| Next changeset 1:c0ea43315baf (2019-10-02) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" |
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README.rst alevin.xml macros.xml static/images/ReadLibraryIllustration.png test-data/alevin_mat.mtx.gz test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv test-data/cached_locally/prebuilt_index/hash.bin test-data/cached_locally/prebuilt_index/header.json test-data/cached_locally/prebuilt_index/indexing.log test-data/cached_locally/prebuilt_index/quasi_index.log test-data/cached_locally/prebuilt_index/refInfo.json test-data/cached_locally/prebuilt_index/rsd.bin test-data/cached_locally/prebuilt_index/sa.bin test-data/cached_locally/prebuilt_index/txpInfo.bin test-data/cached_locally/prebuilt_index/versionInfo.json test-data/cached_locally/salmon_indexes_versioned.loc test-data/fastqs/moreminifastq1.fastq.gz test-data/fastqs/moreminifastq2.fastq.gz test-data/fastqs/reads_1.fastq test-data/fastqs/reads_1.fastq.gz test-data/fastqs/reads_2.fastq test-data/fastqs/reads_2.fastq.gz test-data/fastqs/reads_both.fastq.bz2 test-data/minitranscript.fa test-data/minitxp.tsv test-data/postSample.bam test-data/quant1.sf test-data/quant2.sf test-data/quantmergeout.tsv test-data/salmonbam.bam test-data/salquant.sam test-data/salquant.tsv test-data/transcripts.fasta tool-data/salmon_indexes_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r 908a8d400fa2 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Mon Sep 09 11:12:51 2019 -0400 |
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| @@ -0,0 +1,62 @@ +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 000000000000 -r 908a8d400fa2 alevin.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alevin.xml Mon Sep 09 11:12:51 2019 -0400 |
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| b'@@ -0,0 +1,209 @@\n+<tool id="alevin" name="Alevin" version="@VERSION@">\n+ <description>Quantification and analysis of 3\xe2\x80\x99 tagged-end single-cell sequencing data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+ mkdir ./index\n+ && mkdir ./output\n+ #if \'${refTranscriptSource.TranscriptSource}\' != "indexed":\n+ && salmon index -i ./index\n+ --kmerLen \'${refTranscriptSource.s_index.kmer}\'\n+ --gencode\n+ --transcripts \'${refTranscriptSource.s_index.fasta}\'\n+ #set $index_path = \'./index\'\n+ #else\n+ #set $index_path = $refTranscriptSource.index.fields.path\n+ #end if\n+ #if $pairstraight.readselect == \'paired\':\n+ #if $pairstraight.file1.is_of_type("fastq.gz"):\n+ && cp \'${pairstraight.file1}\' ./mate1.fastq.gz\n+ && gunzip ./mate1.fastq.gz\n+ && cp \'${pairstraight.file2}\' ./mate2.fastq.gz\n+ && gunzip ./mate2.fastq.gz\n+ #else if $pairstraight.file1.is_of_type("fastq.bz2"):\n+ && cp \'${pairstraight.file1}\' ./mate1.fastq.bz2\n+ && bzip2 -d ./mate1.fastq.bz2\n+ && cp \'${pairstraight.file2}\' ./mate2.fastq.bz2\n+ && bzip2 -d ./mate2.fastq.bz2\n+ #else:\n+ && ln -s \'${pairstraight.file1}\' ./mate1.fastq\n+ && ln -s \'${pairstraight.file2}\' ./mate2.fastq\n+ #end if\n+ #else:\n+ #if $pairstraight.unmatedreads.is_of_type("fastq.gz"):\n+ && cp \'${pairstraight.unmatedreads}\' ./unmate.fastq.gz\n+ && gunzip ./unmate.fastq.gz\n+ #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"):\n+ && cp \'${pairstraight.unmatedreads}\' ./unmate.fastq.bz2\n+ && bzip2 -d unmate.fastq.bz2\n+ #else:\n+ && ln -s \'${pairstraight.unmatedreads}\' ./unmate.fastq\n+ #end if\n+ #end if\n+\n+ && ln -s \'${tgmap}\' ./alevinmap.tsv\n+ && salmon alevin -l\n+ #if $pairstraight.readselect == \'paired\':\n+ ${pairstraight.orientation}${pairstraight.strandedness}\n+ -i $index_path\n+ -1 ./mate1.fastq\n+ -2 ./mate2.fastq\n+ #else:\n+ \'${pairstraight.strandedness}\'\n+ -i $index_path\n+ -r zcat ./unmate.fastq\n+ #end if\n+ -o ./output\n+ -p "\\${GALAXY_SLOTS:-4}"\n+ ${protocol}\n+ --tgMap ./alevinmap.tsv\n+ #if $whitelist:\n+ --whitelist \'${optional.whitelist}\'\n+ #end if\n+ #if $optional.numCellBootstraps:\n+ --numCellBootstraps \'${optional.numCellBootstraps}\'\n+ #end if\n+ #if $optional.forceCells:\n+ --forceCells \'${optional.forceCells}\'\n+ #end if\n+ #if $optional.expectCells:\n+ --expectCells \'${optional.expectCells}\'\n+ #end if\n+ #if $optional.mrna:\n+ --mrna \'${optional.mrna}\'\n+ #end if\n+ #if $optional.rrna:\n+ --rrna \'${optional.rrna}\'\n+ #end if\n+ #if $optional.keepCBFraction:\n+ --keepCBFraction \'${optional.keepCBFraction}\'\n+ #end if\n+ ${optional.dumpBfh}\n+ ${optional.dumpFeatures}\n+ ${optional.dumpUmiGraph}\n+ ${optional.dumpMtx}\n+ #if $optional.lowRegionMinNumBarcodes:\n+ --lowregionMinNumBarcodes \'${optional.lowRegionMinNumBarcodes}\'\n+ #end if\n+ #if $optional.maxNumBarcodes:\n+ --maxNumBarcodes \'${optional.maxNumBarcodes}\'\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <expand macro="index"/>\n+ <conditional name="pairstraight">\n+ <param name="readselect" label="Single or paired-end reads?" type="select">\n+ <option value="paired">Paired-end</opti'..b'\n+ <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>\n+ <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>\n+ <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/>\n+ <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">\n+ <filter>allout</filter>\n+ </data>\n+ <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>\n+ <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>\n+ <data name="bfh.txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">\n+ <filter>optional["dumpBfh"] == "Yes"</filter>\n+ </data>\n+ <data name="quants_mean_mat.gz" label="quants_mean_mat.gz" format="mtx" from_work_dir="output/alevin/quants_mean_mat.gz">\n+ <filter>optional["numCellBootstraps"]</filter>\n+ </data>\n+ <data name="quants_var_mat.gz" label="quants_var_mat.gz" format="mtx" from_work_dir="output/alevin/quants_var_mat.gz">\n+ <filter>optional["numCellBootstraps"]</filter>\n+ </data>\n+ <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">\n+ <filter>optional["numCellBootstraps"]</filter>\n+ </data>\n+ <data name="alevinmeta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">\n+ <filter>allout</filter>\n+ </data>\n+ <data name="ambig_info.tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">\n+ <filter>allout</filter>\n+ </data>\n+ <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">\n+ <filter>allout</filter>\n+ </data>\n+ <data name="expected_bias.gz" format="txt" label="expected_bias.gz" from_work_dir="output/aux_info/fld.gz"/>\n+ <data name="observed_bias.gz" format="txt" label="observed_bias.gz" from_work_dir="output/aux_info/observed_bias.gz"/>\n+ <data name="observed_bias_3p.gz" format="txt" label="observed_bias_3p.gz" from_work_dir="output/aux_info/observed_bias_3p.gz"/>\n+ <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>\n+ <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">\n+ <filter>allout</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="11">\n+ <conditional name="refTranscriptSource">\n+ <param name="TranscriptSource" value="history"/>\n+ <section name="s_index">\n+ <param name="fasta" value="minitranscript.fa"/>\n+ </section>\n+ </conditional>\n+ <conditional name="pairstraight">\n+ <param name="readselect" value="paired"/>\n+ <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>\n+ <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>\n+ <param name="orientation" value="I"/>\n+ <param name="strandedness" value="SR"/>\n+ </conditional>\n+ <param name="protocol" value="--chromium"/>\n+ <param name="tgmap" value="minitxp.tsv"/>\n+ <param name="dumpMtx" value="Yes"/>\n+ <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+ @salmonhelp@\n+ @alevinhelp@\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r 908a8d400fa2 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 09 11:12:51 2019 -0400 |
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| b'@@ -0,0 +1,588 @@\n+<macros>\n+ <token name="@VERSION@">0.14.1</token>\n+ <token name="@GALAXY_VERSION@">galaxy0</token>\n+ <token name="@IDX_VERSION@">q5</token>\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="1.0.6">bzip2</requirement>\n+ <requirement type="package" version="1.2">seqtk</requirement>\n+ <requirement type="package" version="0.14.1">salmon</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n+ </requirements>\n+ </xml>\n+ <xml name="stranded">\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 comes from the forward strand (SF)</option>\n+ <option value="SR">read comes from the reverse strand (SR)</option>\n+ </param>\n+ </xml>\n+ <xml name="orient">\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+ <xml name="index">\n+ <conditional name="refTranscriptSource">\n+ <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"\n+ help="Built-ins were indexed using default options">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history" selected="True">Use one from the history</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">\n+ <options from_data_table="salmon_indexes_versioned">\n+ <filter type="sort_by" column="2"/>\n+ <filter type="static_value" column="4" value="@IDX_VERSION@" />\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\n+ </options>\n+ </param>\n+ </when> <!