| Next changeset 1:e0655b546470 (2018-10-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e1031e4c94b25d1ed535bf221764ab801b710ab2 |
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added:
macros.xml obiuniq.xml test-data/illuminapairedend.output.fastq test-data/input_ngsfilter_extrafile.txt test-data/output_ngsfilter.fastq test-data/output_ngsfilter_error_3.fastq test-data/output_ngsfilter_unidentified.fastq test-data/output_obiannotate.fasta test-data/output_obiclean_advanced.fasta test-data/output_obiclean_simple.fasta test-data/output_obiconvert.fasta test-data/output_obigrep_lmin.fastq test-data/output_obigrep_predicat.fasta test-data/output_obisort.fasta test-data/output_obisort.fastq test-data/output_obistat.txt test-data/output_obitab.txt test-data/output_obiuniq.fasta test-data/output_obiuniq_family.fasta test-data/wolf_small.F.fastq test-data/wolf_small.R.fastq |
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| diff -r 000000000000 -r 4c2b715a258a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| @@ -0,0 +1,136 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.0.010">obitools</requirement> + </requirements> + </xml> + + <token name="@WRAPPER_VERSION@">1.0.010</token> + + <xml name="stdio"> + <stdio> + <exit_code range="1:" level="fatal" description="Error in Obitools execution" /> + </stdio> + </xml> + + <token name="@OBITOOLS_LINK@"> +<![CDATA[ +-------- + +**Project links:** + +`OBITools`_ + +.. _OBITools: http://metabarcoding.org/obitools/ +]]> + </token> + + <xml name="attributes"> + <option value="ali_dir" selected="true">ali_dir</option> + <option value="ali_length">ali_length</option> + <option value="avg_quality">avg_quality</option> + <option value="best_match">best_match</option> + <option value="best_identity">best_identity</option> + <option value="class">class</option> + <option value="cluster">cluster</option> + <option value="complemented">complemented</option> + <option value="count">count</option> + <option value="cut">cut</option> + <option value="direction">direction</option> + <option value="distance">distance</option> + <option value="error">error</option> + <option value="experiment">experiment</option> + <option value="family">family</option> + <option value="family_name">family_name</option> + <option value="forward_error">forward_error</option> + <option value="forward_match">forward_match</option> + <option value="forward_primer">forward_primer</option> + <option value="forward_score">forward_score</option> + <option value="forward_tag">forward_tag</option> + <option value="forward_tm">forward_tm</option> + <option value="genus">genus</option> + <option value="genus_name">genus_name</option> + <option value="head_quality">head_quality</option> + <option value="id_status">id_status</option> + <option value="merged_star">merged_star</option> + <option value="merged">merged</option> + <option value="mid_quality">mid_quality</option> + <option value="mode">mode</option> + <option value="obiclean_cluster">obiclean_cluster</option> + <option value="obiclean_count">obiclean_count</option> + <option value="obiclean_head">obiclean_head</option> + <option value="obiclean_headcount">obiclean_headcount</option> + <option value="obiclean_internalcount">obiclean_internalcount</option> + <option value="obiclean_samplecount">obiclean_samplecount</option> + <option value="obiclean_singletoncount">obiclean_singletoncount</option> + <option value="obiclean_status">obiclean_status</option> + <option value="occurrence">occurrence</option> + <option value="order">order</option> + <option value="order_name">order_name</option> + <option value="pairend_limit ">pairend_limit </option> + <option value="partial ">partial </option> + <option value="rank">rank</option> + <option value="reverse_error">reverse_error</option> + <option value="reverse_match">reverse_match</option> + <option value="reverse_primer">reverse_primer</option> + <option value="reverse_score">reverse_score</option> + <option value="reverse_tag">reverse_tag</option> + <option value="reverse_tm">reverse_tm</option> + <option value="sample">sample</option> + <option value="scientific_name">scientific_name</option> + <option value="score">score</option> + <option value="score_norm">score_norm</option> + <option value="select">select</option> + <option value="seq_ab_match">seq_ab_match</option> + <option value="seq_a_single">seq_a_single</option> + <option value="seq_a_mismatch">seq_a_mismatch</option> + <option value="seq_a_deletion">seq_a_deletion</option> + <option value="seq_a_insertion">seq_a_insertion</option> + <option value="seq_b_single">seq_b_single</option> + <option value="seq_b_mismatch">seq_b_mismatch</option> + <option value="seq_b_deletion">seq_b_deletion</option> + <option value="seq_b_insertion">seq_b_insertion</option> + <option value="seq_length">seq_length</option> + <option value="seq_length_ori">seq_length_ori</option> + <option value="seq_rank">seq_rank</option> + <option value="sminL">sminL</option> + <option value="sminR">sminR</option> + <option value="species">species</option> + <option value="species_list">species_list</option> + <option value="species_name">species_name</option> + <option value="status">status</option> + <option value="strand">strand</option> + <option value="tail_quality">tail_quality</option> + <option value="taxid">taxid</option> + </xml> + + <xml name="inputtype"> + <option value="--genbank">genbank</option> + <option value="--embl">embl</option> + <option value="--sanger">sanger</option> + <option value="--solexa">solexa</option> + <option value="--ecopcr">ecopcr</option> + <option value="--ecopcrdb">ecopcrdb</option> + <option value="--fasta" selected="true">fasta</option> + </xml> + + <xml name="sanitizer"> + <sanitizer invalid_char="test"> + <valid initial="default"> + <!--add value="""/--> + </valid> + <mapping initial="default"> + <add source=">" target="\>"/> + <add source=""" target="\""/> + </mapping> + </sanitizer> + </xml> + + <xml name="citation"> + <citations> + <citation type="doi">10.1111/1755-0998.12428</citation> + </citations> + </xml> + +</macros> |
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| diff -r 000000000000 -r 4c2b715a258a obiuniq.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/obiuniq.xml Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| @@ -0,0 +1,92 @@ +<tool id="obi_uniq" name="obiuniq" version="@WRAPPER_VERSION@"> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> +<command> + + <![CDATA[ + + obiuniq + #if str( $options_attribute) == "merge" + -m '$options_uniq' + #else + -c '$options_uniq' + #end if + ${mid} + ${prefix} + '$input' > '$output' + + ]]> + +</command> + +<inputs> + <param name="input" type="data" format="fasta,fastq" label="Input sequences file" /> + <param name="options_uniq" type="select" label="Attribute to merge" > + <expand macro="attributes"/> + </param> + <param name="options_attribute" type="select" label="Use specific option" > + <option value="merge" selected="true">merge</option> + <option value="category_attribute">category_attribute</option> + </param> + <param name="mid" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Add a merged attribute containing the list of sequence record ids merged within this group" /> + <param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching" /> +</inputs> +<outputs> + <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" /> +</outputs> + +<tests> + <test> + <param name="input" value="output_ngsfilter_error_3.fastq" /> + <param name="options_uniq" value="sample" /> + <param name="options_attribute" value="merge" /> + <param name="mid" value="False" /> + <param name="prefix" value="False" /> + <output name="output" file="output_obiuniq.fasta" ftype="fasta"/> + </test> + <test> + <param name="input" value="output_ngsfilter_error_3.fastq" /> + <param name="options_uniq" value="family" /> + <param name="options_attribute" value="category_attribute" /> + <param name="mid" value="True" /> + <param name="prefix" value="True" /> + <output name="output" file="output_obiuniq_family.fasta" ftype="fasta"/> + </test> + +</tests> +<help><![CDATA[ + +.. class:: infomark + +**What it does** + +The obiuniq command is in some way analog to the standard Unix uniq -c command. + +Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records. + +A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself. + +The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed. + +A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option. + +As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported. + +\* By default, only attributes with identical values within a group of sequence records are kept. + +\* A count attribute is set to the total number of sequence records for each group. + +\* For each attribute specified by the -m option, a new attribute whose key is prefixed by merged_ is created. These new attributes contain the number of times each value occurs within the group of sequence records. + + +@OBITOOLS_LINK@ + + + +]]> +</help> +<expand macro="citation" /> +</tool> |
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| diff -r 000000000000 -r 4c2b715a258a test-data/illuminapairedend.output.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/illuminapairedend.output.fastq Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,996 @@\n+@HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS ali_length=62; direction=left; seq_ab_match=47; sminR=40.0; score=115.761290673; seq_a_mismatch=1; seq_b_deletion=1; seq_b_mismatch=13; seq_a_deletion=0; score_norm=1.86711759151; seq_b_insertion=1; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; seq_b_single=46; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttgagctattgccggtagtactctggcgaatgattttgttataataattacttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+dddddddddddbbdaddcddddddcadaddddaadcccWaaddabdx~~|b~~~~cccccccBcBcccBcBcccBccBBcc~}`kXyxu|~Kyr`b~~~~~~b~~~b~d\\cdddddddddddddcacddddcdddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS ali_length=62; direction=left; seq_ab_match=60; sminR=40.0; score=231.881364714; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=2; seq_a_deletion=0; score_norm=3.74002201152; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; seq_b_single=46; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaacaattttgttatattaattacttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+ddddddddddddddddbdddddbddddddddddddddddddddddd~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~Z~~~~~~~~~~~~~b~d]dddddddcdddddcddddddddddddddddddddddcddddddd\n+@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS ali_length=62; direction=left; seq_ab_match=52; sminR=40.0; score=167.91734192; seq_a_mismatch=5; seq_b_deletion=0; seq_b_mismatch=5; seq_a_deletion=0; score_norm=2.70834422451; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; seq_b_single=46; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctcttgccggtagtactctggcgaataattttgttatattaattacttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+ddadddddcd`dcddddddddd^dd]ddddddZad`\\`]Lcca``YT|~~^||v|z|~ts~~~|r~sZ^~~`~~~~~~~~~~~~~~~~V~b~]~~~~b~~~~~~~~`~b\\aadddd`dcdddddc`dddccddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS ali_length=62; direction=left; seq_ab_match=59; sminR=40.0; score=223.982011431; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=3; seq_a_deletion=0; score_norm=3.61261308759; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; seq_b_single=46; \n+ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg\n++\n+dddedddddddddedddddddddedddaddbddddddddddddedd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~b~~~~~~~~b~~~~ddddddddddabbb^bdddddddddddcddddddddcddddddddd\n+@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS ali_length=63; direction=left; seq_ab_match=60; sminR=40.0; score=227.883189945; seq_a_mismatch=3; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; score_norm=3.61719349119; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; seq_b_single=45; \n+ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtttcaggctgttgctagtagtactctggcgaacattcttgtttattgaatgtttatgtttagggctaagcatagtggggtatctaagatattcgg\n++\n+ddcdddddddddddddddeddddddddddddddddddddcddddd~b~~~~~~b~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddddddddddddddddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS ali_length=62; direction=left; seq_ab_match=60; sminR=40.0; score=231.893859399; seq_a_mismatch=2; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; score_norm=3.7402235387; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; seq_b_single=46; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctgttgccgctagtactctggtgaacaattttgtttgtgtaattatttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+ddddddddddddddddddcddddddddddddd\\ddeddecddddddb~~~b~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddddcddddddcdddddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS