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Commit message:
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/mixcr commit b847d69ff272b194e29858c173a7343442f905b2" |
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added:
mixcr_analyze.xml mixcr_macros.xml test-data/sample_IGH_R1.fastq test-data/sample_IGH_R2.fastq |
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| diff -r 000000000000 -r d38cfb922f95 mixcr_analyze.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixcr_analyze.xml Thu Oct 10 18:03:22 2019 -0400 |
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| b'@@ -0,0 +1,271 @@\n+<tool id="mixcr_analyze" name="MiXCR Analyze" version="@VERSION@.0">\n+ <description>immuno clonotyes from sequence data</description>\n+ <macros>\n+ <import>mixcr_macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <command detect_errors="exit_code"><![CDATA[\n+ #import os.path\n+ #import re\n+ #def clean(name)\n+ #set $base_name = $os.path.basename($name)\n+ #set $name_clean = re.sub(\'[^\\w\\-_\\.]\', \'_\', $base_name)\n+ #return $name_clean\n+ #end def\n+ #if $imgt.library_selector == \'history\':\n+ #set $libname = $re.sub(\'.gz$\',\'\',$clean($imgt.library.name))\n+ ln -s -f \'$imgt.library\' $libname &&\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "paired":\n+ #set $fq1 = $clean($fastq_input.fastq_input1.name)\n+ ln -s -f \'$fastq_input.fastq_input1\' $fq1 &&\n+ #set $fq2 = $clean($fastq_input.fastq_input2.name)\n+ ln -s -f \'$fastq_input.fastq_input2\' $fq2 &&\n+ #else:\n+ #set $fq1 = $clean($fastq_input.fastq_input1.name)\n+ ln -s -f \'$fastq_input.fastq_input1\' $fq1 &&\n+ #end if\n+ mixcr analyze $analyze.pipeline --starting-material $starting_material\n+ #if $analyze.pipeline == \'amplicon\':\n+ --5-end $analyze.primers5end\n+ --3-end $analyze.primers3end\n+ --adapters $analyze.adapters\n+ #end if\n+ #if $imgt.library_selector == \'history\':\n+ --align "--library $libname"\n+ #set $taxonId = str($imgt.species).split(\':\')[0]\n+ --species $taxonId\n+ ## #elif $imgt.library_selector == \'cached\':\n+ #else\n+ --species $imgt.species\n+ #end if\n+ $contig_assembly $impute_germline_on_export $only_productive \n+ --receptor-type $receptor_type\n+ #if str( $fastq_input.fastq_input_selector ) == "paired":\n+ $fq1 $fq2\n+ #else:\n+ $fq1\n+ #end if\n+ mixcr_analysis\n+ ]]></command>\n+ <inputs>\n+ <conditional name="analyze">\n+ <param name="pipeline" type="select" label="amplicon or shotgun data" help="">\n+ <option value="amplicon">amplicon: enriched targeted TCR/IG libraries (5\xe2\x80\x99RACE, Amplicon, Multiplex, etc)</option>\n+ <option value="shotgun">shotgun: non-enriched RNA-seq or non-targeted genomic data</option>\n+ </param>\n+ <when value="amplicon">\n+ <param name="primers5end" type="select" label="5\xe2\x80\x99-end of the library.">\n+ <help>\n+ There are two possible values: \n+ no-v-primers \xe2\x80\x94 no V gene primers (e.g. 5\xe2\x80\x99RACE with template switch oligo or a like), \n+ v-primers \xe2\x80\x94 V gene single primer / multiple.