F=8H@G*HHFF0+GEC@@EH.E@ECGE@EEDGGEFGBFG=@EAAAFEEG:E(FGE(E'?GEEG?7E=E?4FEE(G(EEE\n+@level_3-478/2\n+TTGACGTTACGCAATCACCGTATGACACCCCCATACTAAGTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGGGGGCCATCGGGTGGACTTCTTCTGAAGAAGCGTATAGGATACCCCTCCCCCCCGCGAGCAAATGTTACGAC\n++\n+?=???BB?<DDD5DDBFFGGF?FHICIHIIHE.IHIHEAHD5GDHFHCIH@FHF=HH.DHIHIIHGHAHIHIIDAHHHHGDIIIFIFI+HHIFGHIIH,HHHGH8HBHEH=GHIFDHHCHFHHHCGG=EGGHFDEGIFDCFEGEEDGE?(EFGBE**B<D.GCF?GC?EGE>@EGGGE<.EEGCGCC(FECGEGEGEG:?\n+@level_3-476/2\n+GTGTTCCGGTCCTGGAATATTGCGCTTTTTGGTATCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCGTCTCAAAGAATAACGGCTCTAGCTAAAGAAGAGCGAGTAGAGATTCTTTGTAACCTATGATAAATCAAACGAACCTGGTGGCGCACGGGTGGGCGTGCACGTGAAGGGGGCGGATGTTGC\n++\n+???,?B7@--BD@DDBFGGACFH>HI/FEHDIF,IHHI7HIFDAH9GEIGFA>IDHHDI-I@ICAHIHHIGHFHH5HDFHHHHHH.FGFFHDGFGH.FFHFHEHH+HED=)IHHHGHC.BFFF.HHGHD9FF)HDFI1GA@GA;G*GFAGGGDCGA?E?EFG?GGECGF?/G<B*(CGEEEEE*GCA/(EEGEGECDG:8\n+@level_3-474/2\n+GATTCTCTACGCCGACGAATATCTTCTGACATGGGACGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTGTTCGACACAGGATGGTCTTGGCGACTTGCAAAGCATTCGCTACATTACACAGTACTCTTGGCCTCGGTTAAAAGTCCAGCG\n++\n+=??9=B=BDD+DBDDDG*>GGFHFIH/HHBGHHIIIIIGGIHF=FH/EHAIGGHIF?IIH?FFIECH@CDH-HI@-HCEHFE+IIIE-ICH+H+IHDHIFHGFHFHH4HHG9DGH?GBBFEHFHHEG9.GFH?#EEF8FD/AECGEEEEFG(EEGEGFEGD/GE/E:FEG*E*E#GGECE6BEEGE/F;EEEFE?G.CEE\n+@level_3-472/2\n+CCGTATGACACCCCCATACTAAGTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGGGGGCCATCGGGTGGACTTCTTCTGAAGAAGCGTATAGGTTACCCCTCGCCCCCGCGAGCAAATGTTACGACGGGTTGACAGCTCCCCC\n++\n+?=?A?BB3DBDDDAEDGG/GGGBIHHHHIHHFI=C9II@E,HIHIIIHI-HIIHHGDF9.IHFIHHIGE,HEHHIFHI=HIHHHHDEHHFHHIBFHHFIIFHDIF=F+IGHHDAGHFHG*BFF:F*GDEFBGEEGGF8GEFEEGE(G(GE*/GE=EFGG(E*GGEEF8EEF@G6?D8.E)EE3C4AGG;EGGFEF?.CCF\n+@level_3-470/2\n+TGTCTACATTAGCGTGTACGCCGGGGCAGGACGGGATAGTGCCTTCTTGAAGCGGCGGTATTAGTCTGCTACCCGCAAGCCCGAAAGTAGTCACCATAGCAGATGCATATGATTCTCGCACTCCATAATCCAGTCTTTTCAGTAGAGCGGCTCCGGCCTTGGGGCAGATGATTGGCTGAACCATATGATTTGGTAATAGC\n++\n+?