ali_length=62; direction=left; '..b'tagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg\n++\n+ddddddcddddddddddddd`dcdddddaddaddddbdddddddc~~~~~~~~~{~~~~~~~~zxy~~|~~~~ru~~~~~~~~~~~~~~~~~~{~~p~~~~~~~~~~~ddddddddddabaP`ddddabddddddddddddddddcdcdaddd\n+@HELIUM_000100422_612GNAAXX:7:75:9674:16966#0/2_CONS ali_length=58; direction=right; seq_ab_match=57; sminR=40.0; score=224.000075421; seq_a_mismatch=0; seq_b_deletion=50; seq_b_mismatch=1; seq_a_deletion=50; score_norm=3.86207026589; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; seq_b_single=0; \n+ccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg\n++\n+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~~~~\n+@HELIUM_000100422_612GNAAXX:7:59:15367:8376#0/2_CONS ali_length=62; direction=left; seq_ab_match=62; sminR=40.0; score=247.996374666; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; score_norm=3.99994152687; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; seq_b_single=46; \n+ccgaagtagttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctactacttcgg\n++\n+ddddddddddddddddddddddddddddddddddddddddddddad~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddddddddddedddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:29:1328:13185#0/2_CONS ali_length=63; direction=left; seq_ab_match=59; sminR=40.0; score=223.94591652; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=4; seq_a_deletion=0; score_norm=3.55469708763; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; seq_b_single=45; \n+ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg\n++\n+ddddddddddddccdddddddddeddddddddddddddddedadd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W[~~~~~~~~~~~~~~~~~~~~~~~b~~~b~dddcdddddddcddddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:30:16081:4486#0/2_CONS ali_length=63; direction=left; seq_ab_match=62; sminR=40.0; score=243.950667893; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=1; seq_a_deletion=0; score_norm=3.87223282369; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; seq_b_single=45; \n+ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtttcaggctgttgctagtagtactctggcgaacattcttgtttattgaatgtttatgtttagggctaagcatagtggggtatctaagatattcgg\n++\n+ddddddddddddddddddddddddddddddddddddddcdddddd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~dddeddddddddddadddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:104:10274:7999#0/2_CONS ali_length=63; direction=left; seq_ab_match=63; sminR=40.0; score=251.962499638; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; score_norm=3.99940475616; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; seq_b_single=45; \n+ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg\n++\n+dddcdddddddddddedddddddddddccdddddddddddddddd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddd^ddddddddddddddddddddddddcddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:14:7706:12338#0/2_CONS ali_length=62; direction=left; seq_ab_match=59; sminR=40.0; score=223.864093999; seq_a_mismatch=2; seq_b_deletion=0; seq_b_mismatch=1; seq_a_deletion=0; score_norm=3.61071119354; seq_b_insertion=0; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; seq_b_single=46; \n+ccgaagtagtagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaataattttgttatattaattacttgtgtttagggctaagcatagtggggtatctaactacttcgg\n++\n+dddcddcddcdbdbddddddddddddddddddcdddddccaddddd~~~~~~b~~~~~~~~~~~x~~~~wyZq~mv~}}~~~~~~~~~P~~~~~~~~~~~~~~~~~~~d^cddddddddcdddadddddddddddddddddddddddddddddd\n' |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/input_ngsfilter_extrafile.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input_ngsfilter_extrafile.txt Wed Apr 12 17:38:18 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +wolf_diet 13a_F730603 aattaac TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 15a_F730814 gaagtag TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 26a_F040644 gaatatc TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ +wolf_diet 29a_F260619 gcctcct TTAGATACCCCACTATGC TAGAACAGGCTCCTCTAG F @ |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_ngsfilter.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ngsfilter.fastq Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,952 @@\n+@HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP sample=29a_F260619; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gcctcct; reverse_tag=gcctcct; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=47; sminR=40.0; seq_b_mismatch=13; seq_a_mismatch=1; tail_quality=67.0; seq_b_deletion=1; mid_quality=69.1492537313; seq_a_deletion=0; seq_b_single=46; score=115.761290673; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=67.0; avg_quality=68.8701298701; sminL=40.0; seq_a_single=46; score_norm=1.86711759151; seq_b_insertion=1; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaatagctcaaaactcaaaggacttggcggtgctttataccctt\n++\n+cacdddddddddddddc\\d~b~~~b~~~~~~b`ryK~|uxyXk`}~ccBBccBcccBcBcccBcBccccccc~~~~b|~~xdbaddaaWcccdaadddda\n+@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP sample=29a_F260619; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gcctcct; reverse_tag=gcctcct; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=60; sminR=40.0; seq_b_mismatch=2; seq_a_mismatch=0; tail_quality=66.9; seq_b_deletion=0; mid_quality=78.447761194; seq_a_deletion=0; seq_b_single=46; score=231.881364714; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=67.0; avg_quality=76.9545454545; sminL=40.0; seq_a_single=46; score_norm=3.74002201152; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+dddcdddddcddddddd]d~b~~~~~~~~~~~~~Z~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~ddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP sample=29a_F260619; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gcctcct; reverse_tag=gcctcct; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=52; sminR=40.0; seq_b_mismatch=5; seq_a_mismatch=5; tail_quality=67.0; seq_b_deletion=0; mid_quality=75.0820895522; seq_a_deletion=0; seq_b_single=46; score=167.91734192; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=66.6; avg_quality=74.0064935065; sminL=40.0; seq_a_single=46; score_norm=2.70834422451; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+d`cdddddcd`ddddaa\\b~`~~~~~~~~b~~~~]~b~V~~~~~~~~~~~~~~~~`~~^Zs~r|~~~st~|z|v||^~~|TY``accL]`\\`daZddddd\n+@HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB reverse_score=72.0; reverse_match=tagaacaggctcctctag; seq_length=100; sample=29a_F260619; experiment=wolf_diet; forward_tag=gcctcct; reverse_tag=gcctcct; reverse_primer=tagaacaggctcctctag; status=full; forward_score=72.0; direction=forward; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; ali_length=62; seq_ab_match=59; sminR=40.0; seq_b_mismatch=3; seq_a_mismatch=0; tail_quality=66.9; seq_b_deletion=0; mid_quality=78.2537313433; seq_a_deletion=0; seq_b_single=46; score=223.982011431; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=67.1; avg_quality=76.7922077922; sminL=40.0; seq_a_single=46; score_norm=3.61261308759; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+addbddddddddddddedd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~b~~~~~~~~b~~~~ddddddddddabbb^bddd\n+@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP sample=26a_F040644; experiment=wolf_diet; seq_length=99; forward_score=72.0; for'..b'taacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+dddddddddddddddddad~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddddddddddeddddd\n+@HELIUM_000100422_612GNAAXX:7:29:1328:13185#0/2_CONS_SUB_SUB reverse_score=72.0; reverse_match=tagaacaggctcctctag; seq_length=99; sample=26a_F040644; experiment=wolf_diet; forward_tag=gaatatc; reverse_tag=gaatatc; reverse_primer=tagaacaggctcctctag; status=full; forward_score=72.0; direction=forward; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; ali_length=63; seq_ab_match=59; sminR=40.0; seq_b_mismatch=4; seq_a_mismatch=0; tail_quality=67.0; seq_b_deletion=0; mid_quality=78.3007518797; seq_a_deletion=0; seq_b_single=45; score=223.94591652; seq_a_insertion=0; mode=alignment; seq_length_ori=153; head_quality=67.0; avg_quality=76.8235294118; sminL=40.0; seq_a_single=45; score_norm=3.55469708763; seq_b_insertion=0; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+dddddddddddddedadd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W[~~~~~~~~~~~~~~~~~~~~~~~b~~~b~dddcdddddddcdddddd\n+@HELIUM_000100422_612GNAAXX:7:30:16081:4486#0/2_CONS_SUB_SUB_CMP sample=26a_F040644; experiment=wolf_diet; seq_length=99; forward_score=72.0; forward_tag=gaatatc; reverse_tag=gaatatc; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=63; seq_ab_match=62; sminR=40.0; seq_b_mismatch=1; seq_a_mismatch=0; tail_quality=67.0; seq_b_deletion=0; mid_quality=79.0902255639; seq_a_deletion=0; seq_b_single=45; score=243.950667893; seq_a_insertion=0; mode=alignment; seq_length_ori=153; head_quality=67.0; avg_quality=77.5098039216; sminL=40.0; seq_a_single=45; score_norm=3.87223282369; seq_b_insertion=0; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+dddaddddddddddeddd~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddddddcddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:104:10274:7999#0/2_CONS_SUB_SUB reverse_score=72.0; reverse_match=tagaacaggctcctctag; seq_length=99; sample=26a_F040644; experiment=wolf_diet; forward_tag=gaatatc; reverse_tag=gaatatc; reverse_primer=tagaacaggctcctctag; status=full; forward_score=72.0; direction=forward; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; ali_length=63; seq_ab_match=63; sminR=40.0; seq_b_mismatch=0; seq_a_mismatch=0; tail_quality=67.0; seq_b_deletion=0; mid_quality=79.2556390977; seq_a_deletion=0; seq_b_single=45; score=251.962499638; seq_a_insertion=0; mode=alignment; seq_length_ori=153; head_quality=66.9; avg_quality=77.6470588235; sminL=40.0; seq_a_single=45; score_norm=3.99940475616; seq_b_insertion=0; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+ccdddddddddddddddd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddd^ddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:14:7706:12338#0/2_CONS_SUB_SUB_CMP sample=15a_F730814; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gaagtag; reverse_tag=gaagtag; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=59; sminR=40.0; seq_b_mismatch=1; seq_a_mismatch=2; tail_quality=67.0; seq_b_deletion=0; mid_quality=77.6194029851; seq_a_deletion=0; seq_b_single=46; score=223.864093999; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=66.7; avg_quality=76.2207792208; sminL=40.0; seq_a_single=46; score_norm=3.61071119354; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+dddadddcddddddddc^d~~~~~~~~~~~~~~~~~~~P~~~~~~~~~}}~vm~qZyw~~~~x~~~~~~~~~~~b~~~~~~dddddaccdddddcddddd\n' |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_ngsfilter_error_3.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ngsfilter_error_3.fastq Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,952 @@\n+@HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP sample=29a_F260619; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gcctcct; reverse_tag=gcctcct; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=47; sminR=40.0; seq_b_mismatch=13; seq_a_mismatch=1; tail_quality=67.0; seq_b_deletion=1; mid_quality=69.1492537313; seq_a_deletion=0; seq_b_single=46; score=115.761290673; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=67.0; avg_quality=68.8701298701; sminL=40.0; seq_a_single=46; score_norm=1.86711759151; seq_b_insertion=1; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaatagctcaaaactcaaaggacttggcggtgctttataccctt\n++\n+cacdddddddddddddc\\d~b~~~b~~~~~~b`ryK~|uxyXk`}~ccBBccBcccBcBcccBcBccccccc~~~~b|~~xdbaddaaWcccdaadddda\n+@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP sample=29a_F260619; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gcctcct; reverse_tag=gcctcct; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=60; sminR=40.0; seq_b_mismatch=2; seq_a_mismatch=0; tail_quality=66.9; seq_b_deletion=0; mid_quality=78.447761194; seq_a_deletion=0; seq_b_single=46; score=231.881364714; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=67.0; avg_quality=76.9545454545; sminL=40.0; seq_a_single=46; score_norm=3.74002201152; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+dddcdddddcddddddd]d~b~~~~~~~~~~~~~Z~~~~~~~~~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~ddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP sample=29a_F260619; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gcctcct; reverse_tag=gcctcct; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=52; sminR=40.0; seq_b_mismatch=5; seq_a_mismatch=5; tail_quality=67.0; seq_b_deletion=0; mid_quality=75.0820895522; seq_a_deletion=0; seq_b_single=46; score=167.91734192; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=66.6; avg_quality=74.0064935065; sminL=40.0; seq_a_single=46; score_norm=2.70834422451; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+d`cdddddcd`ddddaa\\b~`~~~~~~~~b~~~~]~b~V~~~~~~~~~~~~~~~~`~~^Zs~r|~~~st~|z|v||^~~|TY``accL]`\\`daZddddd\n+@HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB reverse_score=72.0; reverse_match=tagaacaggctcctctag; seq_length=100; sample=29a_F260619; experiment=wolf_diet; forward_tag=gcctcct; reverse_tag=gcctcct; reverse_primer=tagaacaggctcctctag; status=full; forward_score=72.0; direction=forward; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; ali_length=62; seq_ab_match=59; sminR=40.0; seq_b_mismatch=3; seq_a_mismatch=0; tail_quality=66.9; seq_b_deletion=0; mid_quality=78.2537313433; seq_a_deletion=0; seq_b_single=46; score=223.982011431; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=67.1; avg_quality=76.7922077922; sminL=40.0; seq_a_single=46; score_norm=3.61261308759; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+addbddddddddddddedd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~b~~~~~~~~b~~~~ddddddddddabbb^bddd\n+@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP sample=26a_F040644; experiment=wolf_diet; seq_length=99; forward_score=72.0; for'..b'taacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+dddddddddddddddddad~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddddddddddeddddd\n+@HELIUM_000100422_612GNAAXX:7:29:1328:13185#0/2_CONS_SUB_SUB reverse_score=72.0; reverse_match=tagaacaggctcctctag; seq_length=99; sample=26a_F040644; experiment=wolf_diet; forward_tag=gaatatc; reverse_tag=gaatatc; reverse_primer=tagaacaggctcctctag; status=full; forward_score=72.0; direction=forward; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; ali_length=63; seq_ab_match=59; sminR=40.0; seq_b_mismatch=4; seq_a_mismatch=0; tail_quality=67.0; seq_b_deletion=0; mid_quality=78.3007518797; seq_a_deletion=0; seq_b_single=45; score=223.94591652; seq_a_insertion=0; mode=alignment; seq_length_ori=153; head_quality=67.0; avg_quality=76.8235294118; sminL=40.0; seq_a_single=45; score_norm=3.55469708763; seq_b_insertion=0; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+dddddddddddddedadd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W[~~~~~~~~~~~~~~~~~~~~~~~b~~~b~dddcdddddddcdddddd\n+@HELIUM_000100422_612GNAAXX:7:30:16081:4486#0/2_CONS_SUB_SUB_CMP sample=26a_F040644; experiment=wolf_diet; seq_length=99; forward_score=72.0; forward_tag=gaatatc; reverse_tag=gaatatc; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=63; seq_ab_match=62; sminR=40.0; seq_b_mismatch=1; seq_a_mismatch=0; tail_quality=67.0; seq_b_deletion=0; mid_quality=79.0902255639; seq_a_deletion=0; seq_b_single=45; score=243.950667893; seq_a_insertion=0; mode=alignment; seq_length_ori=153; head_quality=67.0; avg_quality=77.5098039216; sminL=40.0; seq_a_single=45; score_norm=3.87223282369; seq_b_insertion=0; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+dddaddddddddddeddd~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddddddcddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:104:10274:7999#0/2_CONS_SUB_SUB reverse_score=72.0; reverse_match=tagaacaggctcctctag; seq_length=99; sample=26a_F040644; experiment=wolf_diet; forward_tag=gaatatc; reverse_tag=gaatatc; reverse_primer=tagaacaggctcctctag; status=full; forward_score=72.0; direction=forward; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; ali_length=63; seq_ab_match=63; sminR=40.0; seq_b_mismatch=0; seq_a_mismatch=0; tail_quality=67.0; seq_b_deletion=0; mid_quality=79.2556390977; seq_a_deletion=0; seq_b_single=45; score=251.962499638; seq_a_insertion=0; mode=alignment; seq_length_ori=153; head_quality=66.9; avg_quality=77.6470588235; sminL=40.0; seq_a_single=45; score_norm=3.99940475616; seq_b_insertion=0; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct\n++\n+ccdddddddddddddddd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddd^ddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:14:7706:12338#0/2_CONS_SUB_SUB_CMP sample=15a_F730814; experiment=wolf_diet; seq_length=100; forward_score=72.0; forward_tag=gaagtag; reverse_tag=gaagtag; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=59; sminR=40.0; seq_b_mismatch=1; seq_a_mismatch=2; tail_quality=67.0; seq_b_deletion=0; mid_quality=77.6194029851; seq_a_deletion=0; seq_b_single=46; score=223.864093999; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=66.7; avg_quality=76.2207792208; sminL=40.0; seq_a_single=46; score_norm=3.61071119354; seq_b_insertion=0; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt\n++\n+dddadddcddddddddc^d~~~~~~~~~~~~~~~~~~~P~~~~~~~~~}}~vm~qZyw~~~~x~~~~~~~~~~~b~~~~~~dddddaccdddddcddddd\n' |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_ngsfilter_unidentified.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_ngsfilter_unidentified.fastq Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| @@ -0,0 +1,44 @@ +@HELIUM_000100422_612GNAAXX:7:1:9007:3289#0/2_CONS_SUB_SUB_CMP error=Cannot assign sequence to a sample; forward_score=72.0; forward_tag=atctctc; reverse_tag=atctctc; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_score=72.0; status=full; direction=reverse; reverse_match=tagaacaggctcctctag; reverse_primer=tagaacaggctcctctag; ali_length=62; seq_ab_match=60; sminR=40.0; seq_b_mismatch=0; seq_a_mismatch=2; tail_quality=67.0; seq_b_deletion=0; mid_quality=78.5671641791; seq_a_deletion=0; seq_b_single=46; score=231.83380127; seq_a_insertion=0; mode=alignment; seq_length_ori=154; head_quality=67.0; avg_quality=77.0649350649; sminL=40.0; seq_a_single=46; score_norm=3.7392548592; seq_b_insertion=0; +ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt ++ +ddddddddddddddcddbd~~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~bddddddddddddddddddd +@HELIUM_000100422_612GNAAXX:7:1:8849:9880#0/2_PairEnd sminR=40.0; pairend_limit=108; tail_quality=64.3; mid_quality=37.8724489796; ali_dir=left; score=25.9064763088; mode=joined; error=No primer match; head_quality=33.0; avg_quality=38.8703703704; sminL=40.0; +ggacgggagagggggggggggggggaaggggggggttttggggggggggggccgttttaaaaaaaaaaaaaaaacaacgtgacatggcacagccgtcacaactgtcagctgacgaccactggcagtgagtctactctcctattttgttttttttttcaagcagaagacggcatacgatatcggtctcggcattcctgctgaaccgctcttccgatc ++ +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB_`X`b[`T[ZWHZTWU]]b]]TZ^__\^`\OOOOO^`^Z^_ba_bbbbbb +@HELIUM_000100422_612GNAAXX:7:1:8649:5297#0/2_CONS ali_length=104; direction=right; seq_ab_match=104; sminR=40.0; seq_b_mismatch=0; seq_a_mismatch=0; tail_quality=93.0; seq_b_deletion=4; mid_quality=93.0; seq_a_deletion=4; seq_b_single=0; score=415.823014771; seq_a_insertion=0; mode=alignment; error=No primer match; head_quality=93.0; avg_quality=93.0; sminL=40.0; seq_a_single=0; score_norm=3.99829821895; seq_b_insertion=0; +ccagcgagatcccattgagtctctgcacctatcctttttttcgttttctgaatctttgtttggaaaaaaacaggatttggctcaggattgcccgatctcgctgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:1:8702:15835#0/2_CONS ali_length=85; direction=left; seq_ab_match=85; sminR=40.0; seq_b_mismatch=0; seq_a_mismatch=0; tail_quality=67.0; seq_b_deletion=0; mid_quality=86.8828828829; seq_a_deletion=0; seq_b_single=23; score=339.959438284; seq_a_insertion=0; mode=alignment; error=No primer match; head_quality=67.0; avg_quality=83.8473282443; sminL=40.0; seq_a_single=23; score_norm=3.99952280334; seq_b_insertion=0; +cccatcgctcagatatccgttgccgagagtcgtgtagattatatagaattgcaactcggggtgcggccagcaagccagccacatcccctcgttaggcacagtgttccttgacgccttcggtgagcgatggg ++ +ddddddddddddddddddddddd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~{~~~~~~~~ddddddddddddddddddddddd +@HELIUM_000100422_612GNAAXX:7:1:8613:9165#0/2_CONS ali_length=101; direction=left; seq_ab_match=99; sminR=40.0; seq_b_mismatch=0; seq_a_mismatch=2; tail_quality=74.8; seq_b_deletion=0; mid_quality=92.4105263158; seq_a_deletion=0; seq_b_single=7; score=387.825112777; seq_a_insertion=0; mode=alignment; error=No primer match; head_quality=74.8; avg_quality=89.347826087; sminL=40.0; seq_a_single=7; score_norm=3.83985260176; seq_b_insertion=0; +ccagagcgagtgggcaatcctgagccaaatctttatttttagaaaaacaaaagggcttcagaaagcaaaaataaacataaaggataggtgcagagactcaatggactcgctctgg ++ +ddddddd~~~~b~~~~~~b~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddddddd +@HELIUM_000100422_612GNAAXX:7:1:8670:8750#0/2_CONS ali_length=90; direction=right; seq_ab_match=90; sminR=40.0; seq_b_mismatch=0; seq_a_mismatch=0; tail_quality=93.0; seq_b_deletion=18; mid_quality=93.0; seq_a_deletion=18; seq_b_single=0; score=359.914979278; seq_a_insertion=0; mode=alignment; error=No primer match; head_quality=93.0; avg_quality=93.0; sminL=40.0; seq_a_single=0; score_norm=3.99905532531; seq_b_insertion=0; +ccgaggcttactaggattagataccctattatttttgaatgttaatgtttgtttgcttgagtagtattagttatgttcttgaaagcctcg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:1:8732:6209#0/2_PairEnd sminR=40.0; pairend_limit=108; tail_quality=57.9; mid_quality=36.5408163265; ali_dir=right; score=15.9727840143; mode=joined; error=No primer match; head_quality=33.0; avg_quality=37.3657407407; sminL=40.0; +gctctacagaggcgggggggggggagaaggggaaatcatggggggggggggcgacatctaaaaacatacatacaacccacacctcctaccacacagctcccagcgcaaagatagatcatgatggtaagtagaggcaaatgagatcatctatttttttcaaagagaagacggcatacgatatcggtctcggcattcctgctaaccgctcttccgatc ++ +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBa[]aa_aaaa]aa`]a\[aZ`\ZcMWR]Z````` +@HELIUM_000100422_612GNAAXX:7:1:8858:2566#0/2_PairEnd sminR=40.0; pairend_limit=108; tail_quality=65.0; mid_quality=40.6581632653; ali_dir=left; score=15.7312871104; mode=joined; error=No primer match; head_quality=33.0; avg_quality=41.4305555556; sminL=40.0; +ggctcggagagagggggggggggggggaggggggggatccgggggggggggggtcttacaaaaaaacacaaaacacataaccactctcacacccacactcgcacacccggatgtggttgtggtgtgcgcgtggatggtgtggtgtggtttttttttcaagcagaagacggcatacgagatcggtctcggcattcctgctgaaccgctcttccgatc ++ +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBa_a_a]aaaa_`Y`_W]Y[S]]aaaabbbbbcbbbbbbbbbbbbb`bbbbbbbbbbbbbb +@HELIUM_000100422_612GNAAXX:7:1:8644:15229#0/2_CONS ali_length=106; direction=left; seq_ab_match=103; sminR=40.0; seq_b_mismatch=2; seq_a_mismatch=1; tail_quality=83.8; seq_b_deletion=0; mid_quality=90.8; seq_a_deletion=0; seq_b_single=2; score=399.617128202; seq_a_insertion=0; mode=alignment; error=No primer match; head_quality=87.8; avg_quality=89.8909090909; sminL=40.0; seq_a_single=2; score_norm=3.76997290756; seq_b_insertion=0; +cacacgctctccattgagtctctgcacctatcctttttgattttcgctttctgaatctttgtttgttttcggaaaacgtgatttggctcaggattgcccagagcgtgtgg ++ +dd~~~~~~~~~~~~~~~~~~~~~~~~{~~~~b~~~~~~~~~{|~~~~s|~v~~|p~~~~~~~~~~~u~qy~a~~~~~~~x~|~~~~z{~|~o|~{yvwwy~~|~~[~~cb +@HELIUM_000100422_612GNAAXX:7:1:8613:5665#0/2_CONS ali_length=90; direction=right; seq_ab_match=89; sminR=40.0; seq_b_mismatch=1; seq_a_mismatch=0; tail_quality=90.2; seq_b_deletion=18; mid_quality=93.0; seq_a_deletion=18; seq_b_single=0; score=351.879189487; seq_a_insertion=0; mode=alignment; error=No primer match; head_quality=93.0; avg_quality=92.6888888889; sminL=40.0; seq_a_single=0; score_norm=3.90976877208; seq_b_insertion=0; +ccttcctggggtagtactctggcgaataattttgttatattaattacttgtgtttagggctaagcatagtggggtatctaaccaggaagg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:1:8823:6682#0/2_PairEnd sminR=40.0; pairend_limit=108; tail_quality=64.9; mid_quality=41.693877551; ali_dir=right; score=15.9839512414; mode=joined; error=No primer match; head_quality=33.0; avg_quality=42.3657407407; sminL=40.0; +gatcgggagagcgtcgtgtaggggaagagggtagatctcggggggggccgtatcattaaaaaaaaaaacaaacatcagcacgaagcacatgacaccgcctagctatcaatcttgagatgagatcagacatctgtttgttttcttttgtttttttttcaagcagaagacggcatacgatatcggtctcggcattcctgctgaaccgctcttccgatc ++ +BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB_aa]a`]^S``aabaab^bbbbab_c``abbbbbbbcbbbbbbbbbbbbbbbbbbbbbbbbbbab |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obiannotate.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obiannotate.fasta Wed Apr 12 17:38:18 2017 -0400 |
| b |