\n+ </help>\n+ <option value="no-v-primers">no-v-primers</option>\n+ <option value="v-primers">v-primers</option>\n+ </param>\n+ <param name="primers3end" type="select" label="3\xe2\x80\x99-end of the library.">\n+ <help>\n+ There are three possible values: \n+ j-primers \xe2\x80\x94 J gene single primer / multiplex, \n+ j-c-intron-primers \xe2\x80\x94 J-C intron single primer / multiplex, \n+ c-primers \xe2\x80\x94 C gene single primer / multiplex (e.g. IGHC primers specific to different immunoglobulin isotypes).\n+ </help>\n+ <option value="j-primers">j-primers</option>\n+ <option value="j-c-intron-primers">j-c-intron-primers</option>\n+ <option value="c-primers">c-primers</option>\n+ </param>\n+ <param name="adapters" type="select" label="Presence of PCR primers and/or adapter sequences">\n+ <help>\n+ '..b'/assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="analyze">\n+ <param name="pipeline" value="amplicon"/>\n+ <param name="primers5end" value="v-primers"/>\n+ <param name="primers3end" value="j-primers"/>\n+ <param name="adapters" value="no-adapters"/>\n+ </conditional>\n+ <param name="starting_material" value="rna"/>\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" value="paired"/>\n+ <param name="fastq_input1" value="sample_IGH_R1.fastq" ftype="fastqsanger"/>\n+ <param name="fastq_input2" value="sample_IGH_R2.fastq" ftype="fastqsanger"/>\n+ </conditional>\n+ <conditional name="imgt">\n+ <param name="library_selector" value="builtin"/>\n+ <param name="species" value="9606"/> \n+ </conditional>\n+ <param name="contig_assembly" value="True"/>\n+ <param name="impute_germline_on_export" value="True"/>\n+ <param name="only_productive" value="False"/>\n+ <param name="receptor_type" value="xcr"/>\n+ <output name="report">\n+ <assert_contents>\n+ <has_text text="Final clonotype count" />\n+ </assert_contents>\n+ </output>\n+ <output name="clonotypes">\n+ <assert_contents>\n+ <has_text text="CARDDGGGKGDYGRLW" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ </tests>\n+ <help><![CDATA[\n+**MiXCR** **a universal tool for fast and accurate analysis of T- and B- cell receptor repertoire sequencing data**\n+\n+MiXCR_ is a universal framework that processes big immunome data from raw sequences to quantitated clonotypes. MiXCR_ efficiently handles paired- and single-end reads, considers sequence quality, corrects PCR errors and identifies germline hypermutations. The software supports both partial- and full-length profiling and employs all available RNA or DNA information, including sequences upstream of V and downstream of J gene segments.\n+\n+**MiXCR is free for academic and non-profit use** (see License_).\n+\n+This tool runs the MiXCR_ analyze_ pipeline. \n+Generally, there two distinct types of library preparation which correspond to the two analyze pipelines:\n+\n+ - analyze_ amplicon_ for analysis of targeted TCR/IG library amplification (5\xe2\x80\x99RACE, Amplicon, Multiplex, etc).\n+ - analyze_ shotgun_ for analysis of random fragments (RNA-Seq, Exome-Seq, etc).