| Previous changeset 11:666bb48b1007 (2019-10-02) Next changeset 13:e3d32471da11 (2020-04-25) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" |
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modified:
macros.xml |
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added:
salmonquant.xml umiout.sh vpolo_convert.py |
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removed:
old/README.rst old/salmon.xml old/static/images/ReadLibraryIllustration.png old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv old/test-data/cached_locally/prebuilt_index/hash.bin old/test-data/cached_locally/prebuilt_index/header.json old/test-data/cached_locally/prebuilt_index/indexing.log old/test-data/cached_locally/prebuilt_index/quasi_index.log old/test-data/cached_locally/prebuilt_index/refInfo.json old/test-data/cached_locally/prebuilt_index/rsd.bin old/test-data/cached_locally/prebuilt_index/sa.bin old/test-data/cached_locally/prebuilt_index/txpInfo.bin old/test-data/cached_locally/prebuilt_index/versionInfo.json old/test-data/cached_locally/salmon_indexes_versioned.loc old/test-data/gene_map.tab old/test-data/reads_1.fastq old/test-data/reads_1.fastq.bz2 old/test-data/reads_1.fastq.gz old/test-data/reads_2.fastq old/test-data/reads_2.fastq.bz2 old/test-data/reads_2.fastq.gz old/test-data/reads_both.fastq old/test-data/reads_both.fastq.bz2 old/test-data/reads_both.fastq.gz old/test-data/salmon_genMap_result1.tab old/test-data/salmon_quant_result1.tab old/test-data/transcripts.fasta old/tool-data/salmon_indexes_versioned.loc.sample old/tool_data_table_conf.xml.sample old/tool_data_table_conf.xml.test |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 macros.xml --- a/macros.xml Wed Oct 02 04:31:53 2019 -0400 +++ b/macros.xml Tue Oct 15 12:01:08 2019 -0400 |
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| @@ -1,5 +1,5 @@ <macros> - <token name="@VERSION@">0.14.1</token> + <token name="@VERSION@">0.14.1.2</token> <token name="@GALAXY_VERSION@">galaxy0</token> <token name="@IDX_VERSION@">q6</token> <xml name="requirements"> @@ -8,6 +8,10 @@ <requirement type="package" version="1.2">seqtk</requirement> <requirement type="package" version="0.14.1">salmon</requirement> <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="0.2.0">vpolo</requirement> + <requirement type="package" version="1.17.2">numpy</requirement> + <requirement type="package" version="0.25.1">pandas</requirement> + <requirement type="package" version="1.3.1">scipy</requirement> </requirements> </xml> <xml name="stranded"> |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/README.rst --- a/old/README.rst Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,62 +0,0 @@ -Galaxy wrappers for salmon -===================================== - -These wrappers are copyright 2014, updated 2018 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. -All rights reserved. See the licence text below. - -Currently tested with salmon 0.11.2. - - -Automated Installation -====================== - -Galaxy should be able to automatically install the salmon for you if you have Conda dependency management enabled in Galaxy. -For more information please read the documentation at: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/conda_faq.rst - - -History -======= - -======== ====================================================================== -Version Changes --------- ---------------------------------------------------------------------- -v0.6.3.0 - First release --------- ---------------------------------------------------------------------- -v0.7.2 - Second release --------- ---------------------------------------------------------------------- -v0.8.2 - Third release --------- ---------------------------------------------------------------------- -v0.9.1 - Fourth release --------- ---------------------------------------------------------------------- -v0.11.2 - Fifth release - -======== ====================================================================== - - -Bug Reports -=========== - -You can file an issue here https://github.com/bgruening/galaxytools/issues or ask -us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev - - -Licence (MIT) -============= - -Permission is hereby granted, free of charge, to any person obtaining a copy -of this software and associated documentation files (the "Software"), to deal -in the Software without restriction, including without limitation the rights -to use, copy, modify, merge, publish, distribute, sublicense, and/or sell -copies of the Software, and to permit persons to whom the Software is -furnished to do so, subject to the following conditions: - -The above copyright notice and this permission notice shall be included in -all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER -LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, -OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN -THE SOFTWARE. |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/salmon.xml --- a/old/salmon.xml Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,885 +0,0 @@\n-<tool id="salmon" name="Salmon" version="@VERSION@">\n-\n- <description>Transcript Quantification from RNA-seq data</description>\n-\n- <macros>\n- <xml name="strandedness">\n- <param name="strandedness" type="select" label="Specify the strandedness of the reads">\n- <option value="U" selected="True">Not stranded (U)</option>\n- <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>\n- <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>\n- </param>\n- </xml>\n- <xml name="orientation">\n- <param name="orientation" type="select" label="Relative orientation of reads within a pair">\n- <option value="M">Mates are oriented in the same direction (M = matching)</option>\n- <option value="O">Mates are oriented away from each other (O = outward)</option>\n- <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>\n- </param>\n- </xml>\n- <token name="@VERSION@">0.11.2</token>\n- <token name="@IDX_VERSION@">q5</token>\n- </macros>\n-\n- <requirements>\n- <requirement type="package" version="1.0.6">bzip2</requirement>\n- <requirement type="package" version="@VERSION@">salmon</requirement>\n- <requirement type="package" version="1.2">seqtk</requirement>\n- </requirements>\n-\n- <stdio>\n- <exit_code range="1:" />\n- <exit_code range=":-1" />\n- <regex match="Error:" />\n- <regex match="Exception:" />\n- <regex match="Exception :" />\n- </stdio>\n- <version_command>salmon -version</version_command>\n- <command><![CDATA[\n- mkdir ./index\n- &&\n- mkdir ./output\n- #if $refTranscriptSource.TranscriptSource == "history":\n- &&\n- salmon index\n- --transcripts $refTranscriptSource.ownFile\n- --kmerLen $refTranscriptSource.kmerLen\n- --threads "\\${GALAXY_SLOTS:-4}"\n- --index \'./index\'\n- --type \'$quasi_orphans.type\'\n- $perfectHash\n- #set $index_path = \'./index\'\n- #else:\n- #set $index_path = $refTranscriptSource.index.fields.path\n- #end if\n- &&\n- #set compressed = \'no\'\n- #if $single_or_paired.single_or_paired_opts == \'single\':\n- #if $single_or_paired.input_singles.ext == \'fasta\':\n- #set $ext = \'fasta\'\n- #else:\n- #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set compressed = \'GZ\'\n- #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set compressed = \'BZ2\'\n- #end if\n- #set $ext = \'fastq\'\n- #end if\n- ln -s $single_or_paired.input_singles ./single.