| b"@@ -0,0 +1,172 @@\n+>HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; seq_rank=1; count=1; seq_length=100; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaat\n+agctcaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; seq_rank=2; count=1; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; seq_rank=3; count=1; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaag\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB merged_sample={'29a_F260619': 30, '15a_F730814': 31}; count=61; seq_length=100; seq_rank=4; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 64}; seq_rank=5; count=64; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 3}; seq_rank=6; count=3; seq_length=100; \n+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS_SUB_SUB merged_sample={'29a_F260619': 2}; seq_rank=7; count=2; seq_length=100; \n+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB merged_sample={'13a_F730603': 46}; count=46; seq_length=100; seq_rank=8; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:24:16230:12703#0/2_CONS_SUB_SUB_CMP merged_sample={'15a_F730814': 1}; seq_rank=9; count=1; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttatcccctt\n+>HELIUM_000100422_612GNAAXX:7:4:4214:9434#0/2_CONS_SUB_SUB merged_sample={'13a_F730603': 1}; seq_rank=10; count=1; seq_length=100; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacaggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:13:6954:13039#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=11; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata\n+gcttaaaactcaaaggacttggcggtgctttatatccct\n+>HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=12; count=1; seq_length=99; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcttaaaactcaaagaactgggcggtgctttatatcccg\n+>HELIUM_000100422_612GNAAXX:7:115:17402:4174#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1, '15a_F730814': 1}; seq_rank=13; count=2; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactacctgcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:78:7151:19928#0/2_CONS_SUB_SUB merged_sample={'26a_F040644': 1}; seq_rank=14; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacgagaatgttcgccagtgtacttctagcaaca\n+ggctgaaactcaaaggacttggcggtggtttacatccct\n+>HELIUM_000100422_612GNAAXX:7:38:10813:16867#0/2_CONS_SUB_SUB merged_sample={'26a_F040644': 2}; seq_rank=15; count=2; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgtttgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB merged_sample={'29a_F260619': 7}; seq_rank=16; count=7; seq_length=4; \n+tttt\n+>HELIUM_000100422_612GNAAXX:7:16:16357:19948#0/2_CONS_SUB_SUB merged_sample={'26a_F040644': 1}; seq_rank=17; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagca"..b"1}; seq_rank=42; count=1; seq_length=100; \n+ctagccttaaacacaaatagttatgcaaacacaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:105:14135:6905#0/2_CONS_SUB_SUB merged_sample={'29a_F260619': 1}; seq_rank=43; count=1; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaattattcaccagagtactagcggcaac\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:76:18268:14980#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; seq_rank=44; count=1; seq_length=100; \n+ttacccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:25:7789:3090#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; seq_rank=45; count=1; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactacaggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:42:19757:3800#0/2_CONS_SUB_SUB_CMP merged_sample={'15a_F730814': 1}; seq_rank=46; count=1; seq_length=99; \n+ttagccctaaacacaagtaattaatatacaaaattattcgccagagtactaccggcaata\n+gcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:116:14244:17926#0/2_CONS_SUB_SUB merged_sample={'26a_F040644': 1}; seq_rank=47; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgttcgcaagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:72:12959:5736#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=48; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacacccct\n+>HELIUM_000100422_612GNAAXX:7:7:15538:8325#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=49; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgtcggccagagtactactagcaaca\n+gcatgaaactcaaagaactgggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:120:16005:7955#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=50; count=1; seq_length=98; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gccgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:10:9237:10532#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; seq_rank=51; count=1; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaataattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:7:11998:4462#0/2_CONS_SUB_SUB merged_sample={'26a_F040644': 1}; seq_rank=52; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtagtactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=53; count=1; seq_length=99; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:3:17077:6562#0/2_CONS_SUB_SUB_CMP merged_sample={'15a_F730814': 1}; seq_rank=54; count=1; seq_length=100; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:19:4311:13343#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=55; count=1; seq_length=99; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactacgagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB merged_sample={'15a_F730814': 1}; seq_rank=56; count=1; seq_length=100; \n+ttagccctaaacacaagacattaatataacgagattaatcgacagagtactaccggctat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB merged_sample={'13a_F730603': 1}; seq_rank=57; count=1; seq_length=100; \n+ctagccttaaacacaaatagttatgcagacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; seq_rank=58; count=1; seq_length=99; \n+ttagccctaaacatgaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obiclean_advanced.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obiclean_advanced.fasta Wed Apr 12 17:38:18 2017 -0400 |
| b |
| b"@@ -0,0 +1,172 @@\n+>HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; obiclean_internalcount=0; obiclean_singletoncount=1; count=1; seq_length=100; obiclean_headcount=0; seq_rank=1; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaat\n+agctcaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=100; obiclean_headcount=0; seq_rank=2; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=100; obiclean_headcount=0; seq_rank=3; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaag\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB merged_sample={'29a_F260619': 30, '15a_F730814': 31}; obiclean_internalcount=0; obiclean_singletoncount=0; count=61; seq_length=100; obiclean_headcount=2; seq_rank=4; obiclean_samplecount=2; obiclean_head=True; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 64}; obiclean_internalcount=0; obiclean_singletoncount=0; count=64; seq_length=99; obiclean_headcount=1; seq_rank=5; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 3}; obiclean_internalcount=0; obiclean_singletoncount=1; count=3; seq_length=100; obiclean_headcount=0; seq_rank=6; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS_SUB_SUB merged_sample={'29a_F260619': 2}; obiclean_internalcount=0; obiclean_singletoncount=1; count=2; seq_length=100; obiclean_headcount=0; seq_rank=7; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB merged_sample={'13a_F730603': 46}; obiclean_internalcount=0; obiclean_singletoncount=0; count=46; seq_length=100; obiclean_headcount=1; seq_rank=8; obiclean_samplecount=1; obiclean_head=True; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:24:16230:12703#0/2_CONS_SUB_SUB_CMP merged_sample={'15a_F730814': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=100; obiclean_headcount=0; seq_rank=9; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttatcccctt\n+>HELIUM_000100422_612GNAAXX:7:4:4214:9434#0/2_CONS_SUB_SUB merged_sample={'13a_F730603': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=100; obiclean_headcount=0; seq_rank=10; obiclean_samplecount=1; obiclean_head=False; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacaggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:13:6954:13039#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; obiclean_internalcount=0; obiclean_singletoncount=1; count=1; seq_length=99; obiclean_headcount=0; seq_rank=11; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata\n+gcttaaaactcaaaggacttggcggtgctttatatc"..b"gaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:72:12959:5736#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=99; obiclean_headcount=0; seq_rank=48; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacacccct\n+>HELIUM_000100422_612GNAAXX:7:7:15538:8325#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; obiclean_internalcount=0; obiclean_singletoncount=1; count=1; seq_length=99; obiclean_headcount=0; seq_rank=49; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgtcggccagagtactactagcaaca\n+gcatgaaactcaaagaactgggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:120:16005:7955#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=98; obiclean_headcount=0; seq_rank=50; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gccgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:10:9237:10532#0/2_CONS_SUB_SUB_CMP merged_sample={'29a_F260619': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=100; obiclean_headcount=0; seq_rank=51; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaataattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:7:11998:4462#0/2_CONS_SUB_SUB merged_sample={'26a_F040644': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=99; obiclean_headcount=0; seq_rank=52; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtagtactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; obiclean_internalcount=0; obiclean_singletoncount=1; count=1; seq_length=99; obiclean_headcount=0; seq_rank=53; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:3:17077:6562#0/2_CONS_SUB_SUB_CMP merged_sample={'15a_F730814': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=100; obiclean_headcount=0; seq_rank=54; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:19:4311:13343#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=99; obiclean_headcount=0; seq_rank=55; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactacgagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB merged_sample={'15a_F730814': 1}; obiclean_internalcount=0; obiclean_singletoncount=1; count=1; seq_length=100; obiclean_headcount=0; seq_rank=56; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagacattaatataacgagattaatcgacagagtactaccggctat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB merged_sample={'13a_F730603': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=100; obiclean_headcount=0; seq_rank=57; obiclean_samplecount=1; obiclean_head=False; \n+ctagccttaaacacaaatagttatgcagacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP merged_sample={'26a_F040644': 1}; obiclean_internalcount=1; obiclean_singletoncount=0; count=1; seq_length=99; obiclean_headcount=0; seq_rank=58; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacatgaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obiclean_simple.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obiclean_simple.fasta Wed Apr 12 17:38:18 2017 -0400 |
| b |
| b"@@ -0,0 +1,67 @@\n+>HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP'}; seq_length=100; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=1; merged_sample={'29a_F260619': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaat\n+agctcaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB count=61; obiclean_count={'XXX': 81}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB'}; seq_length=100; obiclean_internalcount=0; obiclean_status={'XXX': 'h'}; seq_rank=4; merged_sample={'29a_F260619': 30, '15a_F730814': 31}; obiclean_samplecount=1; obiclean_headcount=1; obiclean_singletoncount=0; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP count=64; obiclean_count={'XXX': 77}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 'h'}; seq_rank=5; merged_sample={'26a_F040644': 64}; obiclean_samplecount=1; obiclean_headcount=1; obiclean_singletoncount=0; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP count=3; obiclean_count={'XXX': 3}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP'}; seq_length=100; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=6; merged_sample={'29a_F260619': 3}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB count=46; obiclean_count={'XXX': 52}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB'}; seq_length=100; obiclean_internalcount=0; obiclean_status={'XXX': 'h'}; seq_rank=8; merged_sample={'13a_F730603': 46}; obiclean_samplecount=1; obiclean_headcount=1; obiclean_singletoncount=0; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:13:6954:13039#0/2_CONS_SUB_SUB_CMP count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:13:6954:13039#0/2_CONS_SUB_SUB_CMP'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=11; merged_sample={'26a_F040644': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata\n+gcttaaaactcaaaggacttggcggtgctttatatccct\n+>HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=12; merged_sample={'26a_F040644': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcttaaaactcaaagaactgggcggtgctttatatcccg\n+>HELIUM_000100422_612GNAAXX:7:78:7151:19928#0/2_CONS_SUB_SUB count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:78:7151:19928#0/2_CONS_SUB_SUB'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=14; merged_sample={'26a_F040644': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncoun"..b"ttacaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:111:8478:1127#0/2_CONS_SUB_SUB_CMP