\n+\n+\n+MiXCR_ has builtin libraries for human, mouse and rat. Additional compiled IMGT_ libraries can be imported into your Galaxy history as datatype: *imgt.json* from: https://github.com/repseqio/library-imgt/releases\n+\n+NOTE: The imgt.201822-5.sv4.json.gz release has the rattus genus taxonId:10114 for rat, whereas the mixcr builtin library has the rattus norvegicus species taxId:10116 for rat. If you encounter imgt library loading errors from mixcr, you may have to substitute 10116 for 10114 in the imgt.201822-5.sv4.json.gz file.\n+\n+**Data coming from IMGT server may be used for academic research only**, provided that it is referred to IMGT\xc2\xae, and cited as "IMGT\xc2\xae, the international ImMunoGeneTics information system\xc2\xae http://www.imgt.org (founder and director: Marie-Paule Lefranc, Montpellier, France)."\n+\n+.. _MiXCR: https://mixcr.readthedocs.io/en/latest/index.html\n+.. _analyze: https://mixcr.readthedocs.io/en/latest/analyze.html\n+.. _amplicon: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-targeted-tcr-ig-libraries\n+.. _shotgun: https://mixcr.readthedocs.io/en/latest/analyze.html#analysis-of-non-enriched-or-random-fragments\n+.. _License: https://mixcr.readthedocs.io/en/latest/license.html#license\n+.. _IMGT: https://github.com/repseqio/library-imgt/releases\n+ ]]></help>\n+ <expand macro="citations" />\n+</tool>\n' |
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| diff -r 000000000000 -r d38cfb922f95 mixcr_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mixcr_macros.xml Thu Oct 10 18:03:22 2019 -0400 |
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| @@ -0,0 +1,16 @@ +<macros> + <token name="@VERSION@">3.0.5</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">mixcr</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">doi:10.1038/nmeth.3364</citation> + <citation type="doi">doi:10.1093/nar/gkn838</citation> + <yield /> + </citations> + </xml> +</macros> |
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| diff -r 000000000000 -r d38cfb922f95 test-data/sample_IGH_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_IGH_R1.fastq Thu Oct 10 18:03:22 2019 -0400 |
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| b"@@ -0,0 +1,800 @@\n+@HWI-ST330:342:H11F0ADXX:1:1101:1461:1915 1:N:0:NAGCTT\n+NGCGAGACGGTGACCAGGGTTCCCTGGCCCCAGGGGTCGAACCAGCTGGGACTTAGTAGTAGGTAGCGATGTCTCGCCCTCGCACAGTAATAAATGGCGG\n++\n+#1=DDFFFHHHFDHHHHIJFHGIGEGGIJGGIJEGIJIJJJIJJIDGHHHHFEFEECEEDCDC;@ACBBBBDCDDCDDDDD<@D><C:@ADEDCDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1434:1930 1:N:0:NAGCTT\n+NGGTATCAACGCAGAGTCGCCTGACCTTGTGTCTTGGGGAAGACCCCGCTAACCGCCACCCTCTCAAAATCCGGAAACACATTCCGGCCCGAGGTCCACC\n++\n+#1==DDFFFHHHFGIJHIIIJJIJJJGIJHIJJJJJIJJJJDHHIJJABHHHFEECDDDDDDDDDDDDDDDDBDDDDDDDDDCCEDDDDDBDDD>CCCCD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1461:1989 1:N:0:NAGCTT\n+NGCAAACTCAGTGGTATCAACGCAGAGTTGTTTGACGTTTGATCTTGGGGGTCTGAGAGAGGAGCCCAGCCCTGGGATTTTCAGGTGTTTTCTCTTGGTG\n++\n+#4=DDDFFHHHHHIIIICIIIIIIIIIIIIIIIIIIIHIIIIIIIIIAHIIEHHEHFEFDDDECBDDDBDDDDDDDBDDDDEDDD:@CDDDDDDDDDDCD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1425:1998 1:N:0:NAGCTT\n+NGCAAGGTCAGTGGTATCAACGCAGAGTCAGTTGCTGTCCTTTCTTGGGGGATGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGCACCTG\n++\n+#4=DDFFFHHHHHJJJJJJJJJJJJJJIJJJJJIJJJJJIJJJIIJJIJJJJJJJJJHHHHHHFFFFFFEEEEDEDDDDCDDEDDDDDDDDDDCDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1569:1912 