-- build-in -->\n+ <when value="history">\n+ <section name="s_index" title="Salmon index" expanded="true">\n+ <param name="fasta" type="data" format="fasta" label="Transcripts fasta file"/>\n+ <param name="kmer" type="integer" value="31" label="Kmer length"/>\n+ <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"\n+ help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct"/>\n+ </section>\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="reads">\n+ <section name="input" title="Data input" expanded="True">\n+ <conditional name="single_or_paired">\n+ <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">\n+ <option value="single">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ <option value="paired_collection">Paired-end Dataset Collection</option>\n+ <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>\n+ </param>\n+ <when value="single">\n+ <param name="input_singles" type="data" format="fastq,fasta,fas'..b' ${adv.noGammaDraw}\n+ #if str($adv.numBootstraps):\n+ --numBootstraps \'${adv.numBootstraps}\'\n+ #end if\n+ ${adv.bootstrapReproject}\n+ #if $adv.thinningFactor:\n+ --thinningFactor \'${adv.thinningFactor}\'\n+ #end if\n+ ${adv.perTranscriptPrior}\n+ --sigDigits \'${adv.sigDigits}\'\n+ #if $adv.vbPrior:\n+ --vbPrior \'${adv.vbPrior}\'\n+ #end if\n+ ${adv.writeOrphanLinks}\n+ ${adv.writeUnmappedNames}\n+ -o ./output\n+ ]]>\n+ </token>\n+ <token name="@qmerge@"><![CDATA[\n+ #import re\n+\n+ #for $counter, $input_data in enumerate($quantfiles):\n+ rank_of_series=$counter\n+ mkdir ${counter}.quantmerge &&\n+ ln -s $input_data.quants ${counter}.quantmerge/quant.sf &&\n+ #end for\n+ salmon quantmerge\n+ --quants *.quantmerge\n+ --names\n+ #for $counter, $input_data in enumerate($quantfiles):\n+ #if $input_data.names and re.sub(\' \', \'\', \'$input_data.names\') != \'\':\n+ \'${input_data.names}\'\n+ #else:\n+ #set $identifier=re.sub(\'[^\\w\\-\\s]\', \'_\', str($input_data.quants.element_identifier))\n+ "$identifier"\n+ #end if\n+ #end for\n+ --column \'${column}\'\n+ ${genes}\n+ #if $missing:\n+ --missing \'${missing}\'\n+ #end if\n+ -o qmergeout.tab\n+ ]]>\n+ </token>\n+ <token name="@salmonhelp@"><![CDATA[\n+ Salmon is a lightweight method for quantifying transcript abundance from RNA\xe2\x80\x93seq reads, combining a dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.\n+\n+ The salmon package contains 4 tools:\n+\n+ * Index: creates a salmon index\n+\n+ * Quant: quantifies a sample (Reads or mapping-based)\n+\n+ * Alevin: Single-cell analysis\n+\n+ * Quantmerge: Merges multiple quantifications into a single file\n+\n+ Galaxy divides these four into three separate tools in the IUC toolshed:\n+\n+ * Salmon quant\n+\n+ * Salmon quantmerge\n+\n+ * Alevin\n+ ]]>\n+ </token>\n+ <token name="@alevinhelp@"><![CDATA[\n+ Alevin is a tool \xe2\x80\x94 integrated with the salmon software \xe2\x80\x94 that introduces a family of algorithms for quantification and analysis of 3\xe2\x80\x99 tagged-end single-cell sequencing data. Currently alevin supports the following two major droplet based single-cell protocols:\n+\n+ * Drop-seq\n+\n+ * 10x-Chromium v1/2/3\n+\n+ Alevin works under the same indexing scheme (as salmon) for the reference, and consumes the set of FASTA/Q files(s) containing the Cellular Barcode(CB) + Unique Molecule identifier (UMI) in one read file and the read sequence in the other. Given just the transcriptome and the raw read files, alevin generates a cell-by-gene count matrix (in a fraction of the time compared to other tools).