<?A?B<B6DE@DDD-FGFGFFCIFHIIICIEFHDIEFIFIIHHHDH=BFHHHIG3HFIHHHHIDIIGEII@HFHEHFFHHBFG@IHHEGDICIHFIHIDHHFE5=HHGHFE;HHDHEH)H?H1<GF2EED(;FDAGGGDGBFG,E>GG8GGBFGEECEGGGGGE?:@6*EGACGCG6:G?GEEEE(0GE*FA'EG:G8A\n+@level_3-468/2\n+GCAGACATCAGATTTGAACGACCTTGCGCGTTCGCGAAAAAGCGGCGAATATAGGACAGATTACTCAGGGGGGGTATCCTGGAGATGTATTATGAAAACAGTTTCCCGGAACCTGGTAATTGCTAGCCGCACACTTTGCACGGGTAAAAGTTGCTGCTAGCTACGATGCCTATCATCTCTGACAGGACCGTAACTGCACG\n++\n+??A??<>ADDD,D-DDFFFFFFHHFIBIHIIACIIHI99HHHHHHEEEHHI+@EGFEHDIFB*HIIEIIFGG?-,IFFC++5+BFHHHBHHHIHCIGGIFHFH(FHHHD=HDCHFGE+EFHH2HFDHHGGEF9CFE?FCEG8GGG;EA?GG0GGG@3G=GEEEFG?<*GEEEF<EEC.GEGEFFEE(ED:E)G/FEAGE:\n+@level_3-466/2\n+TTTGAACGACCTTGCGCGTTCGCGAAAAAGCGGCGAATATAGGACCGATTACTCAGGGGGGGTATCCTGGGGATGTATTATGAAAACAGTTTCCCGGAACATGGTAATTGCTAGCCGCACACTTTGCACGGGTAAAAGTTGCTGCTGGCTTCGATGCCTATCATCTCTGACAGGACCGTAACTGCACGTCTTGTTCCTCC\n++\n+??A??==B?-DDDDDD-;FGGFHI-EH8/IHHHG?DHEIHEHCHH.GH?>GIGIIGDGHEF0IIG,A*E=HHHICAIHH-HB-EBIHFFFHHGHHIHIII+HGHGHHFFGFCHGFHFDDHG'G;GF*EEHDEFG83EGEGE0,;FE(7GB)EBGFG@FAFFE6?C?BG;GFEHGGEAGG;8GGDEECG;FEGAE6FGEE0\n+@level_3-464/2\n+CATGCGCCGTCGCAGTGCAACTAACCTTAGGGTACAGGCGTGAGGGGCAGTATGAGCGAGGGATTACCTAGAAAACCACCCCTATTGCAGCAACATTGTCTGACGCATTGCACTACGGCGGTATGTTTAACGCGCCTGATGTCTCACGGTCGTCGGAACAGCTAAATACCCTTGGTGGCGTTGGCTCAATGTATTATGAT\n++\n+A<A????>DDDDDDDBFFCFGGAHI-CHGEFGGFAAHFF/IIGHEIIHCCE+AFG0FHHIICEFGFG=HHAHHHFIGEHHGIHHFDHHIHHIHIDCFHE=GFHB+6=GFHBHHHF+2=HHGFHDF8FHGG)DBGECGFG?DG,,GE4GFGGBEGE*G8GFGG*:FEEE:?GE;GE)CFG.FGC;E(?E8?:0;=?'GGE(\n+@level_3-462/2\n+ATTTAGAATTACCACACTCAAATAGGTCGGTGTTCCGGTCCTGGAATATTGCGCTTTTTGGTATCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCGTCTCAAAGACTAACGGCTCTAGCTAAAGAAGAGCGAGTAGAGATTCTT"..b'++\n+=<????B-BDD7DBEDF8GGFG8HIIFHF;HHEAFIFCIHIHHHIHFEHE#DI5HII=FEC.IFCCEHFBDDH+IHHFIHHIHHIHHHHI-H-IDDAHHHH#HF*HHH=HFHGBEFHHDEHD@HCEBEHHHFHG*#EHGEG;DDDGG/F3EFDEFF(G*GG(EGFEG<EEGCG:F:GE?FEFA*?