count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:111:8478:1127#0/2_CONS_SUB_SUB_CMP'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=33; merged_sample={'26a_F040644': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctggaacgcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:81:15726:2345#0/2_CONS_SUB_SUB_CMP count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:81:15726:2345#0/2_CONS_SUB_SUB_CMP'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=34; merged_sample={'26a_F040644': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaagcactcggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:7:11110:17924#0/2_CONS_SUB_SUB count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:7:11110:17924#0/2_CONS_SUB_SUB'}; seq_length=100; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=35; merged_sample={'15a_F730814': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtcataccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:115:3625:10051#0/2_CONS_SUB_SUB count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:115:3625:10051#0/2_CONS_SUB_SUB'}; seq_length=5; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=38; merged_sample={'13a_F730603': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+caata\n+>HELIUM_000100422_612GNAAXX:7:105:14135:6905#0/2_CONS_SUB_SUB count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:105:14135:6905#0/2_CONS_SUB_SUB'}; seq_length=100; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=43; merged_sample={'29a_F260619': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacacaagtaattaatataacaaaattattcaccagagtactagcggcaac\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:7:15538:8325#0/2_CONS_SUB_SUB_CMP count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:7:15538:8325#0/2_CONS_SUB_SUB_CMP'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=49; merged_sample={'26a_F040644': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacataaacattcaataaacaagaatgtcggccagagtactactagcaaca\n+gcatgaaactcaaagaactgggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP'}; seq_length=99; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=53; merged_sample={'26a_F040644': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB count=1; obiclean_count={'XXX': 1}; obiclean_head=True; obiclean_cluster={'XXX': 'HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB'}; seq_length=100; obiclean_internalcount=0; obiclean_status={'XXX': 's'}; seq_rank=56; merged_sample={'15a_F730814': 1}; obiclean_samplecount=1; obiclean_headcount=0; obiclean_singletoncount=1; \n+ttagccctaaacacaagacattaatataacgagattaatcgacagagtactaccggctat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obiconvert.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obiconvert.fasta Wed Apr 12 17:38:18 2017 -0400 |
| b |
| b"@@ -0,0 +1,172 @@\n+>HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=1; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACACAAGTAATTATTATAACAAAATCATTCGCCAGAGTACTACCGGCAAT\n+AGCTCAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=2; obiclean_samplecount=1; obiclean_head=False; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTGTTCGCCAGAGTACTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=3; obiclean_samplecount=1; obiclean_head=False; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTATTCGCCAGAGTACTACCGGCAAG\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:24:16230:12703#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'15a_F730814': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=9; obiclean_samplecount=1; obiclean_head=False; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTATTCGCCAGAGTACTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATCCCCTT\n+>HELIUM_000100422_612GNAAXX:7:4:4214:9434#0/2_CONS_SUB_SUB count=1; merged_sample={'13a_F730603': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=10; obiclean_samplecount=1; obiclean_head=False; \n+CTAGCCTTAAACACAAATAGTTATGCAAACAAAACTATTCGCCAGAGTACTACAGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:13:6954:13039#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=11; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACATAAACATTCAATAAACAAGAATGTTCGCCAGAGGACTACTAGCAATA\n+GCTTAAAACTCAAAGGACTTGGCGGTGCTTTATATCCCT\n+>HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=12; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACATAGATAATTTTACAACAAAATAATTCGCCAGAGGACTACTAGCAATA\n+GCTTAAAACTCAAAGAACTGGGCGGTGCTTTATATCCCG\n+>HELIUM_000100422_612GNAAXX:7:78:7151:19928#0/2_CONS_SUB_SUB count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=14; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACATAAACATTCAATAAACGAGAATGTTCGCCAGTGTACTTCTAGCAACA\n+GGCTGAAACTCAAAGGACTTGGCGGTGGTTTACATCCCT\n+>HELIUM_000100422_612GNAAXX:7:16:16357:19948#0/2_CONS_SUB_SUB count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=17; obiclean_samplecount=1; obiclean_head=False; \n+TTAGCCCTAAACATAAACATTCAATAAACAAGAATGTTCGCCAGAGTACTACTAGCAACA\n+GCCTGAAACTCACAGGACTTGGCGGTGCTTTACATCCCT\n+>HELIUM_000100422_612GNAAXX:7:107:3570:18147#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=18; obiclean_samplecount=1; obiclean_head=False; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTATTCGCCAGAGTACTACCGGCAAT\n+AGCATAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:114:4511:17596#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=19; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTATTCGCCAGAGTGCTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACGCTT\n+>HELIUM_000"..b" \n+TTAGCCCTAAACACAAGACATTAATATAACGAGATTAATCGACAGAGTACTACCGGCTAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB count=1; merged_sample={'13a_F730603': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=57; obiclean_samplecount=1; obiclean_head=False; \n+CTAGCCTTAAACACAAATAGTTATGCAGACAAAACTATTCGCCAGAGTACTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=58; obiclean_samplecount=1; obiclean_head=False; \n+TTAGCCCTAAACATGAACATTCAATAAACAAGAATGTTCGCCAGAGTACTACTAGCAACA\n+GCCTGAAACTCAAAGGACTTGGCGGTGCTTTACATCCCT\n+>HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS_SUB_SUB count=2; merged_sample={'29a_F260619': 2}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=7; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACACAAGTAATTATTATAACAAAATTATTCGCCAGAGTACTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:115:17402:4174#0/2_CONS_SUB_SUB_CMP count=2; merged_sample={'29a_F260619': 1, '15a_F730814': 1}; obiclean_singletoncount=0; obiclean_internalcount=2; seq_length=100; obiclean_headcount=0; seq_rank=13; obiclean_samplecount=2; obiclean_head=False; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTATTCGCCAGAGTACTACCTGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:38:10813:16867#0/2_CONS_SUB_SUB count=2; merged_sample={'26a_F040644': 2}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=15; obiclean_samplecount=1; obiclean_head=False; \n+TTAGCCCTAAACATAAACATTCAATAAACAAGAATGTTTGCCAGAGTACTACTAGCAACA\n+GCCTGAAACTCAAAGGACTTGGCGGTGCTTTACATCCCT\n+>HELIUM_000100422_612GNAAXX:7:70:11798:2668#0/2_CONS_SUB_SUB count=2; merged_sample={'15a_F730814': 2}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=20; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTATTCGCCAGAGTACTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCTTT\n+>HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP count=3; merged_sample={'29a_F260619': 3}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=6; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACACAAATAATTACACAAACAAAATTGTTCACCAGAGTACTAGCGGCAAC\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB count=7; merged_sample={'29a_F260619': 7}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=4; obiclean_headcount=0; seq_rank=16; obiclean_samplecount=1; obiclean_head=True; \n+TTTT\n+>HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB count=46; merged_sample={'13a_F730603': 46}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=1; seq_rank=8; obiclean_samplecount=1; obiclean_head=True; \n+CTAGCCTTAAACACAAATAGTTATGCAAACAAAACTATTCGCCAGAGTACTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB count=61; merged_sample={'29a_F260619': 30, '15a_F730814': 31}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=2; seq_rank=4; obiclean_samplecount=2; obiclean_head=True; \n+TTAGCCCTAAACACAAGTAATTAATATAACAAAATTATTCGCCAGAGTACTACCGGCAAT\n+AGCTTAAAACTCAAAGGACTTGGCGGTGCTTTATACCCTT\n+>HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP count=64; merged_sample={'26a_F040644': 64}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=99; obiclean_headcount=1; seq_rank=5; obiclean_samplecount=1; obiclean_head=True; \n+TTAGCCCTAAACATAAACATTCAATAAACAAGAATGTTCGCCAGAGTACTACTAGCAACA\n+GCCTGAAACTCAAAGGACTTGGCGGTGCTTTACATCCCT\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obigrep_lmin.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obigrep_lmin.fastq Wed Apr 12 17:38:18 2017 -0400 |
| b |
| @@ -0,0 +1,32 @@ +@HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS ali_length=58; direction=right; seq_ab_match=55; sminR=40.0; seq_a_mismatch=3; seq_b_deletion=50; seq_b_mismatch=0; seq_a_deletion=50; seq_b_single=0; score=207.846895043; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.58356715591; seq_b_insertion=0; +ccgcctcctttagataccccactatgcttttctagaggagcctgttctaaggaggcgg ++ +~~~~~~Z~~~~~~~~~b~~~~~~~~~_~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:7:7916:16505#0/2_CONS ali_length=58; direction=right; seq_ab_match=58; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=50; seq_b_mismatch=0; seq_a_deletion=50; seq_b_single=0; score=231.999536374; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.99999200644; seq_b_insertion=0; +ccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:37:12979:6595#0/2_CONS ali_length=58; direction=right; seq_ab_match=58; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=50; seq_b_mismatch=0; seq_a_deletion=50; seq_b_single=0; score=231.998796685; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.99997925319; seq_b_insertion=0; +ccgcctcctttagataccccactatgcttttctagaggagcctgttctaaggaggcgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:96:8737:4973#0/2_CONS ali_length=58; direction=right; seq_ab_match=57; sminR=40.0; seq_a_mismatch=1; seq_b_deletion=50; seq_b_mismatch=0; seq_a_deletion=50; seq_b_single=0; score=223.980140585; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.86172656181; seq_b_insertion=0; +ccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:115:3625:10051#0/2_CONS ali_length=59; direction=right; seq_ab_match=59; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=49; seq_b_mismatch=0; seq_a_deletion=49; seq_b_single=0; score=235.999642017; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.99999393249; seq_b_insertion=0; +ccaattaacttagataccccactatgccaatactagaggagcctgttctagttaattgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:73:17068:16620#0/2_CONS ali_length=58; direction=right; seq_ab_match=57; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=50; seq_b_mismatch=1; seq_a_deletion=50; seq_b_single=0; score=223.962007947; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.86141393012; seq_b_insertion=0; +ccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~~|~ +@HELIUM_000100422_612GNAAXX:7:95:11283:2557#0/2_CONS ali_length=58; direction=right; seq_ab_match=57; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=50; seq_b_mismatch=1; seq_a_deletion=50; seq_b_single=0; score=223.999078974; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.86205308576; seq_b_insertion=0; +ccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~ +@HELIUM_000100422_612GNAAXX:7:75:9674:16966#0/2_CONS ali_length=58; direction=right; seq_ab_match=57; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=50; seq_b_mismatch=1; seq_a_deletion=50; seq_b_single=0; score=224.000075421; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.86207026589; seq_b_insertion=0; +ccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg ++ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~~~~ |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obigrep_predicat.