\n+\n+ Alevin works in two phases. In the first phase it quickly parses the read file containing the CB and UMI information to generate the frequency distribution of all the observed CBs, and creates a lightweight data-structure for fast-look up and correction of the CB. In the second round, alevin utilizes the read-sequences contained in the files to map the reads to the transcriptome, identify potential PCR/sequencing errors in the UMIs, and performs hybrid de-duplication while accounting for UMI collisions. Finally, a post-abundance estimation CB whitelisting procedure is done and a cell-by-gene count matrix is generated.\n+\n+ For further information regarding the tool and its optional parameters, visit the `Alevin <https://salmon.readthedocs.io/en/latest/alevin.html?highlight=alevin>`__ and `Salmon <https://salmon.readthedocs.io/en/latest/index.html>`__ wikis.\n+ ]]>\n+ </token>\n+</macros>\n' |
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| @@ -0,0 +1,14 @@ +{ + "value0": { + "IndexType": 1, + "IndexVersion": "q6", + "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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| @@ -0,0 +1,2 @@ +[2019-09-08 20:35:10.408] [jLog] [info] building index +[2019-09-08 20:35:10.448] [jLog] [info] done building index |
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| @@ -0,0 +1,12 @@ +[2019-09-08 20:35:10.409] [jointLog] [info] [Step 1 of 4] : counting k-mers +[2019-09-08 20:35:10.412] [jointLog] [info] Replaced 0 non-ATCG nucleotides +[2019-09-08 20:35:10.412] [jointLog] [info] Clipped poly-A tails from 0 transcripts +[2019-09-08 20:35:10.412] [jointLog] [info] Building rank-select dictionary and saving to disk +[2019-09-08 20:35:10.412] [jointLog] [info] done +[2019-09-08 20:35:10.412] [jointLog] [info] Writing sequence data to file . . . +[2019-09-08 20:35:10.412] [jointLog] [info] done +[2019-09-08 20:35:10.412] [jointLog] [info] Building 32-bit suffix array (length of generalized text is 28,577) +[2019-09-08 20:35:10.413] [jointLog] [info] Building suffix array . . . +[2019-09-08 20:35:10.445] [jointLog] [info] khash had 18,902 keys +[2019-09-08 20:35:10.445] [jointLog] [info] saving hash to disk . . . +[2019-09-08 20:35:10.447] [jointLog] [info] done |
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| @@ -0,0 +1,5 @@ +{ + "ReferenceFiles": [ + "test-data/transcripts.fasta" + ] +} \ No newline at end of file |
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| diff -r 000000000000 -r 908a8d400fa2 test-data/cached_locally/salmon_indexes_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/salmon_indexes_versioned.loc Mon Sep 09 11:12:51 2019 -0400 |
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| @@ -0,0 +1,33 @@ +# 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 |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/fastqs/moreminifastq1.fastq.gz |
| b |
| Binary file test-data/fastqs/moreminifastq1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/fastqs/moreminifastq2.fastq.gz |