$ext &&\n- #else if $single_or_paired.single_or_paired_opts == \'paired\':\n- #if $single_or_paired.input_mate1.ext == \'fasta\':\n- #set $ext = \'fasta\'\n- #else:\n- #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):\n- #set compressed = \'GZ\'\n- #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n- #set compressed = \'BZ2\'\n- #end if\n- #set $ext = \'fastq\'\n- #end if\n- ln -s $single_or_paired.input_mate1 ./mate1.$ext &&\n- ln -s $single_or_paired.input_mate2 ./mate2.$ext &&\n- #else if $single_or_paired.single_or_paired_opts == \'paired_collection\':\n- #if $single_or_paired.input_1.forward.ext == \'fasta\':\n- #set $ext = \'fasta\'\n- #else:\n- #if $single_or_paired.input_1.forward.is_of_type('..b'may be unstraned or strand-specific. Finally, paired-end\n-protocols will have a specified relative orientation. To characterize the\n-various different typs of sequencing libraries, we\'ve created a miniature\n-"language" that allows for the succinct description of the many different types\n-of possible fragment libraries. For paired-end reads, the possible\n-orientations, along with a graphical description of what they mean, are\n-illustrated below:\n-.. image:: ReadLibraryIllustration.png\n-The library type string consists of three parts: the relative orientation of\n-the reads, the strandedness of the library, and the directionality of the\n-reads.\n-The first part of the library string (relative orientation) is only provided if\n-the library is paired-end. The possible options are:\n-::\n-\n- I = inward\n- O = outward\n- M = matching\n-\n-The second part of the read library string specifies whether the protocol is\n-stranded or unstranded; the options are:\n-::\n-\n- S = stranded\n- U = unstranded\n-\n-If the protocol is unstranded, then we\'re done. The final part of the library\n-string specifies the strand from which the read originates in a strand-specific\n-protocol \xe2\x80\x94 it is only provided if the library is stranded (i.e. if the\n-library format string is of the form S). The possible values are:\n-::\n-\n- F = read 1 (or single-end read) comes from the forward strand\n- R = read 1 (or single-end read) comes from the reverse strand\n-\n-So, for example, if you wanted to specify a fragment library of strand-specific\n-paired-end reads, oriented toward each other, where read 1 comes from the\n-forward strand and read 2 comes from the reverse strand, you would specify ``-l\n-ISF`` on the command line. This designates that the library being processed has\n-the type "ISF" meaning, **I**\\ nward (the relative orientation), **S**\\ tranded\n-(the protocol is strand-specific), **F**\\ orward (read 1 comes from the forward\n-strand).\n-The single end library strings are a bit simpler than their pair-end counter\n-parts, since there is no relative orientation of which to speak. Thus, the\n-only possible library format types for single-end reads are ``U`` (for\n-unstranded), ``SF`` (for strand-specific reads coming from the forward strand)\n-and ``SR`` (for strand-specific reads coming from the reverse strand).\n-A few more examples of some library format strings and their interpretations are:\n-::\n-\n- IU (an unstranded paired-end library where the reads face each other)\n-\n-::\n-\n- SF (a stranded single-end protocol where the reads come from the forward strand)\n-\n-::\n-\n- OSR (a stranded paired-end protocol where the reads face away from each other,\n- read1 comes from reverse strand and read2 comes from the forward strand)\n-\n-.. note:: Correspondence to TopHat library types\n-\n- The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq\n- read aligner has a different convention for specifying the format of the library.\n- Below is a table that provides the corresponding Salmon/salmon library format\n- string for each of the potential TopHat library types:\n-\n- +---------------------+-------------------------+\n- | TopHat | Salmon (and Sailfish) |\n- +=====================+============+============+\n- | | Paired-end | Single-end |\n- +---------------------+------------+------------+\n- |``-fr-unstranded`` |``-l IU`` |``-l U`` |\n- +---------------------+------------+------------+\n- |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |\n- +---------------------+------------+------------+\n- |``-fr-secondstrand`` |``-l ISF`` |``-l SF`` |\n- +---------------------+------------+------------+\n-\n- The remaining salmon library format strings are not directly expressible in terms\n- of the TopHat library types, and so there is no direct mapping for them.\n-]]> </help>\n- <citations>\n- <citation type="doi">10.1101/021592</citation>\n- </citations>\n-</tool>\n' |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/static/images/ReadLibraryIllustration.png |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv --- a/old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,1 +0,0 @@ -RetainedTxp DuplicateTxp |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/hash.bin |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/header.json --- a/old/test-data/cached_locally/prebuilt_index/header.json Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,14 +0,0 @@ -{ - "value0": { - "IndexType": 1, - "IndexVersion": "q5", - "UsesKmers": true, - "KmerLen": 31, - "BigSA": false, - "PerfectHash": false, - "SeqHash": "238a71484cdcf251805629c612f7edd515eb1a23d9be2e2014b62fd5931eb4ac", - "NameHash": "2fc64c34c65a78d18fec933772e1aa454cfed52b2b48d43eb75d2933a22feb04", - "SeqHash512": "a45ea3d0c5f11c16a45b8b75f902f908996117d7486d72b3d19a8ae619b07b22f3ca0888f5ee6e9dbabf639ae51f7fc74b8eea8808435bbb2ec70b96162849aa", - "NameHash512": "6123f1c58bf2153fca204e97fa72a2d25460242f14b886e421316ff251cc57293e77c02d536122e97f46d2508c626e42a35a1798209766359904ddf49fb7bf33" - } -} \ No newline at end of file |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/indexing.log --- a/old/test-data/cached_locally/prebuilt_index/indexing.log Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -[2019-07-25 13:45:20.599] [jLog] [info] building index -[2019-07-25 13:45:20.654] [jLog] [info] done building index |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/refInfo.json --- a/old/test-data/cached_locally/prebuilt_index/refInfo.json Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -{ - "ReferenceFiles": [ - "tools/salmon/test-data/transcripts.fasta" - ] -} \ No newline at end of file |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/rsd.bin |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/sa.bin |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/txpInfo.bin |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/prebuilt_index/versionInfo.json --- a/old/test-data/cached_locally/prebuilt_index/versionInfo.json Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -{ - "indexVersion": 2, - "hasAuxIndex": false, - "auxKmerLength": 31, - "indexType": 1 -} \ No newline at end of file |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/cached_locally/salmon_indexes_versioned.loc --- a/old/test-data/cached_locally/salmon_indexes_versioned.loc Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,33 +0,0 @@ -# salmon_indexes_versioned.loc.sample -# This is a *.loc.sample file distributed with Galaxy that enables tools -# to use a directory of indexed data files. This one is for Salmon. -# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup -# First create these data files and save them in your own data directory structure. -# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools. -# Copy this file, save it with the same name (minus the .sample), -# follow the format examples, and store the result in this directory. -# The file should include an one line entry for each index set. -# The path points to the "basename" for the set, not a specific file. -# It has four text columns seperated by TABS. -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> <version> -# -# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" - - - -# So, for example, if you had sacCer3 indexes stored in: -# -# /depot/data2/galaxy/sacCer3/salmon_indexes/ -# -# then the salmon_indexes.loc entry could look like this: -# -#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 -# -#More examples: -# -#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 -#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 -# -# -hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q5 |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/gene_map.tab --- a/old/test-data/gene_map.tab Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,4 +0,0 @@ -NM_174914 foo -NM_001168316 bar -NR_003084 baz -NR_031764 foo |
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| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_1.fastq --- a/old/test-data/reads_1.fastq Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,40000 +0,0 @@\n-@1:NM_014620:16:182\n-GTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@2:NM_014620:1094:172\n-ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@3:NM_022658:294:172\n-TGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@4:NM_022658:1362:195\n-ACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@5:NM_173860:323:180\n-GCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@6:NM_022658:1062:146\n-GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@7:NM_022658:1912:184\n-CTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@8:NM_022658:304:172\n-AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9:NM_174914:46:212\n-ATAACATCCAAGAAAGACACCTTGCATATTCTTTCAGTTTCTGTTTTGTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10:NM_022658:25:186\n-CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@11:NM_022658:1031:165\n-AAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@12:NM_022658:1090:157\n-CTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@13:NM_173860:524:97\n-CAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTAT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@14:NM_022658:1471:182\n-CCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@15:NM_022658:1173:198\n-CACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@16:NM_022658:1052:179\n-CAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGGGCAGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@17:NM_022658:1351:186\n-TCCATCAGGTTCCTAGAGAAAGTCAAGGGGGTTTTTCTAAGCAGGGAGCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@18:NM_022658:1777:222\n-TAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTTTAAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@19:NM_018953:838:165\n-GCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCACAGACAAAAGCGCTTTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@20:NM_022658:997:196\n-GGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGAGTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@21:NM_022658:1639:210\n-TCGGGCCCATGCCTTCCTCTCCTTCGCTGTTTGATTTCTATTCTGTTGGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@22:NM_174914:42:131\n-TCAGGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@23:NM_022658:782:137\n-TTCTTTTTTGCTTAGTCCTTGTTTTCTTCCTTTTCCTCCTCTTCTTTCTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@24:NM_022658:623:187\n-AGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAACTAGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@25:NM_022658:1061:175\n-GGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@26:NM_174914:1681:185\n-AGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@27:NM_022658:619:223\n-GGGGAGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAAC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@28:NM_022658:1432:199\n-GAAATAAGGAAAAAAGCAAGGAATATCCCCTCCCCCTCCCCCTCCCCCTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@29:NM_173860:122:191\n-CGCCGCCACCCTCGGCGCACGGCTCGCGGTAGTAACCCTTGCCGTCCTCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@30:NM_022658:1594:160\n-GCCTGCAGTCGCCTCTAAAATCCTACCTAACCATCCCATGGTCACTCGGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@31:NM_153633:1041:170\n-ATTTCCCCTGAAATTCACCCAAGCCAGACCATCACACCTTGCAATATATA\n-'..b'IIIIIIIIIIIIIIIIIIIIIIII\n-@9971:NM_022658:1616:193\n-TTCTTTTTCAAGATTATTGCAGGTTCCCTTTAGGTAGTATGTTAAAGATT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9972:NM_006897:924:149\n-ATATCTCAACACTGAACCCTCCCAAATCGCAAGAGTTTTCTTTTCCCCTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9973:NM_174914:1854:200\n-GGAATCCATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9974:NM_022658:453:180\n-AGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9975:NM_022658:963:167\n-GTTTCTCCGTCTCCCCCCTCCAGCCCCCAAACAAATAAAGAGTGGGGGAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9976:NM_014620:1302:181\n-GTTATGTTTTATAACCTGGTAATGTCCTCTGCCCGTTGCTGCTCCGGCGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9977:NM_022658:175:88\n-CAGCATGAGCTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9978:NM_022658:57:146\n-GCCCAGTCCCGGGGAGCCAGCTGGCCTGGGGTTCGGTCCCGGGGGGAGGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9979:NM_174914:1282:193\n-GGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGATTTCCGGATTCTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9980:NM_014620:772:176\n-GGTGGTGGCCCGCCTGGGCCGGCCCGTGGCCTCGCGAATTGCCGGGCCCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9981:NM_022658:184:203\n-CTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCGGCGAGTCCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9982:NM_022658:1973:206\n-ATGACAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9983:NM_174914:435:160\n-CTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGCTAGCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9984:NM_022658:470:179\n-TCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9985:NM_014620:1158:203\n-GGACAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCAT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9986:NM_022658:1194:170\n-TTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9987:NM_174914:1475:158\n-GTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9988:NM_004503:167:199\n-GAGAGCATGTCTTTCTCCTGGTAAAAGGAATTAGATCCATAGTCATACGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9989:NM_022658:1203:166\n-CTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9990:NM_006897:430:179\n-TTTGTGCTTGCTGCCGGCGAGCGCGTCCGCCTCGGGCGAGGGCAGTGTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9991:NM_173860:200:188\n-ACGGCTCCAGCGGGAGCAGCGCTGCCCCGGGCCCGGCTCCCGGGTCGCGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9992:NM_022658:826:161\n-TAAACTTCTCAATTTATCTGCTACCATAAAACGAAACTTCAAGGGAGTTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9993:NM_014620:1162:157\n-AGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9994:NM_022658:752:194\n-AGGGAGTTGCTAAGGGGGGGGGGGTCTTTCTTTTTTGCTTAGTCCTTGTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9995:NM_022658:1888:191\n-AGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9996:NM_014620:1559:191\n-ATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9997:NM_006897:223:164\n-GAGCCAAGTCCGCATGTAGCGCGTGTCGGCGCCGAGGTGGGGCTGGGGGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9998:NM_022658:1995:180\n-ACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9999:NM_022658:1773:182\n-GCATTACAAATACTCTCAAAGCAGGATTTCTTTCTATAGGTAGTGATAAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10000:NM_014620:1728:181\n-GGAAGGAGGAGGAGGAGAAGGATGAGAATTGGCTTTAAAATTTCTTTCCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_1.fastq.bz2 |
| b |
| Binary file old/test-data/reads_1.fastq.bz2 has changed |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_1.fastq.gz |
| b |
| Binary file old/test-data/reads_1.fastq.gz has changed |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_2.fastq --- a/old/test-data/reads_2.fastq Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,40000 +0,0 @@\n-@1:NM_014620:16:182\n-CCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@2:NM_014620:1094:172\n-AGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@3:NM_022658:294:172\n-CTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTCCGTGGCAGCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@4:NM_022658:1362:195\n-ACCCACATCTCCTTCAGGTTTCCATCAGGTTCCTAGAGAAAGTCAAGGGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@5:NM_173860:323:180\n-GATTCCAGCGACTGGCAGGAGGGCGGGTCGTGCGGAGGTCCTGCGCCGCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@6:NM_022658:1062:146\n-GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@7:NM_022658:1912:184\n-GTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@8:NM_022658:304:172\n-CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9:NM_174914:46:212\n-GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10:NM_022658:25:186\n-GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@11:NM_022658:1031:165\n-TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@12:NM_022658:1090:157\n-CGAGGAGCACGGAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@13:NM_173860:524:97\n-CCAGGGCGCGCCGCTGGCCGAGAGCCCGCCGCCGGGGTTCAACGGCGATA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@14:NM_022658:1471:182\n-AGGCATGGGCCCGAGTGACCATGGGATGGTTAGGTAGGATTTTAGAGGCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@15:NM_022658:1173:198\n-ACATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@16:NM_022658:1052:179\n-TGCAGCTCTGGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@17:NM_022658:1351:186\n-AAGGCTAGTGTACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@18:NM_022658:1777:222\n-GGGTTTTCTTAGTGAAATAAGCAGCAACAAACGACAACAAAACCGCATTA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@19:NM_018953:838:165\n-CCTGCGGAGCTTGCCCTGGGCCCCGGGTACCGAGCTGAGCCGAGCTGAGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@20:NM_022658:997:196\n-TTGCTTTTATAGAGAATAGAATGACACTCACAACTCTAACTACCTGTCAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@21:NM_022658:1639:210\n-TTTTTTTCTCCTATAGCAGGATTTTAAAATTTTTCTCTTTTTCTTTTTCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@22:NM_174914:42:131\n-CCCTGTGCTTGAGAGTTCAGGGCCGGACACAGGCTCACAGGTCTCCACAT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@23:NM_022658:782:137\n-ATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCGGGAGCCCGAGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@24:NM_022658:623:187\n-CCTTGTTGTTCTCCTTTTTCCACTTCATCCTTCGGTTCTGGAACCAGATC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@25:NM_022658:1061:175\n-GAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@26:NM_174914:1681:185\n-ATCATGGATTCCTTAAAGAATGAGAACTTCGACATGGTGATAGTTGAAAC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@27:NM_022658:619:223\n-CTTCTCCTCATCTCGGGCTCCCGGCAGTTTATCCTTGTTGTTCTCCTTTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@28:NM_022658:1432:199\n-GGGATGGTTAGGTAGGATTTTAGAGGCGACTGCAGGCTCCTATCTACCCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@29:NM_173860:122:191\n-GCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@30:NM_022658:1594:160\n-TTATTATTTTCGTGATTATGGTGATTTCTGAGCACTAACACTAATGCAGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@31:NM_153633:1041:170\n-CACTGTTAAGGACCCTTTTAAGCATGTGATGTTGTCTTAGCATGGTACCT\n-'..b'IIIIIIIIIIIIIIIIIIIIIIII\n-@9971:NM_022658:1616:193\n-CTACCTAACCATCCCATGGTCACTCGGGCCCATGCCTTCCTCTCCTTCGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9972:NM_006897:924:149\n-AACCCCACAAAATACCCCAACACAGGCGGGGGAGAGACGAAAAAGAAAAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9973:NM_174914:1854:200\n-TTAAAAAGGAAGAAAAATCATATCAAGTTATCAGTTGGCTTGCACCTGAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9974:NM_022658:453:180\n-CACTGCGCCTCCCCGGAGCGTGGGGTCTCATCCATGGAAACATGAGGCTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9975:NM_022658:963:167\n-GTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9976:NM_014620:1302:181\n-GCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTCAGGTCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9977:NM_022658:175:88\n-GAACCGGCAGTCGTAATAGGCCGGTTCCAGGGACTCGCCGGCTTTGTATT