1:N:0:NAGCTT\n+NGGAAGCCCAGTGGTATCAACGCAGAGTACATTGATTTGGTGTCTTGGGGGAGATCCGCTAGCGCTACCGGACTCAGATCCCAGTCTGGACCTGAGGTGC\n++\n+#1=DDFFFHHHHHJJJJJJJJJJJJJJFDHHGIJFHIJJIBGIJIJJIJJJHIHHHHFFFDDDBDDDDDDD;@BDCCADCDDDDDDDDDCDDDDCDD?AC\n+@HWI-ST330:342:H11F0ADXX:1:1101:1613:1915 1:N:0:GAGCTT\n+NTGAGACGGTGACCAGGGTTCCCTGGCCCCAGGTTAGGCTAAAATCCCATCGGCCTCCAGGATCTCTCGCACAGTAATACACGGCCGTGTCCTCGGCTCT\n++\n+#1=DDFFFHHHHHJJJJJJJJJJIJIJJIJJJJGIIJJJJJIIIJJJJJJJJJIJIJHHHHFFFFFFCDD@BDDCDCDEDDDDBDDDDDBDDDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1522:1922 1:N:0:NAGCTT\n+NAGAGACGGTGACCAGGGTTCCCTGGCCCCAAAGTCTTCCGTAGTCACCCTTTCCCCCGCCATCATCTCTCGCACAGTAATAGAAGGCCGTGTCGTCAAG\n++\n+#1=DDFDDHHHHHIFIIDHGIGIIIIIIIGECHHIGIIII<FHGBGBCBGGBHHGGIEHFFDDC@ADCDEABBBD:?C;A@CDCCDBDB9@B<A@8?ABD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1658:1922 1:N:0:GAGCTT\n+NTGAGACGGTGACCAGGGTTCCCTGGCCCCAGGGGTCGAACCAGTTGTAGGCGTTACCACCGTAGTCTCTCGCACAATAATAGACGGCCGTGTCTGCGGC\n++\n+#1:DDDDDHHHHHIIII@FHIIIICHIIIGIIIIIFHIIIHHGIIIEHEHBHHDDDCCCCCB?BBBE@CCCBBBBBBCCCDD>AC5>BBB9<8?CCCBB<\n+@HWI-ST330:342:H11F0ADXX:1:1101:1591:1923 1:N:0:NAGCTT\n+NCGAGACGGTGACCGGGGTTCCCTGGCCCCAGTACTCAGCTGGGACTCCCGCGCGGTAGTCTCTTGCACAGAAACAGACAACCGTGTCCTCGGCTCTCAG\n++\n+#1=DDDDDHFFHHJEGEIHIIGHEHEIIIJJJ=8BGABHEEDGG2@GEH9:9=B>'8=/++:>AC3::4>9ACCCC9?ABCA<@<8(<:@A<@@@BCA@>\n+@HWI-ST330:342:H11F0ADXX:1:1101:1729:1931 1:N:0:GAGCTT\n+NGAGACGGTGACCGGGGTTCCCTGGCCCCAAAGTCTTCCGTAGTCACCCTTTCCCCCGCCATCATCTCTCGCACAGTAATAGAAGGCCGTGTCGTCAAGT\n++\n+#1=DDFFFHHGHHJGIJIJJJJJJFHIHFHGFB==F@BF@C@G;D>EIHGFHHFFEFDBDBBCCADCDCCBBD@DD>@CDDCCDD??B<)98?<88<BDC\n+@HWI-ST330:342:H11F0ADXX:1:1101:1655:1947 1:N:0:TAGCTT\n+NCAAAGGTCAGTGGTATCAACGCAGAGTCAACTGTGGTTAATTCTTGTGGCACCATGGACTGGACCTGGAGGTTCCTCTTTGTGGTGGCAGCAGCTACAG\n++\n+#1=DDFFFHGHHHJJJJJJJJIJIJIJHJIJJJJHJJJIJJJIIIJJ0?FEHIGIGJJJJJIJJIJHHHHFFDEEEEAAEDC;CB(<?B?BBD@BCD@CC\n+@HWI-ST330:342:H11F0ADXX:1:1101:1505:1958 1:N:0:NAGCTT\n+NGGAAGGTCAGTGGTATCAACGCAGAGTTGGTTGCAATCTTTTCTTGGGGGGCATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCAC\n++\n+#4=DDDFFHHHHHJIJJFJJJJJJJJJJJJJIIJJJJJJJJJJIJJJHIJJDDDDDDDDDDDDDDDDDDDDDDEDDDDDDDDDDDBDDDDDDDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1660:1964 1:N:0:GAGCTT\n+NCTAAGGTCAGTGGTATCAACGCAGAGTCCGCTTCTTTCTGGTCTTGGGGGACACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCACAGC\n++\n+#1:BBDDDHHHHHJIJJ4AIHIJJJJHHI?FGIEDDHHCD<9BGHIJIJJIGHE?=B@C@BEAA???CCDEAACC?A>ACAC?A?BB>8088<<@8<<CB\n+@HWI-ST330:342:H11F0ADXX:1:1101:1527:1967 1:N:0:NAGCTT\n+NGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAGTCAAAATACCCTTGGCCCTTTGGAAGGTACCAGCCACTGCTATACAGGGGATTCCTCGCACAGTAA\n++\n+#1=DADDDFDAFFI9E@FIACEFFF@EDFDFGFFF<??FEG@BFEFE8=)=BFII@A:=@=.?A>AE9?@3;>ACC>>AD;?@BB8AADABB55>@@4@B\n+@HWI-ST330:342:H11F0ADXX:1:1101:1630:1977 1:N:0:GAGCTT\n+NGAGACGGTGACCATGGTCCCTAGGCCCCAGACGTCCATTCCGTAATAGTACCCCCCAGTTAATGTAGTCATGGGACCCGCCTCTCTCGCACAGTAATAC\n++\n+#1=DDDDFHHFHHEHGAGHGIHIIIIGIIIIGGBHIIBHHEEFFFBFCH=CHGGIIHFFFFCEEECEEDD:;@CBC<@BBBCBBCCCC-?