| b |
| Binary file test-data/fastqs/moreminifastq2.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/fastqs/reads_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqs/reads_1.fastq Mon Sep 09 11:12:51 2019 -0400 |
| b |
| b'@@ -0,0 +1,40000 @@\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 000000000000 -r 908a8d400fa2 test-data/fastqs/reads_1.fastq.gz |
| b |
| Binary file test-data/fastqs/reads_1.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/fastqs/reads_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqs/reads_2.fastq Mon Sep 09 11:12:51 2019 -0400 |
| b |
| b'@@ -0,0 +1,40000 @@\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 000000000000 -r 908a8d400fa2 test-data/fastqs/reads_2.fastq.gz |
| b |
| Binary file test-data/fastqs/reads_2.fastq.gz has changed |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/fastqs/reads_both.fastq.bz2 |
| b |
| Binary file test-data/fastqs/reads_both.fastq.bz2 has changed |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/minitranscript.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minitranscript.fa Mon Sep 09 11:12:51 2019 -0400 |
| b |
| b'@@ -0,0 +1,10000 @@\n+>ENST00000641515.2|ENSG00000186092.6|OTTHUMG00000001094.4|OTTHUMT00000003223.4|OR4F5-202|OR4F5|2618|UTR5:1-60|CDS:61-1041|UTR3:1042-2618|\n+CCCAGATCTCTTCAGTTTTTATGCCTCATTCTGTGAAAATTGCTGTAGTCTCTTCCAGTT\n+ATGAAGAAGGTAACTGCAGAGGCTATTTCCTGGAATGAATCAACGAGTGAAACGAATAAC\n+TCTATGGTGACTGAATTCATTTTTCTGGGTCTCTCTGATTCTCAGGAACTCCAGACCTTC\n+CTATTTATGTTGTTTTTTGTATTCTATGGAGGAATCGTGTTTGGAAACCTTCTTATTGTC\n+ATAACAGTGGTATCTGACTCCCACCTTCACTCTCCCATGTACTTCCTGCTAGCCAACCTC\n+TCACTCATTGATCTGTCTCTGTCTTCAGTCACAGCCCCCAAGATGATTACTGACTTTTTC\n+AGCCAGCGCAAAGTCATCTCTTTCAAGGGCTGCCTTGTTCAGATATTTCTCCTTCACTTC\n+TTTGGTGGGAGTGAGATGGTGATCCTCATAGCCATGGGCTTTGACAGATATATAGCAATA\n+TGCAAGCCCCTACACTACACTACAATTATGTGTGGCAACGCATGTGTCGGCATTATGGCT\n+GTCACATGGGGAATTGGCTTTCTCCATTCGGTGAGCCAGTTGGCGTTTGCCGTGCACTTA\n+CTCTTCTGTGGTCCCAATGAGGTCGATAGTTTTTATTGTGACCTTCCTAGGGTAATCAAA\n+CTTGCCTGTACAGATACCTACAGGCTAGATATTATGGTCATTGCTAACAGTGGTGTGCTC\n+ACTGTGTGTTCTTTTGTTCTTCTAATCATCTCATACACTATCATCCTAATGACCATCCAG\n+CATCGCCCTTTAGATAAGTCGTCCAAAGCTCTGTCCACTTTGACTGCTCACATTACAGTA\n+GTTCTTTTGTTCTTTGGACCATGTGTCTTTATTTATGCCTGGCCATTCCCCATCAAGTCA\n+TTAGATAAATTCCTTGCTGTATTTTATTCTGTGATCACCCCTCTCTTGAACCCAATTATA\n+TACACACTGAGGAACAAAGACATGAAGACGGCAATAAGACAGCTGAGAAAATGGGATGCA\n+CATTCTAGTGTAAAGTTTTAGATCTTATATAACTGTGAGATTAATCTCAGATAATGACAC\n+AAAATATAGTGAAGTTGGTAAGTTATTTAGTAAAGCTCATGAAAATTGTGCCCTCCATTC\n+CCATATAATTTAGTAATTGTCTAGGAACTTCCACATACATTGCCTCAATTTATCTTTCAA\n+CAACTTGTGTGTTATATTTTGGAATACAGATACAAAGTTATTATGCTTTCAAAATATTCT\n+TTTGCTAATTCTTAGAACAAAGAAAGGCATAAATATATTAGTATTTGTGTACACCTGTTC\n+CTTCCTGTGTGACCCTAAGTTTAGTAGAAGAAAGGAGAGAAAATATAGCCTAGCTTATAA\n+ATTTAAAAAAAAATTTATTTGGTCCATTTTGTGAAAAACATAAAAAAAGAACTGTCACAT\n+CTTAATTTAAAAAATATATGCTTAGTGGTAAGGAGATATATGTCAACTTTTAAGAGGTTG\n+AAAAACAAACGCCTCCCATTATAAGTTTATACTTCACCTCCCACCACTATAACAACCCAG\n+AATCCATGAGGGCATTATCAGGAGTGAGTGGAAGAGTAAGTTTGCCAATGTGAAATGTGC\n+CTTCTAGGTCCTAGACGTCTGTGGTATAACTGCTCATAAGCAGTAGAAAGAATTTAGAGG\n+GATCCAGGCTCTCATCACGTTGGCACAAAGTATATTACTTGGATCCATCTATGTCATTTT\