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9978:NM_022658:57:146\n-GGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACCCGCGGCCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9979:NM_174914:1282:193\n-CTCTGCTTCCCAACACTGTTTATGTTGGAGGCTTGATGGAAAAACCTATT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9980:NM_014620:772:176\n-ACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9981:NM_022658:184:203\n-AGTTGGAGATGCCGGAGGTGCCGTGGTGGAAGAAGTCTTGAACGTGGTGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9982:NM_022658:1973:206\n-TGCTGCTTATTTCACTAAGAAAACCCAACAACTGAGACTGCCTAGCCCGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9983:NM_174914:435:160\n-TCTAGTCCTTCTAGTTATCTCCTGTTTTCTTGAAGAACAGGAAAAATGGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9984:NM_022658:470:179\n-CTGTAAGTTTGCCGTCCACTGCGCCTCCCCGGAGCGTGGGGTCTCATCCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9985:NM_014620:1158:203\n-CGGGGGTGCTGACCTGACTTTGGTGTTGGGGAGTCGGTGGTCCTTCTTCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9986:NM_022658:1194:170\n-GTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTGCATTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9987:NM_174914:1475:158\n-CTTTAGTTTCTGCAGGAGGCAACAGCACATGCAGTCTACATTTGACAACA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9988:NM_004503:167:199\n-ACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9989:NM_022658:1203:166\n-ATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9990:NM_006897:430:179\n-GGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9991:NM_173860:200:188\n-CTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9992:NM_022658:826:161\n-CCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9993:NM_014620:1162:157\n-CTTCTTCCATTTCATGCGACGGTTTTGGAACCAGATTTTGATCTGCCTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9994:NM_022658:752:194\n-CAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9995:NM_022658:1888:191\n-TGCAATTTAGTTCTACTCTACTGGGGTTAGAAGCACAATAAAAGCGCACA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9996:NM_014620:1559:191\n-GGCCTTTTAAAAAAAAACACCCAGCAGGTACCATGCTAAGACAACATCAC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9997:NM_006897:223:164\n-TGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9998:NM_022658:1995:180\n-CAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCGAGCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9999:NM_022658:1773:182\n-TACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10000:NM_014620:1728:181\n-GGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_2.fastq.bz2 |
| b |
| Binary file old/test-data/reads_2.fastq.bz2 has changed |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_2.fastq.gz |
| b |
| Binary file old/test-data/reads_2.fastq.gz has changed |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_both.fastq --- a/old/test-data/reads_both.fastq Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,80000 +0,0 @@\n-@1:NM_014620:16:182\n-GTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@1:NM_014620:16:182\n-CCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@2:NM_014620:1094:172\n-ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@2:NM_014620:1094:172\n-AGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@3:NM_022658:294:172\n-TGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@3:NM_022658:294:172\n-CTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTCCGTGGCAGCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@4:NM_022658:1362:195\n-ACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@4:NM_022658:1362:195\n-ACCCACATCTCCTTCAGGTTTCCATCAGGTTCCTAGAGAAAGTCAAGGGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@5:NM_173860:323:180\n-GCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@5:NM_173860:323:180\n-GATTCCAGCGACTGGCAGGAGGGCGGGTCGTGCGGAGGTCCTGCGCCGCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@6:NM_022658:1062:146\n-GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@6:NM_022658:1062:146\n-GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@7:NM_022658:1912:184\n-CTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@7:NM_022658:1912:184\n-GTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@8:NM_022658:304:172\n-AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@8:NM_022658:304:172\n-CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9:NM_174914:46:212\n-ATAACATCCAAGAAAGACACCTTGCATATTCTTTCAGTTTCTGTTTTGTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9:NM_174914:46:212\n-GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10:NM_022658:25:186\n-CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10:NM_022658:25:186\n-GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@11:NM_022658:1031:165\n-AAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@11:NM_022658:1031:165\n-TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@12:NM_022658:1090:157\n-CTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@12:NM_022658:1090:157\n-CGAGGAGCACGGAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@13:NM_173860:524:97\n-CAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTAT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@13:NM_173860:524:97\n-CCAGGGCGCGCCGCTGGCCGAGAGCCCGCCGCCGGGGTTCAACGGCGATA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@14:NM_022658:1471:182\n-CCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@14:NM_022658:1471:182\n-AGGCATGGGCCCGAGTGACCATGGGATGGTTAGGTAGGATTTTAGAGGCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@15:NM_022658:1173:198\n-CACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@15:NM_022658:1173:198\n-ACATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@16:NM_022658:1052:179\n-CAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGGGCAGG\n-+\n-IIIIIIIII'..b'IIIIIIIIIIIIIIIIII\n-@9986:NM_022658:1194:170\n-TTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9986:NM_022658:1194:170\n-GTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTGCATTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9987:NM_174914:1475:158\n-GTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9987:NM_174914:1475:158\n-CTTTAGTTTCTGCAGGAGGCAACAGCACATGCAGTCTACATTTGACAACA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9988:NM_004503:167:199\n-GAGAGCATGTCTTTCTCCTGGTAAAAGGAATTAGATCCATAGTCATACGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9988:NM_004503:167:199\n-ACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9989:NM_022658:1203:166\n-CTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9989:NM_022658:1203:166\n-ATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9990:NM_006897:430:179\n-TTTGTGCTTGCTGCCGGCGAGCGCGTCCGCCTCGGGCGAGGGCAGTGTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9990:NM_006897:430:179\n-GGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9991:NM_173860:200:188\n-ACGGCTCCAGCGGGAGCAGCGCTGCCCCGGGCCCGGCTCCCGGGTCGCGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9991:NM_173860:200:188\n-CTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9992:NM_022658:826:161\n-TAAACTTCTCAATTTATCTGCTACCATAAAACGAAACTTCAAGGGAGTTG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9992:NM_022658:826:161\n-CCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9993:NM_014620:1162:157\n-AGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9993:NM_014620:1162:157\n-CTTCTTCCATTTCATGCGACGGTTTTGGAACCAGATTTTGATCTGCCTCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9994:NM_022658:752:194\n-AGGGAGTTGCTAAGGGGGGGGGGGTCTTTCTTTTTTGCTTAGTCCTTGTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9994:NM_022658:752:194\n-CAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9995:NM_022658:1888:191\n-AGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9995:NM_022658:1888:191\n-TGCAATTTAGTTCTACTCTACTGGGGTTAGAAGCACAATAAAAGCGCACA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9996:NM_014620:1559:191\n-ATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9996:NM_014620:1559:191\n-GGCCTTTTAAAAAAAAACACCCAGCAGGTACCATGCTAAGACAACATCAC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9997:NM_006897:223:164\n-GAGCCAAGTCCGCATGTAGCGCGTGTCGGCGCCGAGGTGGGGCTGGGGGC\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9997:NM_006897:223:164\n-TGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9998:NM_022658:1995:180\n-ACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9998:NM_022658:1995:180\n-CAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCGAGCA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9999:NM_022658:1773:182\n-GCATTACAAATACTCTCAAAGCAGGATTTCTTTCTATAGGTAGTGATAAA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@9999:NM_022658:1773:182\n-TACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10000:NM_014620:1728:181\n-GGAAGGAGGAGGAGGAGAAGGATGAGAATTGGCTTTAAAATTTCTTTCCT\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n-@10000:NM_014620:1728:181\n-GGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\n-+\n-IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_both.fastq.bz2 |
| b |
| Binary file old/test-data/reads_both.fastq.bz2 has changed |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/reads_both.fastq.gz |
| b |
| Binary file old/test-data/reads_both.fastq.gz has changed |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/salmon_genMap_result1.tab --- a/old/test-data/salmon_genMap_result1.tab Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,5 +0,0 @@ -Name Length EffectiveLength TPM NumReads -baz 1640 1052.77 1.09566 0.00943897 -NR_031764 1853 1214.33 10407.1 103.415 -foo 348.949 235.269 976889 9737.65 -bar 2283 1528.95 12702.4 158.926 |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/salmon_quant_result1.tab --- a/old/test-data/salmon_quant_result1.tab Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,16 +0,0 @@ -Name Length EffectiveLength TPM NumReads -NM_001168316 2283 2106.09 12428 158.641 -NM_174914 2385 2208.09 112348 1503.55 -NR_031764 1853 1676.09 10021.5 101.805 -NM_004503 1681 1504.09 36259.8 330.551 -NM_006897 1541 1364.09 80313.1 664 -NM_014212 2037 1860.09 4878.54 55 -NM_014620 2300 2123.09 45879.2 590.368 -NM_017409 1959 1782.09 4351.4 47 -NM_017410 2396 2219.09 3122.74 42 -NM_018953 1612 1435.09 26213 228 -NM_022658 2288 2111.09 381473 4881 -NM_153633 1666 1489.09 40073.1 361.67 -NM_153693 2072 1895.09 6478.45 74.4115 -NM_173860 849 672.091 236161 962 -NR_003084 1640 1463.09 0.00490872 4.3529e-05 |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/test-data/transcripts.fasta --- a/old/test-data/transcripts.fasta Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,498 +0,0 @@\n->NM_001168316\n-TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n-TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n-CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n-CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n-GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n-GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n-GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n-ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n-TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n-TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n-GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n-CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n-GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n-AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n-GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n-GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n-CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n-CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n-AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n-CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n-CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n-ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n-TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n-CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n-CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n-AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGACAAAACTGGCCTAGAGCC\n-TTCTGTGAAATGTTCCTTGATGGTGTTGTCAAATGTAGACTGCATGTGCTGTTGCCTCCT\n-GCAGAAACTAAAGAACATCAGAAAATTCTTCACTCGGCCCCAGAAGTCCATGTGATCAGT\n-CAGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAATTCCAAAGA\n-GCCGAATGAAGTGGAAAGAATGGCCACAAATGGCTTCCCAAGCTTCTCAGCAATCAGGAA\n-AGGACAGTAGTCAAAAGTTTCAACTATCACCATGTCGAAGTTCTCATTCTTTAAGGAATC\n-CATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCAAGTATTCTAGAACATT\n-TAATAAGTTTTCAAATTTTCCTCTGCCACCTAAAGTTTCTTCCAGAAAGAAATCAAAACT\n-CTTTTTAAATTCTCTTTGATGATCTTCAGGTGCAAGCCAACTGATAACTTGATATGATTT\n-TTCTTCCTTTTTAAAATCTACTGTAGATATTGTCAGGATTTTGGCAGCCTCTGAGAGCAG\n-GACCCCAGGGAGAAGGAAGCCCACTAGAAGAAGCACTCGCTGCCCAGCCATGCTCACTTC\n-TACGGAAGCCGCGGATCTCAGCCTGGGCTGCGCGCCCTGCGCCCGGCTAAGGGACCCTGT\n-GCACCTCAGTGCGCCAAAGGCACTGGCTGTGGGTAGAGGTAGGAGTAAGGATCCTGCCAG\n-TCT\n->NM_174914\n-TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n-TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n-CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n-CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n-GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n-GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n-GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n-ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n-TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n-TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n-GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n-CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n-GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n-AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n-GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