@B<C@CCD@C\n+@HWI-ST330:342:H11F0ADXX:1:1101:166"..b'IHGHHHFDEFEDEDDDDDDDBDCCDDEDCCCDDDDDBBDDDDDDDDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4879:1921 1:N:0:TAGCTT\n+NGGAGACGGTGACCATGGTTCCCTGGCCCCAAAGTCTTCCGTAGTCACCCTTTCCCCCGCCATCATCTCTCGCACAGTAATAGAAGGCCGTGTCGTCAAG\n++\n+#4=DDDFFHHHHHJHIJJJJJJJJJHHIJJJJJJJJJJJJJHIJIJJJJJJJJJJJJJGHFFDEEEEEDEDDDBDDCDEDEFDDDCDDDBDDDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4828:1925 1:N:0:TAGCTT\n+NGCAAAGACAGTGGTATCAACGCAGAGTGTCTTCATTTACAGTCTTGGGGGAGATCCGCTAGCGCTACCGGACTCAGATCCCAGTCTGGACCTGAGGTGC\n++\n+#1=DDDFFHHHHHJJJJFJJJJJJJJJGHIJIJJIJJJJJIJJJJIJHIJJJJJJHHHHFFDEDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDCBD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4769:1933 1:N:0:TAGCTT\n+NGAAAAGACAGTGGTATCAACGCAGAGTAATGTCATTTGGTATCTTGGGGGACACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCACAGC\n++\n+#4=DDDFFHHHHHJJJJGJJJJJJJJJIJJJJIJJJJJJJGIIJJJJGIJJJJIJJJHHHHHFFFFDEEEEEDDDDDDDDDDDDDDDDDDDDBDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4919:1935 1:N:0:TAGCTT\n+NAAGAGACGGTGACCAGGGTTCCCTGGCCCCAAAGTCTTCCGTAGTCACCCTTTCCCCCGCCATCATCTCTCGCACAGTAATAGAAGGCCGTGTCGTCAA\n++\n+#1=DDDDDHFHHHIHII7FFHIIIIIHGHIIIIIIIIIIIIIIIIIICHIIIIIIIIIIHECCCCCCCFCECBBBBBCCDCDECCCCBBBBBBBBBBBBB\n+@HWI-ST330:342:H11F0ADXX:1:1101:4850:1938 1:N:0:TAGCTT\n+NTGGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAGTCAAAGTAGGTCACCGTAGTCACTCCCCACCACCTCGCACAGTAATACACGGCCGTGTCGTCAG\n++\n+#1:DDBDDFFFFFFGGI;CAGFIFIIIIIIIIFFGFIIIIIIFIIIIBFFIIIIFFGIIIIIIFCFD?DCCCCBB?@?@ABBEBBB@BBBB@BBBBBB?@\n+@HWI-ST330:342:H11F0ADXX:1:1101:4806:1954 1:N:0:TAGCTT\n+NATGAGACGGTGACCAGGGTTCCCCGGCCCCAGGACTCTCGTGGGCGAGCCGCCATAGTCTGCCCCAGATTCCGGTCTTTCACACAGTAATACACAGCCG\n++\n+#1=BBDDFHHHHGJJIIJJJIEIIIGIIJJJJJJJJJJJJJGGJIFHFDDDBDDDDDDEEDDDDDDDDBCDDEDDDDDDDDCCDDBDADDDEDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4920:1959 1:N:0:GAGCTT\n+NTGAAGGTCAGTGGTATCAACGCAGAGTGTGGTACTATCCTTTCTTGGGGGAGCTCTGAGAGAGGAGCCCAGCCCTGGGATTTTCAGGTGTTTTCATTTG\n++\n+#1=DDDFFHHHHGJJJJFJJJJJJJIIHIJJJHHJJJJIJJJJJJJJ?FHJIJJHHHHEFCEFFDEDDDDDDDDDDDDDDDDDDDCCD:ACDDDCCDDEE\n+@HWI-ST330:342:H11F0ADXX:1:1101:4852:1963 1:N:0:TAGCTT\n+NGCAAACTCAGTGGTATCAACGCAGAGTTCAATCTTAGGGTCTTGGGGGAGCCCCATTGCTGATCAGGACTGCACACAGAGAACTCACCATGGAGTTTGG\n++\n+#1BDDDFFHHHHHJJJJGJIJJJJJJJHJJJJJJJJJJJJJJJJJIJFHHIJJHHHFFFFFFEEEEEDDDDDDDDDDDDDDDDDDDDDDDDDDCDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4781:1970 1:N:0:GAGCTT\n+NAAAAAGACAGTGGTACAACGCAGAGTTGGCTATATTGTCTTCTTGGGGGATGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGCACCTGT\n++\n+#1=DDDFFHHHHHJJJJJJJJJJJHIGHIJJJJJJJJJHIJJIJJJJFHHIIJJJHHHHHHFFEEFFDEEEEEDDDDDCDDEDDDDDDCDDDDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4806:1979 1:N:0:TAGCTT\n+NGGGAGACGGTGACCGGGGTTCCCTGGCCCCAACCAGGACGACCTCCTACACGACCTCCAAGGTTACGGCCTCTCGCACAGTAATAGACAGCCGTGTCCG\n++\n+#4=DDDFFHHHHHIIIJJJJJJJJJIIIJJJJJJJJJJJJJHHFFFD;AEEDDDBDDDDDDDDDDCCBBBDBDDDDD@BBDDEDDDDDDCDDD<@@BBCB\n+@HWI-ST330:342:H11F0ADXX:1:1101:4824:1983 1:N:0:TAGCTT\n+NAGAGACGGTGACCGGGGTTCCCTGGCCCCACATGTCGGATGCTTCCCAACCACCTCCAGTATTCGTATCTCTCGCACAGTAATAAACAGCCGTGTCCTC\n++\n+#1=DDDFFHHHHHIHIJJHIIJJJJJJJJJJJJGGIIJJJJIHHHHHHHFFFCDDDDDDDCCFFFDACDDEDEDBD@BBDDEDDDDDCC?BDBBDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4859:1994 