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obigrep_predicat.fasta Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,980 @@\n+@HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS ali_length=62; direction=left; seq_ab_match=47; sminR=40.0; seq_a_mismatch=1; seq_b_deletion=1; seq_b_mismatch=13; seq_a_deletion=0; seq_b_single=46; score=115.761290673; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; score_norm=1.86711759151; seq_b_insertion=1; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttgagctattgccggtagtactctggcgaatgattttgttataataattacttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+dddddddddddbbdaddcddddddcadaddddaadcccWaaddabdx~~|b~~~~cccccccBcBcccBcBcccBccBBcc~}`kXyxu|~Kyr`b~~~~~~b~~~b~d\\cdddddddddddddcacddddcdddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS ali_length=62; direction=left; seq_ab_match=60; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=2; seq_a_deletion=0; seq_b_single=46; score=231.881364714; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; score_norm=3.74002201152; seq_b_insertion=0; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaacaattttgttatattaattacttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+ddddddddddddddddbdddddbddddddddddddddddddddddd~~~~~~~~~~~~~~~~~~}~~~~~~~~~~~~~~~~~~~~~~~~~~~Z~~~~~~~~~~~~~b~d]dddddddcdddddcddddddddddddddddddddddcddddddd\n+@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS ali_length=62; direction=left; seq_ab_match=52; sminR=40.0; seq_a_mismatch=5; seq_b_deletion=0; seq_b_mismatch=5; seq_a_deletion=0; seq_b_single=46; score=167.91734192; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; score_norm=2.70834422451; seq_b_insertion=0; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctcttgccggtagtactctggcgaataattttgttatattaattacttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+ddadddddcd`dcddddddddd^dd]ddddddZad`\\`]Lcca``YT|~~^||v|z|~ts~~~|r~sZ^~~`~~~~~~~~~~~~~~~~V~b~]~~~~b~~~~~~~~`~b\\aadddd`dcdddddc`dddccddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS ali_length=62; direction=left; seq_ab_match=59; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=3; seq_a_deletion=0; seq_b_single=46; score=223.982011431; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; score_norm=3.61261308759; seq_b_insertion=0; \n+ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg\n++\n+dddedddddddddedddddddddedddaddbddddddddddddedd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~b~~~~~~~~b~~~~ddddddddddabbb^bdddddddddddcddddddddcddddddddd\n+@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS ali_length=63; direction=left; seq_ab_match=60; sminR=40.0; seq_a_mismatch=3; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; seq_b_single=45; score=227.883189945; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; score_norm=3.61719349119; seq_b_insertion=0; \n+ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtttcaggctgttgctagtagtactctggcgaacattcttgtttattgaatgtttatgtttagggctaagcatagtggggtatctaagatattcgg\n++\n+ddcdddddddddddddddeddddddddddddddddddddcddddd~b~~~~~~b~~~~~~~~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddddddddddddddddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS ali_length=62; direction=left; seq_ab_match=60; sminR=40.0; seq_a_mismatch=2; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; seq_b_single=46; score=231.893859399; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; score_norm=3.7402235387; seq_b_insertion=0; \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctgttgccgctagtactctggtgaacaattttgtttgtgtaattatttgtgtttagggctaagcatagtggggtatctaaaggaggcgg\n++\n+ddddddddddddddddddcddddddddddddd\\ddeddecddddddb~~~b~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ddddcddddddcdddddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS ali_length=62; direction=left; '..b'tagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg\n++\n+ddddddcddddddddddddd`dcdddddaddaddddbdddddddc~~~~~~~~~{~~~~~~~~zxy~~|~~~~ru~~~~~~~~~~~~~~~~~~{~~p~~~~~~~~~~~ddddddddddabaP`ddddabddddddddddddddddcdcdaddd\n+@HELIUM_000100422_612GNAAXX:7:75:9674:16966#0/2_CONS ali_length=58; direction=right; seq_ab_match=57; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=50; seq_b_mismatch=1; seq_a_deletion=50; seq_b_single=0; score=224.000075421; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=0; score_norm=3.86207026589; seq_b_insertion=0; \n+ccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg\n++\n+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~b~~~~~~~~~~~~~~~\n+@HELIUM_000100422_612GNAAXX:7:59:15367:8376#0/2_CONS ali_length=62; direction=left; seq_ab_match=62; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; seq_b_single=46; score=247.996374666; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; score_norm=3.99994152687; seq_b_insertion=0; \n+ccgaagtagttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctactacttcgg\n++\n+ddddddddddddddddddddddddddddddddddddddddddddad~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddddddddddedddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:29:1328:13185#0/2_CONS ali_length=63; direction=left; seq_ab_match=59; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=4; seq_a_deletion=0; seq_b_single=45; score=223.94591652; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; score_norm=3.55469708763; seq_b_insertion=0; \n+ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg\n++\n+ddddddddddddccdddddddddeddddddddddddddddedadd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~W[~~~~~~~~~~~~~~~~~~~~~~~b~~~b~dddcdddddddcddddddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:30:16081:4486#0/2_CONS ali_length=63; direction=left; seq_ab_match=62; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=1; seq_a_deletion=0; seq_b_single=45; score=243.950667893; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; score_norm=3.87223282369; seq_b_insertion=0; \n+ccgaatatctagaacaggctcctctagagggatgtaaagcaccgccaagtcctttgagtttcaggctgttgctagtagtactctggcgaacattcttgtttattgaatgtttatgtttagggctaagcatagtggggtatctaagatattcgg\n++\n+ddddddddddddddddddddddddddddddddddddddcdddddd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~c~~~dddeddddddddddadddddddddddddddddddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:104:10274:7999#0/2_CONS ali_length=63; direction=left; seq_ab_match=63; sminR=40.0; seq_a_mismatch=0; seq_b_deletion=0; seq_b_mismatch=0; seq_a_deletion=0; seq_b_single=45; score=251.962499638; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=45; score_norm=3.99940475616; seq_b_insertion=0; \n+ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccctctagaggagcctgttctagatattcgg\n++\n+dddcdddddddddddedddddddddddccdddddddddddddddd~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dddddd^ddddddddddddddddddddddddcddddddddddddd\n+@HELIUM_000100422_612GNAAXX:7:14:7706:12338#0/2_CONS ali_length=62; direction=left; seq_ab_match=59; sminR=40.0; seq_a_mismatch=2; seq_b_deletion=0; seq_b_mismatch=1; seq_a_deletion=0; seq_b_single=46; score=223.864093999; seq_a_insertion=0; mode=alignment; sminL=40.0; seq_a_single=46; score_norm=3.61071119354; seq_b_insertion=0; \n+ccgaagtagtagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaataattttgttatattaattacttgtgtttagggctaagcatagtggggtatctaactacttcgg\n++\n+dddcddcddcdbdbddddddddddddddddddcdddddccaddddd~~~~~~b~~~~~~~~~~~x~~~~wyZq~mv~}}~~~~~~~~~P~~~~~~~~~~~~~~~~~~~d^cddddddddcdddadddddddddddddddddddddddddddddd\n' |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obisort.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obisort.fasta Wed Apr 12 17:38:18 2017 -0400 |
| b |
| b"@@ -0,0 +1,172 @@\n+>HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=1; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaat\n+agctcaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=2; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=3; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaag\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:24:16230:12703#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'15a_F730814': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=9; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttatcccctt\n+>HELIUM_000100422_612GNAAXX:7:4:4214:9434#0/2_CONS_SUB_SUB count=1; merged_sample={'13a_F730603': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=10; obiclean_samplecount=1; obiclean_head=False; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacaggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:13:6954:13039#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=11; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata\n+gcttaaaactcaaaggacttggcggtgctttatatccct\n+>HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=12; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcttaaaactcaaagaactgggcggtgctttatatcccg\n+>HELIUM_000100422_612GNAAXX:7:78:7151:19928#0/2_CONS_SUB_SUB count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=14; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacgagaatgttcgccagtgtacttctagcaaca\n+ggctgaaactcaaaggacttggcggtggtttacatccct\n+>HELIUM_000100422_612GNAAXX:7:16:16357:19948#0/2_CONS_SUB_SUB count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=17; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcacaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:107:3570:18147#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=18; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcataaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:114:4511:17596#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=19; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtgctaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttatacgctt\n+>HELIUM_000"..b" \n+ttagccctaaacacaagacattaatataacgagattaatcgacagagtactaccggctat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB count=1; merged_sample={'13a_F730603': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=57; obiclean_samplecount=1; obiclean_head=False; \n+ctagccttaaacacaaatagttatgcagacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=58; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacatgaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS_SUB_SUB count=2; merged_sample={'29a_F260619': 2}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=7; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:115:17402:4174#0/2_CONS_SUB_SUB_CMP count=2; merged_sample={'29a_F260619': 1, '15a_F730814': 1}; obiclean_singletoncount=0; obiclean_internalcount=2; seq_length=100; obiclean_headcount=0; seq_rank=13; obiclean_samplecount=2; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactacctgcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:38:10813:16867#0/2_CONS_SUB_SUB count=2; merged_sample={'26a_F040644': 2}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=15; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgtttgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:70:11798:2668#0/2_CONS_SUB_SUB count=2; merged_sample={'15a_F730814': 2}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=20; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccttt\n+>HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP count=3; merged_sample={'29a_F260619': 3}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=6; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB count=7; merged_sample={'29a_F260619': 7}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=4; obiclean_headcount=0; seq_rank=16; obiclean_samplecount=1; obiclean_head=True; \n+tttt\n+>HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB count=46; merged_sample={'13a_F730603': 46}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=1; seq_rank=8; obiclean_samplecount=1; obiclean_head=True; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB count=61; merged_sample={'29a_F260619': 30, '15a_F730814': 31}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=2; seq_rank=4; obiclean_samplecount=2; obiclean_head=True; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP count=64; merged_sample={'26a_F040644': 64}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=99; obiclean_headcount=1; seq_rank=5; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obisort.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obisort.fastq Wed Apr 12 17:38:18 2017 -0400 |
| b |