n-GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n-CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n-CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n-AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n-CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n-CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n-ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n-TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n-CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n-CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n-AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGA'..b'G\n-GATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAG\n-GACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGC\n-CCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACA\n-GTGGGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGA\n-CCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACGCGGCGCCGGCGCATCG\n-AGATCGCCAACGCGCTTTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCC\n-GGATGAAGTGGAAAAAAGAATCTAATCTCACATCCACTCTCTCGGGGGGCGGCGGAGGGG\n-CCACCGCCGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGC\n-AGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTCTCCCTTTCTCCCTCGCTCCCCAC\n-CAACTCTCCCCTAATCACACACTCTGTATTTATCACTGGCACAATTGATGTGTTTTGATT\n-CCCTAAAACAAAATTAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCCTCCC\n-TCACCGCACAACTCTCTTTCACCACGCGCCTCCTCCTCCTCGCTCCCTTGCTAGCTCGTT\n-CTCGGCTTGTCTACAGGCCCTTTTCCCCGTCCAGGCCTTGGGGGCTCGGACCCTGAACTC\n-AGACTCTACAGATTGCCCTCCAAGTGAGGACTTGGCTCCCCCACTCCTTCGACGCCCCCA\n-CCCCCGCCCCCCGTGCAGAGAGCCGGCTCCTGGGCCTGCTGGGGCCTCTGCTCCAGGGCC\n-TCAGGGCCCGGCCTGGCAGCCGGGGAGGGCCGGAGGCCCAAGGAGGGCGCGCCTTGGCCC\n-CACACCAACCCCCAGGGCCTCCCCGCAGTCCCTGCCTAGCCCCTCTGCCCCAGCAAATGC\n-CCAGCCCAGGCAAATTGTATTTAAAGAATCCTGGGGGTCATTATGGCATTTTACAAACTG\n-TGACCGTTTCTGTGTGAAGATTTTTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGT\n-TTAGCACCGTCAGTGTTCCTATCCAATTTCAAAAAAGGAAAAAAAAGAGGGAAAATTACA\n-AAAAGAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAATAA\n-ATAAATCCCTTCGTGTTACCCTCCTGTATAAATCCAACCTCTGGGTCCGTTCTCGAATAT\n-TTAATAAAACTGATATTATTTTTAAAACTTTA\n->NM_173860\n-ATGGGCGAGCATAATCTCCTGAATCCCGGGTTTGTGGGGCCGCTGGTAAACATCCACACG\n-GGAGACACCTTCTACTTCCCCAACTTCCGCGCGTCCGGGGCGCAGCTTCCCGGGCTGCCT\n-TCGCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGGCGGAGCCG\n-TGCAATGGCTACCCGCAGCCCTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGC\n-CGCACGTGCGAGCTGGCGCGCGTGGAGGACGGCAAGGGTTACTACCGCGAGCCGTGCGCC\n-GAGGGTGGCGGCGGGGGCCTGAAGCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCC\n-GGGGCAGCGCTGCTCCCGCTGGAGCCGTCGGGGCCGCCTGCGCTCGGCTTCAAGTACGAC\n-TACGCGGCGGGCGGCGGCGGTGGCGACGGCGGCGGCGGCGCAGGACCTCCGCACGACCCG\n-CCCTCCTGCCAGTCGCTGGAATCCGACTCCAGTTCGTCCCTGCTCAACGAGGGCAACAAG\n-GGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTATCGCCGTTGAACCCCGGCGGCGGGCTC\n-TCGGCCAGCGGCGCGCCCTGGTACCCGATCAACAGCCGCTCTCGGAAGAAGCGCAAGCCC\n-TATTCGAAGTTGCAACTGGCAGAGCTGGAGGGCGAGTTTCTGGTCAACGAGTTCATCACA\n-CGCCAGCGCCGGAGGGAACTCTCAGACCGCTTGAATCTTAGTGACCAGCAGGTCAAGATC\n-TGGTTTCAGAACCGGAGAATGAAAAAGAAAAGACTTCTGTTGAGGGAGCAAGCTCTCTCC\n-TTCTTTTAA\n->NR_003084\n-TTATTGTGGTTTGTCCGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAAC\n-CATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAA\n-TCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGA\n-AGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCT\n-CTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTT\n-GAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCC\n-CTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTT\n-TGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCAC\n-AGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAG\n-AGTGACAGCAGCGCTCGAGACGGACGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCA\n-GACTCTGGAACTCGAGAAAGAATTCCACTTTAACCGCTACCTCACTCGCCGCAGGCGCAT\n-AGAGATCGCCAACAACTTGTGTCTCAATGAGAGACAGATCAAGATCTGGTTCCAGAACCG\n-CAGGATGAAGTGGAAGAAAGATTCCAAAATGAAAAGCAAAGAGGCTCTTTAGAGGCAGCG\n-GGGGAGGCCCGCAGAGCGCGCCCCTAGCCGGTTCCTGTCCCTGCGCCTTTCCTTTTCGCC\n-TTTCCTCTCTATATTTCGGGTCGGGGGCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCAC\n-AGACAAAAGCGCTTTTCCTTGGCATTCCGCATCCCTACCGACCCAGGGTTCCCGCGGGGC\n-TGTCGGCGCTGCCCCATCTCCCCTCAGCTCGGCTCAGCTCGGTACCCGGGGCCCAGGGCA\n-AGCTCCGCAGGACTTCCCCGGAGGGCTGCGGCGTACAGGCTGGCGCAGAACGAACCTTGG\n-CCTGGGCCGTATCTCCGGCTCCCAGCCTCAGCGCGGCCCTCCCGAGTTAAGGTGGGCCCG\n-GCCCGCGCCACAGGACCCTCGCCGGACCCTCTAACCTCGCCCTCTCCTTTGTTCCCGGCT\n-GGACGGGTTAGACAGCCAAAGGCTGGCGAGAGTCTGGCCCTAGACTCGGGGTGCTTCCTT\n-GTAGCGACTAAACTAGATTTTCACTTATGAATGATTTGCATATGAAAGGAGAGCATCGGC\n-CTAGGGCCCCCACAGTTGCTCTATGCTTTCCAAACCTTATCTCCACAACCTCTTCCCCCC\n-AAAACCCGGGAACCTCCCCAGCCTGCGCCTGCTGCATGCCCTCTCAGGCCGGCAGCCCCA\n-GCCTGCTAGCTAGCTCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTA\n-GAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGC\n-TGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAA\n-TAAAGAGAGAACAGGACTAA\n' |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/tool-data/salmon_indexes_versioned.loc.sample --- a/old/tool-data/salmon_indexes_versioned.loc.sample Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,32 +0,0 @@ -# salmon_indexes_versioned.loc.sample -# This is a *.loc.sample file distributed with Galaxy that enables tools -# to use a directory of indexed data files. This one is for Salmon. -# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup -# First create these data files and save them in your own data directory structure. -# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools. -# Copy this file, save it with the same name (minus the .sample), -# follow the format examples, and store the result in this directory. -# The file should include an one line entry for each index set. -# The path points to the "basename" for the set, not a specific file. -# It has four text columns seperated by TABS. -# -# <unique_build_id> <dbkey> <display_name> <file_base_path> <version> -# -# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" - - - -# So, for example, if you had sacCer3 indexes stored in: -# -# /depot/data2/galaxy/sacCer3/salmon_indexes/ -# -# then the salmon_indexes.loc entry could look like this: -# -#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 -# -#More examples: -# -#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 -#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 -# -# |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/tool_data_table_conf.xml.sample --- a/old/tool_data_table_conf.xml.sample Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -<tables> - <!-- Locations of indexes in salmon mapper format --> - <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, path, version</columns> - <file path="tool-data/salmon_indexes_versioned.loc" /> - </table> -</tables> |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 old/tool_data_table_conf.xml.test --- a/old/tool_data_table_conf.xml.test Wed Oct 02 04:31:53 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,7 +0,0 @@ -<tables> - <!-- Locations of indexes in salmon mapper format --> - <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False"> - <columns>value, dbkey, name, path, version</columns> - <file path="${__HERE__}/test-data/cached_locally/salmon_indexes_versioned.loc" /> - </table> -</tables> |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 salmonquant.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/salmonquant.xml Tue Oct 15 12:01:08 2019 -0400 |