(FAGGAGGGEEEEG:\n+@level_3-18/2\n+GTGCCTTCTTGAAGCGGCGGTATTAGTCTGCTACCCGCAAGCCCGAAAGTAGTCACCATAGCAGATCCATATGATTCTCGCACTCCATAATCCAGTCTTTTCAGTAGAGCGGCTCCGGCCTTGGGGCAGATGAGTGGATGAACCATATGATTTGGTAATAGCACGGGCCTGTAGCTTTTGGCGAGTCTGAGACCTCGGCA\n++\n+?<????B>D@-DD-@BGCF?/GHIFDHG>I8G>FHIHH@EHCDFCFHIHD=HAHHGI=II++F>F?5IHB?EFFHGHEGEHHIHDHD?HC:HDGHHHHFCIGFEH3HGFDHHHHH;DHDH=EFEG@HEHDFHG(@F0#AEB4E:G4A:*E(;GEEEFE(FGEEEEGAFGE8/EE=EFEFF(FGG:DEGGEEE68?F(ECG\n+@level_3-16/2\n+AACTTCGGATTTCAGAACATCGGACACGTAGCACCTGCGATACCAATCGGTTCCTCCTTTCCCCCGTTCCAATGTGTGTACGATCTAAAATTTCCAGTCTCATAGATGCGGTCACTTCTTCCACAAGAAAATCAAAACCGGATTGACGTCTGGACTCAACTGGAATCGGTAGCCGTAGGTGCCGTGCCCAAGGGGTCGCC\n++\n+???,?BBBDDD5DB@DGGAGGFFIFHHIEHHIF9IIHHHHFHH=HHIHG/HFHIFIH@IIHHIIHHIEFHIH)GIHEHGHICDGCHFIHEHFHHFFFEHHHHHH=GHFE@DCEFHF=-EHD@E=HGFC*D4GHGG/CEEFEGGG@EECEGAG(E/GCF0C(;@GG*)<EEG*?FGE@CGG>6G=FG0/E;EECGEAGEE?\n+@level_3-14/2\n+GTACAACAATTTGAACTTCCCTGGATTGGCAATAACCGGGAACTATGTTCTTACGGGTAGCATACGCTGTTTACAATATTGGACGGCAGGGGGCCATCGGGTGGACTTCTTCTGAAGAAGCGTATAGGATACCCCTCCCCCCCGCGAGCAAATGTTACCACGGGTTGACAGCTCCCCCAGCCAGCATTTTCAACGGGTCT\n++\n+??<5?B??BD@-@D<DFFGG>EHI>IIBCEHHCIHHHIHIHIIIF0HIHHHH.DH@>GEEH-HIIFHHDEGICFHHGHF5ECHFGEHHHHIHHHHH5,EEEHCGBI6HFFHHHF@@HGHFFG=DDG+EGDF(.GEBGFGC4F:G<CGGGGEECFGFCG).8F0<EEEC=CFB*G8?86<6GGE;DAGG:GGAE*E;E(EG\n+@level_3-12/2\n+TAAGTGGGTCCATATGAATATTAACGTAAAGCGTCAGTACATTATGGAAGATCAGCCTTTCTTCGCCTTGGGTGGTGAAGCACGCTCCCTCTTCTAGACGGGCGACCCCTTGGGCACGGCACCTACGGATACCGATTCCGGTTGAGTCCAGACGTCAATCCGGTTTTGATTTTCTTGTGGAAGAAGTGACCGCATCTATG\n++\n+5AA??B?BDDBD?D@DCGF6FF-IAHFHI>HI/HEHDHH9III-H?IHIFIFIIC8HHHFHHEHCHDFIHGIHFIAHIIFDHHCH+EDH=HFHI=HFFDF5HDH>BHH3H;EFHF.HHDFHHHFG*E=EFFEDG+EIG9*EADG;GG2F?FE0E8GEEGG9EEEAEGA?0CFCFEEEEEAGAGGG*FEEEEF;G<EC:GE\n+@level_3-10/2\n+CAACCATTGCCATCGTGCCTAACTCGCTATACAAGTCCGGCTCACCCAATATGGTGGGGATTCTCTACGCCGACGAATATCTTCTGACATGGGAGGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTATTCGACACAGGATGGTCTTGGCG\n++\n+?5<?