| b"@@ -0,0 +1,172 @@\n+>HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP count=64; merged_sample={'26a_F040644': 64}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=99; obiclean_headcount=1; seq_rank=5; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB count=61; merged_sample={'29a_F260619': 30, '15a_F730814': 31}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=2; seq_rank=4; obiclean_samplecount=2; obiclean_head=True; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB count=46; merged_sample={'13a_F730603': 46}; obiclean_singletoncount=0; obiclean_internalcount=0; seq_length=100; obiclean_headcount=1; seq_rank=8; obiclean_samplecount=1; obiclean_head=True; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB count=7; merged_sample={'29a_F260619': 7}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=4; obiclean_headcount=0; seq_rank=16; obiclean_samplecount=1; obiclean_head=True; \n+tttt\n+>HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP count=3; merged_sample={'29a_F260619': 3}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=6; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS_SUB_SUB count=2; merged_sample={'29a_F260619': 2}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=7; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:115:17402:4174#0/2_CONS_SUB_SUB_CMP count=2; merged_sample={'29a_F260619': 1, '15a_F730814': 1}; obiclean_singletoncount=0; obiclean_internalcount=2; seq_length=100; obiclean_headcount=0; seq_rank=13; obiclean_samplecount=2; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactacctgcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:38:10813:16867#0/2_CONS_SUB_SUB count=2; merged_sample={'26a_F040644': 2}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=15; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgtttgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:70:11798:2668#0/2_CONS_SUB_SUB count=2; merged_sample={'15a_F730814': 2}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=20; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccttt\n+>HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=1; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaat\n+agctcaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=2; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP count=1; merged_s"..b"gaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:72:12959:5736#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=48; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacacccct\n+>HELIUM_000100422_612GNAAXX:7:7:15538:8325#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=49; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacataaacattcaataaacaagaatgtcggccagagtactactagcaaca\n+gcatgaaactcaaagaactgggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:120:16005:7955#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=98; obiclean_headcount=0; seq_rank=50; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gccgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:10:9237:10532#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'29a_F260619': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=51; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaataattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:7:11998:4462#0/2_CONS_SUB_SUB count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=52; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtagtactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=99; obiclean_headcount=0; seq_rank=53; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:3:17077:6562#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'15a_F730814': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=54; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:19:4311:13343#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=55; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactacgagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB count=1; merged_sample={'15a_F730814': 1}; obiclean_singletoncount=1; obiclean_internalcount=0; seq_length=100; obiclean_headcount=0; seq_rank=56; obiclean_samplecount=1; obiclean_head=True; \n+ttagccctaaacacaagacattaatataacgagattaatcgacagagtactaccggctat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB count=1; merged_sample={'13a_F730603': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=100; obiclean_headcount=0; seq_rank=57; obiclean_samplecount=1; obiclean_head=False; \n+ctagccttaaacacaaatagttatgcagacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP count=1; merged_sample={'26a_F040644': 1}; obiclean_singletoncount=0; obiclean_internalcount=1; seq_length=99; obiclean_headcount=0; seq_rank=58; obiclean_samplecount=1; obiclean_head=False; \n+ttagccctaaacatgaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obistat.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obistat.txt Wed Apr 12 17:38:18 2017 -0400 |
| b |
| @@ -0,0 +1,8 @@ +count merged min_seq_length count total +2 None 99 4 8 +61 None 100 1 61 +46 None 100 1 46 +7 None 4 1 7 +64 None 99 1 64 +1 None 5 49 49 +3 None 100 1 3 |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obitab.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obitab.txt Wed Apr 12 17:38:18 2017 -0400 |
| b |
| @@ -0,0 +1,59 @@ +id count sample:13a_F730603 sample:15a_F730814 sample:26a_F040644 sample:29a_F260619 obiclean_head obiclean_headcount obiclean_internalcount obiclean_samplecount obiclean_singletoncount seq_length seq_rank +HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP 64 0 0 64 0 True 1 0 1 0 99 5 +HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB 61 0 31 0 30 True 2 0 2 0 100 4 +HELIUM_000100422_612GNAAXX:7:6:9274:14951#0/2_CONS_SUB_SUB 46 46 0 0 0 True 1 0 1 0 100 8 +HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB 7 0 0 0 7 True 0 0 1 1 4 16 +HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP 3 0 0 0 3 True 0 0 1 1 100 6 +HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/2_CONS_SUB_SUB 2 0 0 0 2 True 0 0 1 1 100 7 +HELIUM_000100422_612GNAAXX:7:115:17402:4174#0/2_CONS_SUB_SUB_CMP 2 0 1 0 1 False 0 2 2 0 100 13 +HELIUM_000100422_612GNAAXX:7:38:10813:16867#0/2_CONS_SUB_SUB 2 0 0 2 0 False 0 1 1 0 99 15 +HELIUM_000100422_612GNAAXX:7:70:11798:2668#0/2_CONS_SUB_SUB 2 0 2 0 0 True 0 0 1 1 100 20 +HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 True 0 0 1 1 100 1 +HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 False 0 1 1 0 100 2 +HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 False 0 1 1 0 100 3 +HELIUM_000100422_612GNAAXX:7:24:16230:12703#0/2_CONS_SUB_SUB_CMP 1 0 1 0 0 False 0 1 1 0 100 9 +HELIUM_000100422_612GNAAXX:7:4:4214:9434#0/2_CONS_SUB_SUB 1 1 0 0 0 False 0 1 1 0 100 10 +HELIUM_000100422_612GNAAXX:7:13:6954:13039#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 True 0 0 1 1 99 11 +HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 True 0 0 1 1 99 12 +HELIUM_000100422_612GNAAXX:7:78:7151:19928#0/2_CONS_SUB_SUB 1 0 0 1 0 True 0 0 1 1 99 14 +HELIUM_000100422_612GNAAXX:7:16:16357:19948#0/2_CONS_SUB_SUB 1 0 0 1 0 False 0 1 1 0 99 17 +HELIUM_000100422_612GNAAXX:7:107:3570:18147#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 False 0 1 1 0 100 18 +HELIUM_000100422_612GNAAXX:7:114:4511:17596#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 True 0 0 1 1 100 19 +HELIUM_000100422_612GNAAXX:7:29:18416:16620#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 True 0 0 1 1 100 21 +HELIUM_000100422_612GNAAXX:7:120:1900:13295#0/2_CONS_SUB_SUB_CMP 1 0 1 0 0 True 0 0 1 1 100 22 +HELIUM_000100422_612GNAAXX:7:76:10822:18722#0/2_CONS_SUB_SUB 1 0 0 1 0 False 0 1 1 0 99 23 +HELIUM_000100422_612GNAAXX:7:76:8491:8900#0/2_CONS_SUB_SUB_CMP 1 0 1 0 0 True 0 0 1 1 100 24 +HELIUM_000100422_612GNAAXX:7:9:10358:4089#0/2_CONS_SUB_SUB_CMP 1 1 0 0 0 True 0 0 1 1 100 25 +HELIUM_000100422_612GNAAXX:7:59:11971:12063#0/2_CONS_SUB_SUB 1 0 0 0 1 False 0 1 1 0 100 26 +HELIUM_000100422_612GNAAXX:7:111:19168:18517#0/2_CONS_SUB_SUB 1 0 1 0 0 False 0 1 1 0 100 27 +HELIUM_000100422_612GNAAXX:7:41:9316:2256#0/2_CONS_SUB_SUB 1 0 0 0 1 False 0 1 1 0 100 28 +HELIUM_000100422_612GNAAXX:7:33:9900:9541#0/2_CONS_SUB_SUB 1 1 0 0 0 False 0 1 1 0 100 29 +HELIUM_000100422_612GNAAXX:7:95:1688:9598#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 True 0 0 1 1 99 30 +HELIUM_000100422_612GNAAXX:7:55:16528:11418#0/2_CONS_SUB_SUB 1 1 0 0 0 True 0 0 1 1 100 31 +HELIUM_000100422_612GNAAXX:7:19:6313:16567#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 False 0 1 1 0 99 32 +HELIUM_000100422_612GNAAXX:7:111:8478:1127#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 True 0 0 1 1 99 33 +HELIUM_000100422_612GNAAXX:7:81:15726:2345#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 True 0 0 1 1 99 34 +HELIUM_000100422_612GNAAXX:7:7:11110:17924#0/2_CONS_SUB_SUB 1 0 1 0 0 True 0 0 1 1 100 35 +HELIUM_000100422_612GNAAXX:7:89:9710:20652#0/2_CONS_SUB_SUB 1 0 0 1 0 False 0 1 1 0 99 36 +HELIUM_000100422_612GNAAXX:7:71:17473:7401#0/2_CONS_SUB_SUB_CMP 1 0 1 0 0 False 0 1 1 0 100 37 +HELIUM_000100422_612GNAAXX:7:115:3625:10051#0/2_CONS_SUB_SUB 1 1 0 0 0 True 0 0 1 1 5 38 +HELIUM_000100422_612GNAAXX:7:99:8183:13912#0/2_CONS_SUB_SUB 1 1 0 0 0 False 0 1 1 0 100 39 +HELIUM_000100422_612GNAAXX:7:22:1798:3790#0/2_CONS_SUB_SUB_CMP 1 1 0 0 0 False 0 1 1 0 100 40 +HELIUM_000100422_612GNAAXX:7:115:14354:10118#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 False 0 1 1 0 99 41 +HELIUM_000100422_612GNAAXX:7:103:3594:15996#0/2_CONS_SUB_SUB 1 1 0 0 0 False 0 1 1 0 100 42 +HELIUM_000100422_612GNAAXX:7:105:14135:6905#0/2_CONS_SUB_SUB 1 0 0 0 1 True 0 0 1 1 100 43 +HELIUM_000100422_612GNAAXX:7:76:18268:14980#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 False 0 1 1 0 100 44 +HELIUM_000100422_612GNAAXX:7:25:7789:3090#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 False 0 1 1 0 100 45 +HELIUM_000100422_612GNAAXX:7:42:19757:3800#0/2_CONS_SUB_SUB_CMP 1 0 1 0 0 False 0 1 1 0 99 46 +HELIUM_000100422_612GNAAXX:7:116:14244:17926#0/2_CONS_SUB_SUB 1 0 0 1 0 False 0 1 1 0 99 47 +HELIUM_000100422_612GNAAXX:7:72:12959:5736#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 False 0 1 1 0 99 48 +HELIUM_000100422_612GNAAXX:7:7:15538:8325#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 True 0 0 1 1 99 49 +HELIUM_000100422_612GNAAXX:7:120:16005:7955#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 False 0 1 1 0 98 50 +HELIUM_000100422_612GNAAXX:7:10:9237:10532#0/2_CONS_SUB_SUB_CMP 1 0 0 0 1 False 0 1 1 0 100 51 +HELIUM_000100422_612GNAAXX:7:7:11998:4462#0/2_CONS_SUB_SUB 1 0 0 1 0 False 0 1 1 0 99 52 +HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 True 0 0 1 1 99 53 +HELIUM_000100422_612GNAAXX:7:3:17077:6562#0/2_CONS_SUB_SUB_CMP 1 0 1 0 0 False 0 1 1 0 100 54 +HELIUM_000100422_612GNAAXX:7:19:4311:13343#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 False 0 1 1 0 99 55 +HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB 1 0 1 0 0 True 0 0 1 1 100 56 +HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB 1 1 0 0 0 False 0 1 1 0 100 57 +HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP 1 0 0 1 0 False 0 1 1 0 99 58 |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obiuniq.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obiuniq.fasta Wed Apr 12 17:38:18 2017 -0400 |
| b |
| b"@@ -0,0 +1,172 @@\n+>HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2_CONS_SUB_SUB_CMP ali_length=62; seq_ab_match=47; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'29a_F260619': 1}; forward_score=72.0; score=115.761290673; seq_a_mismatch=1; forward_tag=gcctcct; seq_b_mismatch=13; experiment=wolf_diet; mid_quality=69.1492537313; avg_quality=68.8701298701; seq_a_single=46; score_norm=1.86711759151; status=full; direction=reverse; seq_b_insertion=1; seq_b_deletion=1; seq_a_insertion=0; seq_length_ori=154; reverse_tag=gcctcct; count=1; seq_length=100; mode=alignment; head_quality=67.0; seq_b_single=46; \n+ttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaat\n+agctcaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2_CONS_SUB_SUB_CMP ali_length=62; seq_ab_match=60; sminR=40.0; tail_quality=66.9; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'29a_F260619': 1}; forward_score=72.0; score=231.881364714; seq_a_mismatch=0; forward_tag=gcctcct; seq_b_mismatch=2; experiment=wolf_diet; mid_quality=78.447761194; avg_quality=76.9545454545; seq_a_single=46; score_norm=3.74002201152; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=gcctcct; count=1; seq_length=100; mode=alignment; head_quality=67.0; seq_b_single=46; \n+ttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2_CONS_SUB_SUB_CMP ali_length=62; seq_ab_match=52; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'29a_F260619': 1}; forward_score=72.0; score=167.91734192; seq_a_mismatch=5; forward_tag=gcctcct; seq_b_mismatch=5; experiment=wolf_diet; mid_quality=75.0820895522; avg_quality=74.0064935065; seq_a_single=46; score_norm=2.70834422451; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=gcctcct; count=1; seq_length=100; mode=alignment; head_quality=66.6; seq_b_single=46; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaag\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2_CONS_SUB_SUB sminR=40.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'29a_F260619': 30, '15a_F730814': 31}; forward_score=72.0; experiment=wolf_diet; reverse_score=72.0; seq_length_ori=154; count=61; seq_length=100; status=full; mode=alignment; seq_b_single=46; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/2_CONS_SUB_SUB_CMP ali_length=63; sminR=40.