1:N:0:GAGCTT\n+NATGAGACGGTGACCGTGGTCCCTTGGCCCCAGACGTCCAGACCGTAGTAGTAGTAAGGGCGAGATGATAAGGTCCGGTCTCTTGCACAGAAGTAAATGG\n++\n+#1=DDDFFHFHHHJIJGHIGIJJIJJIIIJJJJJIIJJJJJJJIJFGGEHEHHEEHHHFFDC;@BBD>CDDCD@CDBDBDDDDDCCCDDDDDDCCDDE@C\n+@HWI-ST330:342:H11F0ADXX:1:1101:4998:1997 1:N:0:TAGCTT\n+NGGAAGGTCAGTGGTATCAACGCAGAGTTTGTTGGAATACTGTCTTGGGGGATGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGCACCTG\n++\n+#1=DDFFFHHHHHJIIJHIJJJIJJJIIJJJGIJGIJJJJJJGIIJI9DHIIIJJHHHHHHFFDEFFEDEDCEDDDDDDCDDEDCDC?CDDDDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4956:1999 1:N:0:TAGCTT\n+NGAGACGGTGACCGGGGTTCCCTGGCCCCAGTAGTCAAATATGCCCCCCCTCGTTTCTGACACTGTCGCACAGTAATACACGGCCGTGTCCTCAGATCTC\n++\n+#4=DDFFFHHHHHIJJJJJJJJJJJJJJJJJIJJJJJJJJGGIJJIJJFD@@@?@BDDD:@@AC>>CBB>BDDDDDCA@>@<>BD955ABCCD>C@@CDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:5031:1912 1:N:0:GAGCTT\n+NTCAAACTCAGTGGTATCAACGCAGAGTTGCCTCCGATATTCTCTTGGGGGATACTCTCTGAGAGTCCTGGACCTCCTGTGCAAGAACATGAAACACCTG\n++\n+#1=DDDFFHHHHHJIJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJHJJJHHHHFFFFFFEEEEEEDDDDDDDDDDDCDDDEDDDDDDDDDDDDDDDDD\n' |
| b |
| diff -r 000000000000 -r d38cfb922f95 test-data/sample_IGH_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_IGH_R2.fastq Thu Oct 10 18:03:22 2019 -0400 |
| b |
| b'@@ -0,0 +1,800 @@\n+@HWI-ST330:342:H11F0ADXX:1:1101:1461:1915 2:N:0:NAGCTT\n+NCGAAGCCCAGTGGTATCAACGCAGAGTACGATAATTTCGTTTCTTGGGGGAGTCTCCCTCACTGCCCAGCTGGGATCTCAGGGCTTCATTTTCTGTCCT\n++\n+#11ABDDDFFBHHEHEGIGGGDGHIIEIHHIIIIIGGGIIIIBGIDG@GIIEHEEEEECC@CBCCCCAC?55@?8?@?ACCCCB@BBCCDDD@A@4:@C:\n+@HWI-ST330:342:H11F0ADXX:1:1101:1434:1930 2:N:0:NAGCTT\n+NNANACGGTGACCAGGGTCCCCTGACCCCAGGGGTCGAACCAGTCGTAGCAGCTGTCACCAGGACAAAATGCCCCGCCTCTCGCGCAGTAATAAGTAGCC\n++\n+##0#22@?@??@@????@@?@?@?<????????????????>????9>???????=????<===<>;<<<<=<;;;9:995:88:9::8:<=========\n+@HWI-ST330:342:H11F0ADXX:1:1101:1461:1989 2:N:0:NAGCTT\n+NGAGACGGTGACCAGGGTTCCCTGGCCCCAATTGTCAAAGTAGTATAATAACCACTACCGGGGGCCTTTCGCGCAGTAATATACGGCCGTGTCCTCGGCT\n++\n+#4:DDDDDFDHBFEFGGHHHIJ<>AHGDGIHEFGBDHIGB09DF8?DG9BF@BAHE)8CGGFB6=88(+4+5>;B<@AC@C:@C8<95-0&2834>3>B8\n+@HWI-ST330:342:H11F0ADXX:1:1101:1425:1998 2:N:0:NAGCTT\n+NNNNACGGTGACCAGGGTTCCCTGGCTCCAGGGGTCGAACCAGTTGTAGGCGTTACCACCGTAGTCTGTCGCACAGTAATAGACGGCCGTGTCTGCGGCG\n++\n+####22@@@?@?@?@@@@@@@@>@?@?@@????????????>?????????????????====<<=>?=?<<7;<<:;<==::<9::998:8;===::95\n+@HWI-ST330:342:H11F0ADXX:1:1101:1569:1912 2:N:0:NAGCTT\n+AAGAGACGGTGACCGGGGTTCCCTGGCCCCAAAGTCTTCCGTAGTCACCCTTTCCCCCGCCATCATCTCTCGCACAGTAATAGAAGGCCGTGTCGTCAAG\n++\n+CCCFFFFFHHHHHJJJJJHHFIJJIJJJJJJJGIIJIJJJICHEDHEHIGHHHFFFFE?BDDDDDDDDDCDBBDDDCDEDEECCDDDCDBBBDDBBD?BC\n+@HWI-ST330:342:H11F0ADXX:1:1101:1613:1915 2:N:0:GAGCTT\n+CTAAAGCCCAGTGGTATCAACGCAGAGTTGTTTCGGATGTTTTCTTGGGGGAGCACTGGGATTCCGAGGTGTTTCCATTCGGTGATCAGCACTGAACACA\n++\n+@@@FDEDDHHHHHJIJIJJJIHGGHHGHIJJJJIJJIJGEHIIHHIHGHJJHHDFEFDE@ECCCDD:@B;?CBDCCDEEDCBDDDCDEDADDDDDCDDD<\n+@HWI-ST330:342:H11F0ADXX:1:1101:1522:1922 2:N:0:NAGCTT\n+GGCAAGCCCAGTGGTATCAACGCAGAGTTCAATTGTCTGAGCTCTTGGGGGAGATCCGCTAGCGCTACCGGACTCAGATCCCAGTCTGGACCTGAGGTGC\n++\n+@CCFF?FFHH;FHEIGFFHIEHIIHIJJGIIJJGDGHIIJII@HHD?DDGHHEEEHEBBBBBEDDBBDCDDDDBCD@AADDCCDAACDDCACCDCDD>AC\n+@HWI-ST330:342:H11F0ADXX:1:1101:1658:1922 