=BBB-DDDDADAAGFGEFFHAEHFIEHHFIFHHIFHHDBHFHIHGEHHHIFIC=E+FIGHHHAFHFAFHE--+IHHA>FI2HIEHCE@AHHHHIEEEFHIHHIHHGDHHGHHDG+7HECH;IGGH5HAEG?@E<G,G?GEGE?1:@=GEEGFEGCBGCEC0FEEGEEFFE6E#BE6EG/8<(GEG?(EEE(GAEA?\n+@level_3-8/2\n+GGCTCACCCAATATGGTGGGGATTCTCTACGCCGACGAATATCTTCTGACATGGGAGGCTCCGTATACTTTCGTCAGTGGCTCAAACTCAGGACCCAACACCTAGAGCGAGCTATTTAACGTGAAACATCCTCGAACTGTTCGACACAGGATGGTCTTGGCGACTTGCAAAGCATTCGCTACATTACACAGTACACTTGG\n++\n+???A?@B?D<5DDBDDBGAFCFCEAFAHHHAHIGHHHGHFHIEHA.IEH9IIF@CHFE0AICHHHEAEHIHEHIHHIH5HH+HDBIIHDIH78GHHHIIGHHHFFFDFCE=)EHDFG;=H*HH9EGG=GGFEBDGGG;7*EA,G*CCFEEEEDEEGCCG(*EEAGC(GE8G*CGGC><6FFF:/AGGE9GE;E:ECEE:8\n+@level_3-6/2\n+TAAACTCTTAAGAGCGTGGCTCGTGTAGAGCGGGATAACATACCAGAACACGCGGTGGGAATCGTATTGGTCGCAACTTGTCTGTACGTGTTGCACCATTGAGGCCGCGCCGACATTATTCTGGCAATTTGACTGCACTCGGGTGAATGCAGATAAGTCTAAACCCGCGGCCCATGGATGGAAAAAGCAGAAATCAGATT\n++\n+=??<<B?BB--?<BB@FCACGFEIFIIFEFFH9HHC9ICFIDH.HIDC>FFIHHH-GHFHIHC+FHCFHFHHHDHA>IFDDH5IEH-HFFHE7HEFHGHDHGHFHGHHFH?HGCHHHHGE;CFBHHFFEEGCGFGF2CFE?G>GGGFGEDAFEGGEGE4;GGEGC:EEE6(EG<EG/:GEE+C:G?GFGGGFGCE:E*F*\n+@level_3-4/2\n+CGATCCTAGCGAGCGTCGGAGAGCATGTCTACATTAGCGTGTACGCCGGGGCAGGACGGGATAGTGCCTTCTTGAAGCGGCGGTATTAGTCTGCTACCCGCAAGCCCGAAAGTAGTCACCATAGCAGATCCATATGAATCTCGCACTCCATAATCTAGTCTTTTCAGTAGAGCGGCTCCGGCCTTGGCGCAGATGATTGG\n++\n+A??=,BBBDBB@DD-EGGFGFFBC8CH+HHEH@HI@FHHA-IFHHFHHFCFHHGIHHFHF58?CH+EIHI=HHFGFIAIAFDI=HIIFDHHEIIGHIHGHHHHD+-HHCF)GHHHFHGHHEGDCGGGFFDE?GHEG#*G?EGGBFEGE/FEEDFF/EEF0G6AE.FE.GC@B6,EGEC?E.F/EDGE(A?06CCGE6CEG\n+@level_3-2/2\n+TCAACCGTTGTGTGCAGTGAAAGATTCATAGTGATATTTCGTCTCGTCTCAAAGAATAACGGCTCTAGCTAAAGAAGAGCGAGTAGAGATTCTTTGTAACCTATGATAAATCAAACGAACCTGGTGGCGCACGGGTGGGCGAGCACGTGCAGGGGGCGGATGTTGCCATGCCGATCCTAGCGAGCTTCGGAGAGCATGTC\n++\n+????AB-BDABDBD@DEFFGGC>>FH8IFII7HIHHHHHHII@AHEHIIIHHBIIGFIFHIEIH5H=HCHE5GFD-HHIHHHGIHFFIEHH=(HH5AHHEECFHHHHEFH+3EFHHHEH1+G@+EG:FFHGG>CFGGE5B2:DEFCEEEEEF;FFEEG1*GGG(?EG8GGD**GEF/G6FCECEA/4GG<GG;GGECEEC\n' 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