| [ |
| b'@@ -0,0 +1,267 @@\n+<tool id="salmon" name="Salmon quant" version="@VERSION@">\n+ <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="aggressive"><![CDATA[\n+ #if $quant_type.qtype == "reads":\n+ @indexing@\n+ @salreads@\n+ #else:\n+ @salalign@\n+ #end if\n+ @salquant@\n+ #if $quant_type.qtype == "reads":\n+ #if $quant_type.writeMappings:\n+ && samtools view -S -b ./output/samout.sam > ./output/bamout.bam\n+ #end if\n+ #end if\n+ #if $quant_type.qtype == "alignment":\n+ #if $quant_type.sampleOut:\n+ && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam\n+ #end if\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="quant_type">\n+ <param name="qtype" type="select" label="Select salmon quantification mode:">\n+ <option value="reads" selected="True">Reads</option>\n+ <option value="alignment">Alignment</option>\n+ </param>\n+ <when value="reads">\n+ <expand macro="index"/>\n+ <expand macro="reads"/>\n+ </when>\n+ <when value="alignment">\n+ <expand macro="align"/>\n+ </when>\n+ </conditional>\n+ <expand macro="quantboth"/>\n+ </inputs>\n+ <outputs>\n+ <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />\n+ <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">\n+ <filter>geneMap</filter>\n+ </data>\n+ <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)">\n+ <filter>quant_type[\'qtype\'] == "reads" and quant_type[\'writeMappings\']</filter>\n+ </data>\n+ <data name="postSample" format="bam" from_work_dir="./output/postSample_sorted.bam" label="Sampled input alignments on ${on_string}(BAM format)">\n+ <filter>quant_type[\'qtype\'] == "alignment" and quant_type[\'sampleOut\']</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="2">\n+ <conditional name="quant_type">\n+ <param name="qtype" value="reads"/>\n+ <conditional name="refTranscriptSource">\n+ <param name="TranscriptSource" value="history"/>\n+ <section name="s_index">\n+ <param name="fasta" value="transcripts.fasta"/>\n+ </section>\n+ </conditional>\n+ <section name="input">\n+ <param name="single_or_paired.single_or_paired_opts" value="paired" />\n+ <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />\n+ <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />\n+ <param name="single_or_paired.strandedness" value="U"/>\n+ </section>\n+ <param name="writeMappings" value="true"/>\n+ </conditional>\n+ <output name="output_quant" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="NM_001168316" />\n+ <has_text text="NM_174914" />\n+ <has_text text="NM_018953" />\n+ <has_text text="NR_003084" />\n+ <has_text text="NM_017410" />\n+ <has_text text="NM_153693" />\n+ <has_text'..b'allowDovetail"/>\n+ <param name="recoverOrphans" value="--recoverOrphans"/>\n+ </conditional>\n+ <output name="output_quant" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="NM_001168316" />\n+ <has_text text="NM_174914" />\n+ <has_text text="NM_018953" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="quant_type">\n+ <param name="qtype" value="reads"/>\n+ <conditional name="refTranscriptSource">\n+ <param name="TranscriptSource" value="history"/>\n+ <section name="s_index">\n+ <param name="fasta" value="transcripts.fasta"/>\n+ </section>\n+ </conditional>\n+ <section name="input">\n+ <param name="single_or_paired.single_or_paired_opts" value="paired" />\n+ <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />\n+ <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />\n+ <param name="single_or_paired.strandedness" value="U"/>\n+ </section>\n+ </conditional>\n+ <param name="seqBias" value="--seqBias"/>\n+ <param name="gcBias" value="--gcBias"/>\n+ <section name="adv">\n+ <param name="dumpEq" value="--dumpEq"/>\n+ <param name="minAssignedFrags" value="10"/>\n+ <param name="noLengthCorrection"/>\n+ <param name="initUniform" value="--initUniform"/>\n+ <param name="useEM" value="--useEM"/>\n+ <param name="noGammaDraw" value="--noGammaDraw"/>\n+ </section>\n+ <output name="output_quant" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <conditional name="quant_type">\n+ <param name="qtype" value="reads"/>\n+ <conditional name="refTranscriptSource">\n+ <param name="TranscriptSource" value="indexed"/>\n+ <param name="index" value="hg19_transcript_subset" />\n+ </conditional>\n+ <section name="input">\n+ <conditional name="single_or_paired">\n+ <param name="single_or_paired_opts" value="paired" />\n+ <param name="input_mate1" value="fastqs/reads_1.fastq" />\n+ <param name="input_mate2" value="fastqs/reads_2.fastq" />\n+ <param name="strandedness" value="U"/>\n+ </conditional>\n+ </section>\n+ </conditional>\n+ <output name="output_quant" ftype="tabular">\n+ <assert_contents>\n+ <has_text text="EffectiveLength" />\n+ <has_text text="TPM" />\n+ <has_text text="NM_001168316" />\n+ <has_text text="NM_174914" />\n+ <has_text text="NM_018953" />\n+ <has_text text="NR_003084" />\n+ <has_text text="NM_017410" />\n+ <has_text text="NM_153693" />\n+ <has_text text="NR_031764" />\n+ <has_n_columns n="5" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ @salmonhelp@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 umiout.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/umiout.sh Tue Oct 15 12:01:08 2019 -0400 |
| b |
| @@ -0,0 +1,11 @@ +#!/usr/bin/bash + +mkdir fixed; +for file in ./umiout/*; +do prefix="${file%.dot.gz}"; +prefix=${prefix/.\/umiout\//}; +gunzip $file; +sed "s/umiout\/$prefix.dot.gz/$prefix/" umiout/$prefix.dot > fixed/$prefix.dot; +dot -Tpdf fixed/$prefix.dot -o fixed/$prefix.pdf; +done +ls fixed |
| b |
| diff -r 666bb48b1007 -r 7fdb9d1591e2 vpolo_convert.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/vpolo_convert.py Tue Oct 15 12:01:08 2019 -0400 |
| b |
| @@ -0,0 +1,19 @@ +#!/usr/bin/env python + +from vpolo.alevin import parser as par +import argparse +import os + +parser = argparse.ArgumentParser() +parser.add_argument("--mtx", "-m", action="store_true", help="--dumpMtx flag set") +parser.add_argument("--umi", "-u", action="store_true", help="--dumpUmiGraph flag set") +args = parser.parse_args() + +if args.mtx: + alevin_df = par.read_quants_bin("output") + with open("quants_mat.tsv", "w") as f: + f.write(alevin_df.to_csv(sep="\t")) + +if args.umi: + os.mkdir("umiout") + par.read_umi_graph("output", "umiout") |