2:N:0:GAGCTT\n+CTGAAAGACAGTGGTATCAACGCAGAGTATACTCCACTAACTTCTTGGGGGATGCTTTCTGAGAGTCATGGACCTCCTGTGCAAGAACATGAAGCACCTG\n++\n+CC@FDFFFHHHHHIIIHIIICHGDHIIIEHHIIIIIII>DHIIGGIGIIGII<EEEEH:CEEECF?D;;;3>@ECCBCCA@CDCCCCCCCCCCCCCCBCC\n+@HWI-ST330:342:H11F0ADXX:1:1101:1591:1923 2:N:0:NAGCTT\n+ATAAAAATTAGTGGCAGCAAGGCAGCGTTATCTAATCTGAAGTCCTGGGGGGGACCAACCCTGGAATTCCAACTGGCTTCGCCTTGTTGGTGAGGCTCGC\n++\n+??7D;:+222<<A;<A2<;<3<;AC+:?C)1*0*:::B?499?909?8(7@#################################################\n+@HWI-ST330:342:H11F0ADXX:1:1101:1729:1931 2:N:0:GAGCTT\n+GACAAAGACAGTGGTATCAACGCAGAGTCGCTTGCTATCTAATCTTGGGGGAGATCCGCTAGCGCTACCGGGCTCAGATCCCAGTCTGGACCTGAGGTGC\n++\n+88:BA?D>DF>DDGIIIIIIIEHGCFGICE0@GHIG@B9F@<BDHIIIIIIFHECD;;,93;C>?B?2589;59?>C>@?>944>::A<(2?393<@3<>\n+@HWI-ST330:342:H11F0ADXX:1:1101:1655:1947 2:N:0:TAGCTT\n+CGAGACGGTGACCGTGGTCCCTTTGCCCCAGACGTCCATGTAGTAGTAGTGACGACCGATAGCAGCTGGTACTACTACAATACCTCTCGCACAGTAATAC\n++\n+B@@FDDFFHHGHHJJJIIJIJAHHIEIIIICGIGHGHCGHDDIHIIHGICHGIJIGHB>BBDDDDBCCCCDDDDCCACDDDDDCDDCDDD><@C:>@DCD\n+@HWI-ST330:342:H11F0ADXX:1:1101:1505:1958 2:N:0:NAGCTT\n+TGAGACGGTGACCGTGGTCCCTTGGCCCCAGACGTCCATACCGTAGTAGTAGTAGTAATAAGGGGTGTAAGGCTGCTTACCACTCCAAAAATCGCGTTGG\n++\n+@CCFDDFFHHHHHJJJJJJJJJJJGIJIJJJJJJJJJIJJJIJIJIHIIHJIEHIGHGHHHFEFF6>@CEDCDCBDCDDDDCDDDCDDDDDBDDDDBBBB\n+@HWI-ST330:342:H11F0ADXX:1:1101:1660:1964 2:N:0:GAGCTT\n+CAAAGACGGTGACCGTGGTCCCTTGGCCCCAGACGTCCGTACCGTAGTAGTAGGGGCAGCTGGTACTGCTACAATCCTCTCTCGCACAGTAATACACCGC\n++\n+=?7+=22=C<<<AE11<E<CFEEEEEADID60)0??@?(8B7ADC#######################################################\n+@HWI-ST330:342:H11F0ADXX:1:1101:1527:1967 2:N:0:NAGCTT\n+TTAAAAGACAGTGGTATCAACGCAGAGTTCGTTTAATTTGGTTCTTGGGGGACTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAACATGAAACACCTGTG\n++\n+;==AAAA<=@+2?+2??+7<<3=<)):1:@;?;AB>B?BBB)9???<ABAA<AAAA7A9;?#######################################\n+@HWI-ST330:342:H11F0ADXX:1:1101:1630:1977 2:N:0:GAGCTT\n+GTTAAAGACAGTGGTATCAACGCAGAGTTGGCTAAGCTTTGTTCTTGGGGGCTTTCTGAGAGTCCTGGACCTCCTGTGCAAGAACATGAAACATCTGTGG\n++\n+B@CFDFFFHHHHHJJJJJJJJJJJJGIJJIIIJJJJJJIJJFHHIJJIIJJGIIJHHHHFEFBDFFFEEECDDDDDCCDDDDDDDDDDCCCDDDDDCCDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:166'..b'JJJGIJGIIJJHHHH?CE?BAECEEDDD=:B@B<@BACCDDCDDDDDBDD<AC\n+@HWI-ST330:342:H11F0ADXX:1:1101:4879:1921 2:N:0:TAGCTT\n+AACAAACTCAGTGGTATCAACGCAGAGTACAGTCCGTTTTAGTCTTGGGGGCAGATCCGCTAGCGCTACCGGACTCAGATCCCAGTCTGGACCTGAGGTG\n++\n+CCCFFFFFHHHHHJJJJJJJJJJJJJJJIJJJJJJJHIJJJEGHIJJJJJJJJHHHGHEDFDDDDDDDBDDDDDBDDDCDDDDDDDDDDD>BCDDDDD9A\n+@HWI-ST330:342:H11F0ADXX:1:1101:4828:1925 2:N:0:TAGCTT\n+GACGGTGACCGGGGTTCCCTGGCCCCAAAGTCTTCCGTAGTCACCCTTTCCCCCGCCATCATCTCTCGCACAGTAATAGAAGGCCGTGTCGTCAAGTCTC\n++\n+CBCFFDDFHHHHHJIJCCFHIIJJJJJIJJHIJJJJJJJJGHGHIJJJJJHGHGFDDD?CDDDCDCDBBDDDDDEDEEDDDDDDDDDDDDD@D<@DCDED\n+@HWI-ST330:342:H11F0ADXX:1:1101:4769:1933 2:N:0:TAGCTT\n+AGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAGTCAAAGTCATCCGAATAATCGGTAGTTCCAGTGCGTGTTCTCGCACAGTAATACACGGCCGTGTCC\n++\n+BCCFDFFFHHHHHJJJJJJJJJJJJIJJJJJJJJIJJJJJHIIJJJJHIJIIIIJJ;EHGHHHFHACDEDCDECDDDCDDDDCCDDEDDDDDDDD<BBDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4919:1935 2:N:0:TAGCTT\n+AGAAAGCCCAGTGGTATCAACGCAGAGTTTTTTGCCGTCGATTCTTGGGGGAGATCCGCTAGCGCTACCGGACTCAGATCCCAGTCTGGACCTGAGGTGC\n++\n+@CCFDFFFHHHHHJJJJJJJJJJJJJJJJJJJJJGIJJIJIJIJJJJJIJHFD@CDCDBDDDDD@?;>C>;9>BCCDCACDDDDDDCDC:?CDDDDD?BA\n+@HWI-ST330:342:H11F0ADXX:1:1101:4850:1938 2:N:0:TAGCTT\n+ATTAAAGACAGTGGTATCAACGCAGAGTGTAGTACGTTACTTTCTTGGGGGGAGCATCACCCAGCAACCACATCTGTCCTCTAGAGAATCCCCTGAGAGC\n++\n+@@@DDDDDFDFFFIFF4EBHFII6FFDGIIIIIEFFEGIFFIIFIFIFFBBB-:<BB<AABB<B@BB?BB??B:>BDAA@>A>B<>:9@A>>?