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'26a_F040644': 64}; forward_score=72.0; forward_tag=gaatatc; experiment=wolf_diet; seq_a_single=45; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=153; reverse_tag=gaatatc; count=64; seq_length=99; status=full; mode=alignment; seq_b_single=45; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/2_CONS_SUB_SUB_CMP ali_length=62; sminR=40.0; tail_quality=67.0; revers"..b"e=223.876050008; seq_a_mismatch=3; forward_tag=gaagtag; seq_b_mismatch=0; experiment=wolf_diet; mid_quality=77.6567164179; avg_quality=76.1818181818; seq_a_single=46; score_norm=3.61090403239; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=gaagtag; count=1; seq_length=100; mode=alignment; head_quality=66.0; seq_b_single=46; \n+ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:19:4311:13343#0/2_CONS_SUB_SUB_CMP ali_length=63; seq_ab_match=58; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'26a_F040644': 1}; forward_score=72.0; score=211.837822462; seq_a_mismatch=4; forward_tag=gaatatc; seq_b_mismatch=1; experiment=wolf_diet; mid_quality=77.7969924812; avg_quality=76.385620915; seq_a_single=45; score_norm=3.36250511845; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=153; reverse_tag=gaatatc; count=1; seq_length=99; mode=alignment; head_quality=67.0; seq_b_single=45; \n+ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactacgagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:30:1800:7833#0/2_CONS_SUB_SUB ali_length=62; seq_ab_match=52; sminR=40.0; tail_quality=65.6; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'15a_F730814': 1}; forward_score=72.0; score=167.712615339; seq_a_mismatch=0; forward_tag=gaagtag; seq_b_mismatch=10; experiment=wolf_diet; mid_quality=59.9104477612; avg_quality=58.6623376623; seq_a_single=46; score_norm=2.70504218289; status=full; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=gaagtag; count=1; seq_length=100; mode=alignment; head_quality=35.0; seq_b_single=46; \n+ttagccctaaacacaagacattaatataacgagattaatcgacagagtactaccggctat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:108:9222:18258#0/2_CONS_SUB_SUB ali_length=62; seq_ab_match=60; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'13a_F730603': 1}; forward_score=72.0; score=231.857703869; seq_a_mismatch=0; forward_tag=aattaac; seq_b_mismatch=2; experiment=wolf_diet; mid_quality=78.5; avg_quality=77.0194805195; seq_a_single=46; score_norm=3.73964038498; status=full; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=aattaac; count=1; seq_length=100; mode=alignment; head_quality=67.2; seq_b_single=46; \n+ctagccttaaacacaaatagttatgcagacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP ali_length=63; seq_ab_match=60; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; merged_sample={'26a_F040644': 1}; forward_score=72.0; score=227.901935995; seq_a_mismatch=3; forward_tag=gaatatc; seq_b_mismatch=0; experiment=wolf_diet; mid_quality=78.5939849624; avg_quality=77.0784313725; seq_a_single=45; score_norm=3.61749104754; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=153; reverse_tag=gaatatc; count=1; seq_length=99; mode=alignment; head_quality=67.0; seq_b_single=45; \n+ttagccctaaacatgaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/output_obiuniq_family.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_obiuniq_family.fasta Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| b"@@ -0,0 +1,172 @@\n+>HELIUM_000100422_612GNAAXX:7:75:9674:16966#0/2_CONS_SUB_SUB_CMP ali_length=58; sminR=40.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=50; sample=29a_F260619; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; forward_tag=gcctcct; experiment=wolf_diet; seq_a_single=0; merged=['HELIUM_000100422_612GNAAXX:7:75:9674:16966#0/2_CONS_SUB_SUB_CMP', 'HELIUM_000100422_612GNAAXX:7:95:11283:2557#0/2_CONS_SUB_SUB_CMP', 'HELIUM_000100422_612GNAAXX:7:73:17068:16620#0/2_CONS_SUB_SUB_CMP', 'HELIUM_000100422_612GNAAXX:7:96:8737:4973#0/2_CONS_SUB_SUB_CMP', 'HELIUM_000100422_612GNAAXX:7:37:12979:6595#0/2_CONS_SUB_SUB', 'HELIUM_000100422_612GNAAXX:7:7:7916:16505#0/2_CONS_SUB_SUB_CMP', 'HELIUM_000100422_612GNAAXX:7:13:5742:9859#0/2_CONS_SUB_SUB']; reverse_score=72.0; seq_b_insertion=0; seq_b_deletion=50; seq_a_insertion=0; seq_length_ori=58; reverse_tag=gcctcct; count=7; seq_length=4; status=full; mode=alignment; seq_b_single=0; \n+tttt\n+>HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP ali_length=63; seq_ab_match=60; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; sample=26a_F040644; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; score=227.901935995; seq_a_mismatch=3; forward_tag=gaatatc; seq_b_mismatch=0; experiment=wolf_diet; mid_quality=78.5939849624; avg_quality=77.0784313725; seq_a_single=45; score_norm=3.61749104754; merged=['HELIUM_000100422_612GNAAXX:7:38:3005:20881#0/2_CONS_SUB_SUB_CMP']; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=153; reverse_tag=gaatatc; count=1; seq_length=99; mode=alignment; head_quality=67.0; seq_b_single=45; \n+ttagccctaaacatgaacattcaataaacaagaatgttcgccagagtactactagcaaca\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP ali_length=63; seq_ab_match=59; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; sample=26a_F040644; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; score=219.686655506; seq_a_mismatch=0; forward_tag=gaatatc; seq_b_mismatch=4; experiment=wolf_diet; mid_quality=67.7443609023; avg_quality=67.3986928105; seq_a_single=45; score_norm=3.48708976993; merged=['HELIUM_000100422_612GNAAXX:7:38:6201:12003#0/2_CONS_SUB_SUB_CMP']; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=153; reverse_tag=gaatatc; count=1; seq_length=99; mode=alignment; head_quality=63.2; seq_b_single=45; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcttaaaactcaaagaactgggcggtgctttatatcccg\n+>HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP ali_length=63; seq_ab_match=61; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; sample=26a_F040644; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; score=235.877819976; seq_a_mismatch=2; forward_tag=gaatatc; seq_b_mismatch=0; experiment=wolf_diet; mid_quality=78.8646616541; avg_quality=77.3137254902; seq_a_single=45; score_norm=3.74409238057; merged=['HELIUM_000100422_612GNAAXX:7:111:18277:17779#0/2_CONS_SUB_SUB_CMP']; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=153; reverse_tag=gaatatc; count=1; seq_length=99; mode=alignment; head_quality=67.0; seq_b_single=45; \n+ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata\n+gcctgaaactcaaaggacttggcggtgctttacatccct\n+>HELIUM_000100422_612GNAAXX:7:78:7151:19928#0/2_CONS_SUB_SUB ali_length=63; seq_ab_match=56; sminR=40.0; tail_quality=47.6; reverse_match="..b"00422_612GNAAXX:7:99:8183:13912#0/2_CONS_SUB_SUB']; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=aattaac; count=1; seq_length=100; status=full; mode=alignment; head_quality=67.0; seq_b_single=46; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctc\n+>HELIUM_000100422_612GNAAXX:7:4:4214:9434#0/2_CONS_SUB_SUB ali_length=62; seq_ab_match=58; sminR=40.0; tail_quality=63.3; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; sample=13a_F730603; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; score=215.812703412; seq_a_mismatch=3; forward_tag=aattaac; seq_b_mismatch=1; experiment=wolf_diet; mid_quality=76.2388059701; avg_quality=74.6883116883; seq_a_single=46; score_norm=3.48085005502; merged=['HELIUM_000100422_612GNAAXX:7:4:4214:9434#0/2_CONS_SUB_SUB']; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=aattaac; count=1; seq_length=100; status=full; mode=alignment; head_quality=65.3; seq_b_single=46; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacaggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:9:10358:4089#0/2_CONS_SUB_SUB_CMP ali_length=61; seq_ab_match=54; sminR=40.0; tail_quality=66.9; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; sample=13a_F730603; reverse_score=72.0; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; score=181.620394786; seq_a_mismatch=1; forward_tag=aattaac; seq_b_mismatch=6; experiment=wolf_diet; mid_quality=66.3880597015; avg_quality=66.4545454545; seq_a_single=46; score_norm=2.97738352108; merged=['HELIUM_000100422_612GNAAXX:7:9:10358:4089#0/2_CONS_SUB_SUB_CMP']; status=full; direction=reverse; seq_b_insertion=0; seq_b_deletion=1; seq_a_insertion=0; seq_length_ori=154; reverse_tag=aattaac; count=1; seq_length=100; mode=alignment; head_quality=66.9; seq_b_single=47; \n+ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacaggcaat\n+agctcaaaactcaaagaacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:33:9900:9541#0/2_CONS_SUB_SUB ali_length=62; seq_ab_match=62; sminR=40.0; tail_quality=67.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=0; sample=13a_F730603; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; score=247.949713348; seq_a_mismatch=0; forward_tag=aattaac; seq_b_mismatch=0; experiment=wolf_diet; mid_quality=78.8955223881; avg_quality=77.3506493506; seq_a_single=46; score_norm=3.99918892497; merged=['HELIUM_000100422_612GNAAXX:7:33:9900:9541#0/2_CONS_SUB_SUB']; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=0; seq_a_insertion=0; seq_length_ori=154; reverse_tag=aattaac; count=1; seq_length=100; status=full; mode=alignment; head_quality=67.0; seq_b_single=46; \n+ctagccctaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat\n+agcttaaaactcaaaggacttggcggtgctttataccctt\n+>HELIUM_000100422_612GNAAXX:7:115:3625:10051#0/2_CONS_SUB_SUB ali_length=59; seq_ab_match=59; sminR=40.0; tail_quality=93.0; reverse_match=tagaacaggctcctctag; seq_a_deletion=49; sample=13a_F730603; forward_match=ttagataccccactatgc; forward_primer=ttagataccccactatgc; reverse_primer=tagaacaggctcctctag; sminL=40.0; forward_score=72.0; score=235.999642017; seq_a_mismatch=0; forward_tag=aattaac; seq_b_mismatch=0; experiment=wolf_diet; mid_quality=93.0; avg_quality=93.0; seq_a_single=0; score_norm=3.99999393249; merged=['HELIUM_000100422_612GNAAXX:7:115:3625:10051#0/2_CONS_SUB_SUB']; reverse_score=72.0; direction=forward; seq_b_insertion=0; seq_b_deletion=49; seq_a_insertion=0; seq_length_ori=59; reverse_tag=aattaac; count=1; seq_length=5; status=full; mode=alignment; head_quality=93.0; seq_b_single=0; \n+caata\n" |
| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/wolf_small.F.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wolf_small.F.fastq Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,998 @@\n+@HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/1 \n+ccgcctcctttagataccccactatgcttagccctaaacacaagtaattattataacaaaatcattcgccagagtactaccggcaatagctcaaaactcaaagaactt\n++\n+bbbbbbbbbbbbbbbbbbbbbbabbbba_abbbbbbbbbbbbbaZbbb`bbbbbbb``b`QXK^[TWXXJ`\\`BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 \n+ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggactt\n++\n+bbbbbbbabbbbbbbbbbbbbbbbbbbbbbabbbbbabbbbbbb[bbbb`bbZb^bbbb_`Z\\KaZXRYZbb\\bZ\\\\^^BBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 \n+ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccgccactagcttaaaactcaaagaactc\n++\n+bbbbbbbbbbbbbbbbbbbbbbbaabbb^abbbbbab^bbbb__Z`````Tb_b_bbb_b]]Zb_Vbb_bXRZRPYYT[[``[_BBBBBBBBBBBBBBBBBBBBBBBB\n+@HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/1 \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaataattttgttatattaat\n++\n+bbbbbbbbbabbbbbbbbabbbbbbbbbbb`\\```_bbbbbbbbbbb^b`bbb^bb_b_b`bb^b`\\a^O`Z```UZ]R^`b^b^W```R[[LW[a`b_QQ[U^BBBB\n+@HELIUM_000100422_612GNAAXX:7:57:18459:16145#0/1 \n+ccgaatatcttagataccccactatgcttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaccagcctgaaactcacaggactcg\n++\n+bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbcbbba^b^b``bb`Z`Z`^^^W^BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HELIUM_000100422_612GNAAXX:7:89:10281:5930#0/1 \n+ccgcctcctttagataccccactatgcttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaagtactc\n++\n+bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbabbbbbbabbbbbbbb`bb_bbbbbaaa`a```^\\UXW[XU`[W`BBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HELIUM_000100422_612GNAAXX:7:29:15520:18035#0/1 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| b |
| diff -r 000000000000 -r 4c2b715a258a test-data/wolf_small.R.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wolf_small.R.fastq Wed Apr 12 17:38:18 2017 -0400 |
| [ |
| b'@@ -0,0 +1,998 @@\n+@HELIUM_000100422_612GNAAXX:7:119:14871:19157#0/2 \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaacctactcccgctacacgtccgccgaataatactgttatcatatt\n++\n+bbbbbbbbbbb``b_bbabbbbbba_b_bbbb__baaaU__bb_`bWbb[b]b__BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB\n+@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/2 \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctattgccggtagtactctggcgaacacttttgttatattact\n++\n+bbbbbbbbbbbbbbbb`bbbbb`bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbabbbbbbbbbb\\bbbbbbbbbbY\\][`bbbbabb`WZUWMUX``^]G]`b_b`R`\n+@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/2 \n+ccgcctccttagaacaggctcctctagaagggtataaagcaccgccaagtcctttgagttttaagctcttgccggtagtactctggcgcacacttttcttatattact\n++\n+bb_bbbbbab^babbbbbbbbb\\bb[bbbbbbX_b^Z^[Jaa_^^WT[^]^[[U[Y[^SR^^^[Q^RZ^^b`_bTTQGW[T[]YHMGNNPNNKPFUYRVT\\bbbb_^U\n+@HELIUM_000100422_612GNAAXX:7:22:8540:14708#0/2 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