<B<<AA@\n+@HWI-ST330:342:H11F0ADXX:1:1101:4806:1954 2:N:0:TAGCTT\n+AGAAAACTCAGTGGTATCAACGCAGAGTTGAATTGCCTACGTTCTTGGGGGGTGCTTTCTGAGAGTCATGGACCTCCTGCACAAGAACATGAAACACCTG\n++\n+CCCFDFFFHHHHHJJJIJJJJJJJJJIJJJJJJJJJJJJJIEIIIIIIIIJD5<BDDDDDDEDDD@CCDDCDDDDDDDDDDCDDDDDDDDDCDDDDDDDC\n+@HWI-ST330:342:H11F0ADXX:1:1101:4920:1959 2:N:0:GAGCTT\n+CGGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAGTCAAAGTAGTACAAGATAGTAGGTCCCCCTAGTCTCGCACAGTAATAGACGGCCGTGTCCTCGGC\n++\n+CCCFFFFFHHHGHJJJGJIHHIJJJJJJJJJJJJJJJJJJIFHIGIJJJIHFGIIGIJAHIIJJHHH>DCEFFDDDDACCDECCDDDDDDBBDDDDDDDD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4852:1963 2:N:0:TAGCTT\n+TGCGAGACGGTGACCAGGGTTCCCTGACCCGAGTACTCAGCTGGGACTCCCGCGCGGAAGTCTCTTGCACAGTAATAAACAGCCGTGTCCTCGGCTCTCA\n++\n+BCCFDFFFHHHHHJJJJJJIIJJJJJJJJJJHJIJJJJJJIIGIJIIEHHJJIHFDDBBDDDEDDDDDDDCDACCDEDDDACAADBDDDDCD@DB?<CDC\n+@HWI-ST330:342:H11F0ADXX:1:1101:4781:1970 2:N:0:GAGCTT\n+AGACGGTGACCAGGGTTCCCTGGCCCCAGGGGTCGAACCAGTTGTAGGCGTTACCACCGTAGTCTCTCGCACAATAATAGACGGCCGTGTCTGCGGCGGT\n++\n+CCCFDFDDHHHHHJJIIJJJJIHHJJJJIJJJHIJIIJJJJGIICEGIJIEHFFFFFDDABD?DCDCDDB=BDDDDDEEDACDDDDB9>ABCDDBDD>B#\n+@HWI-ST330:342:H11F0ADXX:1:1101:4806:1979 2:N:0:TAGCTT\n+CATAAGCCCAGTGGTATCAACGCAGAGTCATGTAGCGTATAATCTTGGGGGGCTTTCTGAGAGTCATGGACCTCCTGCACAAGAACATGAAGCACCTGTG\n++\n+BCCDDDDFHHHHHJJJIJJJIJGHHIIIIGDHJIIHJJJJFIIJIGHIJJJD@DDCCDDEDDDDDDEDCDDCDDBDDDDDDDDDDDDDDCDDDDDBCC>C\n+@HWI-ST330:342:H11F0ADXX:1:1101:4824:1983 2:N:0:TAGCTT\n+CCGAAGGTCAGTGGTATCAACGCAGAGTAGCTTGGCTTCCGGTCTTGGGGGAGAGGTGCCTTAGCCCTGGATTCCAAGGCATTTCCACTTGGTGATCAGC\n++\n+CCCFFFFDHHHHHJJJIJJJJJJJJJJJIJIIJJJJIJIIGHIIJIJJIII:=4=A;;@CCCA@CDC?AA<ACDEE>C<?8CCACDA>CACC4<4:@ACD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4859:1994 2:N:0:GAGCTT\n+GGCAAGCCCAGTGGTATCAACGCAGAGTTACGTAGAGTGCAGTCTTGGGGCTCAGGTGAAGAAGCCCGGGGCCTCAGTGGAAGTCTTCTGCGCGGCGTCT\n++\n+B@CFFFFFHHHHHJJJJJJJJJJJJJJIJJJJJIGGJJIIEIEHJJJGIJJIJGHIDHIJHHHGHFFFCDDBDDDDC:ACCCD>CDEDDDDBDDDBB<BD\n+@HWI-ST330:342:H11F0ADXX:1:1101:4998:1997 2:N:0:TAGCTT\n+AGGAGACGGTGACCAGGGTTCCCTGGCCCCAGTAGTCAGCGCCACCCACGGGGGGGGGGGGAACTACCCCCCAAATTTCCCCCCCCCCCCCCACACGGTA\n++\n+@@CFBDFDFCBH>FIHBHEGFEHEHHEIFHC@GEGBGA@ADG:@AGGGIIIB9278BB5<0&)84>@A?BBB9@8@C@C>CCB@BB##############\n+@HWI-ST330:342:H11F0ADXX:1:1101:4956:1999 2:N:0:TAGCTT\n+GGGAAACTCAGTGGTATCAACGCAGAGTATCATCGTCTTGCTTCTTGGGGGATCACATAACAACCACATTCCTCCTCTAAAGAAGCCCCTGGGAGCACAG\n++\n+@@@FFFFFHHHHHJIJJJJJJJJJJJJJGGGJJJGIGIGIIIJJJJJJJJJAAEGHFHCEHFFB?BC=@CDDDDCD?C:@@CCD:ABBBDDDDABBBBD<\n+@HWI-ST330:342:H11F0ADXX:1:1101:5031:1912 2:N:0:GAGCTT\n+AAGAGACGGTGACCAGGGTTCCCTGGCCCCAGTTGTCGGGAGGACCATAGCTGTATTTTACCCCCCTCGCACAATAATACACGGCCGTGTCCGCAGCGGT\n++\n+CCCFFFFDGHHGHJJIJJFGHGIJIJJJJJJIGHIGIIIJJIIJIICGEGGEHCHHGHFBEFFDDDDD?BDDDDDDDEDCCCBDDDBD>BDDDDDDD390\n' |