n+CCATGGTTAATGTTTAAAAGCACAGGCTTTAAAGTAAAAAACAAAGAGCTGGATTCAACT\n+CTACTGACTCTTATTAATCATGATTTTGGGCACATTACGTAGCTTTCATGAGCTTTAGTT\n+TCTACATTTATAAACAGGAGATTATACCTATTATGCATGGTTATTATGAAGGAAAATGAC\n+AAAATAGATATAAATCAAATAGCCCACTTCGAGACATATTAAGCATGAATAAACATTAGA\n+TACTATTAAAATCCTATATATTAACAAAGCCAAAAGTTTCAAACTTTACTTTTTCCCAAC\n+ATTCTTGTGAAATATGACACATCCCAATCTTAACAGATGCTCATTTGGGATACTGTACTT\n+GTGAGTGGAAGTGTGTATATTTGTGTGCAAGTGTGTACTCATATACTTCCACCTTACCAC\n+CCTAGAAAGGCATGATGAAAATTTAAGATAGAAGGAAAATATAAATTGAAAAAAAAAAAC\n+CTTAACAAATGATTCTGACAAATATCTTCTCTTTCCAGGGAGAATCACTGAGCCAGAATA\n+AAATTGAACACTAAATATTCTAAGAAAAAAGGAATCTAGTTTGTCAAAATGTGACTTGAA\n+TTAATAGATAAGGAGAGTCAGATGATAAGAGGGTCAAAATTATGTTTATCTTAGGAAAAG\n+TAGAATAGAAAATTTATAAGCAGATTAAAAACACATAATAAAAGTAGTAAATAATAATGA\n+CAGTATCTCAAATCAGTGCAGGGGGGAAAGGCCTACTAATGTGATGGTGGGATAATTGGA\n+TAGCAATATGGGAAAAGATATATTTAATTTATTTGCTACACCAAATGCCAGGACAATCTC\n+TAAGTGAATTCAAGACATAACTCTTTTTTCAAAAAAAC\n+>ENST00000335137.4|ENSG00000186092.6|OTTHUMG00000001094.4|-|OR4F5-201|OR4F5|1054|UTR5:1-36|CDS:37-954|UTR3:955-1054|\n+TCCTGGAATGAATCAACGAGTGAAACGAATAACTCTATGGTGACTGAATTCATTTTTCTG\n+GGTCTCTCTGATTCTCAGGAACTCCAGACCTTCCTATTTATGTTGTTTTTTGTATTCTAT\n+GGAGGAATCGTGTTTGGAAACCTTCTTATTGTCATAACAGTGGTATCTGACTCCCACCTT\n+CACTCTCCCATGTACTTCCTGCTAGCCAACCTCTCACTCATTGATCTGTCTCTGTCTTCA\n+GTCACAGCCCCCAAGATGATTACTGACTTTTTCAGCCAGCGCAAAGTCATCTCTTTCAAG\n+GGCTGCCTTGTTCAGATATTTCTCCTTCACTTCTTTGGTGGGAGTGAGATGGTGATCCTC\n+ATAGCCATGGGCTTTGACAGATATATAGCAATATGCAAGCCCCTACACTACACTACAATT\n+ATGTGTGGCAACGCATGTGTCGGCATTATGGCTGTCACATGGGGAATTGGCTTTCTCCAT\n+TCGGTGAGCCAGTTGGCGTTTGCCGTGCACTTACTCTTCTGTGGTCCCAATGAGGTCGAT\n+AGTTTTTATTGTGACCTTCCTAGGGTAATCAAACTTGCCTGTACAGATACCTACAGGCTA\n+GATATTATGGTCATTGCTAACAGTGGTGTGCTCACTGTGTGTTCTTTTGTTCTTCTAATC\n+ATCTCATACACTATCATCCTAATGACCATCCAGCATCGCCCTTTAGATAAGTCGTCCAAA\n+GCTCTGTCCACTTTGACTGCTCACATTACAGTAGTTCTTTTGTTCTTTGGACCATGTGTC\n+TTTATTTATGCCTGGCCATTCCCCATCAAGTCATTAGATAAATTCCTTGCTGTATTTTAT\n+TCTGTGATCACCCCTCTCTTGAACCCAATTATATACACACTGAGGAACAAAGACATGAAG\n+ACGGCAATAAGACAGCTGAGAAAATGGGATGCACATTCTAGTGTAAAGTTTTAGATCTTA\n+TATAACTGTGAGATTAATCTCAG'..b'25|UTR5:1-531|CDS:532-1225|\n+CTGGTGCCTGCCTTGGGGCTCCGGGACTGTGGGCTGTCTCCATCCGGAGGTCTCCCTACC\n+ACCAGGCTCTGTGGGGCAGGGAAGCCCAGTGGGGTGCAGGGAGCCAGGAAGCTGGGGTGG\n+GGTCAGGGCAGGGTCCACAGGGAGACCGGGCGAGGCTGGCAGCCTTCCCAGTCCGCGCAG\n+CGTCTCTGCAGGGGGAGCAAGAGCTGCCCTTCCACCCCTCCCAGGGGACGGGTAGGGGCA\n+CTCTGGGCTTTTCCCACCCCCTCACGCAGGGACACAGGCCTGGTGGGTCTATGACTGAAA\n+TTGGCCAGACCGCATTCTGGTGGTTTTATTCGGAAGGGAAGTTTACCCTGTTCAGCAGAA\n+GCTGAGATGGGAACAGGAAACCCACAGGGCCCCTTTATTCGGCAAAAATGTCAGTCAGCG\n+CCCCGGGGAGCAGCCGAGGGTCCCTGAGTGTCCGCAGCAATGGCGCTGAGTTCCTCTGCT\n+GGAGTTCATCCTGCTAGCTGGGTTCCCGAGCTGCCGGTCTGAGCCTGAGGCATGGAGCCT\n+CCTGGAGACTGGGGGCCTCCTCCCTGGAGATCCACCCCCAAAACCGACGTCTTGAGGCTG\n+GTGCTGTATCTCACCTTCCTGGGAGCCCCCTGCTACGCCCCAGCTCTGCCGTCCTGCAAG\n+GAGGACGAGTACCCAGTGGGCTCCGAGTGCTGCCCCAAGTGCAGTCCAGGTTATCGTGTG\n+AAGGAGGCCTGCGGGGAGCTGACGGGCACAGTGTGTGAACCCTGCCCTCCAGGCACCTAC\n+ATTGCCCACCTCAATGGCCTAAGCAAGTGTCTGCAGTGCCAAATGTGTGACCCAGCCATG\n+GGCCTGCGCGCGAGCCGGAACTGCTCCAGGACAGAGAACGCCGTGTGTGGCTGCAGCCCA\n+GGCCACTTCTGCATCGTCCAGGACGGGGACCACTGCGCCGCGTGCCGCGCTTACGCCACC\n+TCCAGCCCGGGCCAGAGGGTGCAGAAGGGAGGCACCGAGAGTCAGGACACCCTGTGTCAG\n+AACTGCCCCCCGGGGACCTTCTCTCCCAATGGGACCCTGGAGGAATGTCAGCACCAGACC\n+AAGTGCAGCTGGCTGGTGACGAAGGCCGGAGCTGGGACCAGCAGCTCCCACTGGGTATGG\n+TGGTTTCTCTCAGGGAGCCTCGTCATCGTCATTGTTTGCTCCACAGTTGGCCTAATCATA\n+TGTGTGAAAAGAAGAAAGCCAAGGG\n+>ENST00000451778.5|ENSG00000157873.17|OTTHUMG00000000792.18|OTTHUMT00000002093.13|TNFRSF14-207|TNFRSF14|827|UTR5:1-133|CDS:134-827|\n+AGCGTCTCTGCAGGGGGAGCAAGAGCTGCCCTTCCACCCCTCCCAGGGGACGGCCGCAGC\n+AATGGCGCTGAGTTCCTCTGCTGGAGTTCATCCTGCTAGCTGGGTTCCCGAGCTGCCGGT\n+CTGAGCCTGAGGCATGGAGCCTCCTGGAGACTGGGGGCCTCCTCCCTGGAGATCCACCCC\n+CAAAACCGACGTCTTGAGGCTGGTGCTGTATCTCACCTTCCTGGGAGCCCCCTGCTACGC\n+CCCAGCTCTGCCGTCCTGCAAGGAGGACGAGTACCCAGTGGGCTCCGAGTGCTGCCCCAA\n+GTGCAGTCCAGGTTATCGTGTGAAGGAGGCCTGCGGGGAGCTGACGGGCACAGTGTGTGA\n+ACCCTGCCCTCCAGGCACCTACATTGCCCACCTCAATGGCCTAAGCAAGTGTCTGCAGTG\n+CCAAATGTGTGACCCAGCCATGGGCCTGCGCGCGAGCCGGAACTGCTCCAGGACAGAGAA\n+CGCCGTGTGTGGCTGCAGCCCAGGCCACTTCTGCATCGTCCAGGACGGGGACCACTGCGC\n+CGCGTGCCGCGCTTACGCCACCTCCAGCCCGGGCCAGAGGGTGCAGAAGGGAGGCACCGA\n+GAGTCAGGACACCCTGTGTCAGAACTGCCCCCCGGGGACCTTCTCTCCCAATGGGACCCT\n+GGAGGAATGTCAGCACCAGACCAAGTGCAGCTGGCTGGTGACGAAGGCCGGAGCTGGGAC\n+CAGCAGCTCCCACTGGGTATGGTGGTTTCTCTCAGGGAGCCTCGTCATCGTCATTGTTTG\n+CTCCACAGTTGGCCTAATCATATGTGTGAAAAGAAGAAAGCCAAGGG\n+>ENST00000409119.5|ENSG00000157873.17|OTTHUMG00000000792.18|OTTHUMT00000002096.2|TNFRSF14-202|TNFRSF14|896|UTR5:1-120|CDS:121-702|UTR3:703-896|\n+CCCCGGGGAGCAGCCGAGGGTCCCTGAGTGTGTGAGTGAGCCGCAGCAATGGCGCTGAGT\n+TCCTCTGCTGGAGTTCATCCTGCTAGCTGGGTTCCCGAGCTGCCGGTCTGAGCCTGAGGC\n+ATGGAGCCTCCTGGAGACTGGGGGCCTCCTCCCTGGAGATCCACCCCCAAAACCGACGTC\n+TTGAGGCTGGTGCTGTATCTCACCTTCCTGGGAGCCCCCTGCTACGCCCCAGCTCTGCCG\n+TCCTGCAAGGAGGACGAGTACCCAGTGGGCTCCGAGTGCTGCCCCAAGTGCAGTCCAGGT\n+TATCGTGTGAAGGAGGCCTGCGGGGAGCTGACGGGCACAGTGTGTGAACCCTGCCCTCCA\n+GGCACCTACATTGCCCACCTCAATGGCCTAAGCAAGTGTCTGCAGTGCCAAATGTGTGAC\n+CCAGCCATGGGCCTGCGCGCGAGCCGGAACTGCTCCAGGACAGAGAACGCCGTGTGTGGC\n+TGCAGCCCAGGCCACTTCTGCATCGTCCAGGACGGGGACCACTGCGCCGCGTGCCGCGCT\n+TACGCCACCTCCAGCCCGGGCCAGAGGGTGCAGAAGGGAGGCACCGAGAGTCAGGACACC\n+CTGTGTCAGAACTGCCCCCCGGGGACCTTCTCTCCCAATGGGACCCTGGAGGAATGTCAG\n+CACCAGACCAACCGAGCTTGGAAAAGTCAGACAGACCTCTGAGGTCTCATCCTGGAGCTG\n+CCACCAGCCCAGCCTCCCTGGGACCTGTCTTCACTGCCTGGGGCCCTGGGAGCCAGGGAG\n+GCTCCCTGAGGCTGAGTGAACACTGGGCGCTGCACCTGCCTCTCCCACGTCCTCGGCCCC\n+ACTCCCGCAGGTGCAGCTGGCTGGTGACGAAGGCCGGAGCTGGGACCAGCAGCTCC\n+>ENST00000355716.4|ENSG00000157873.17|OTTHUMG00000000792.18|OTTHUMT00000002088.1|TNFRSF14-201|TNFRSF14|1707|UTR5:1-299|CDS:300-1151|UTR3:1152-1707|\n+CCTTCATACCGGCCCTTCCCCTCGGCTTTGCCTGGACAGCTCCTGCCTCCCGCAGGGCCC\n+ACCTGTGTCCCCCAGCGCCGCTCCACCCAGCAGGCCTGAGCCCCTCTCTGCTGCCAGACA\n+CCCCCTGCTGCCCACTCTCCTGCTGCTCGGGTTCTGAGGCACAGCTTGTCACACCGAGGC\n+GGATTCTCTTTCTCTTTCTCTTTCTCTTCTGGCCCACAGCCGCAGCAATGGCGCTGAGTT\n+CCTCTGCTGGAGTTCATCCTGCTAGCTGGGTTCCCGAGCTGCCGGTCTGAGCCTGAGGCA\n+TGGAGCCTCCTGGAGACTGGGGGCCTCCTCCCTGGAGATCCACCCCCAAAACCGACGTCT\n+TGAGGCTGGTGCTGTATCTCACCTTCCTGGGAGCCCCCTGCTACGCCCCAGCTCTGCCGT\n+CCTGCAAGGAGGACGAGTACCCAGTGGGCTCCGAGTGCTGCCCCAAGTGCAGTCCAGGTT\n' |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/minitxp.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minitxp.tsv Mon Sep 09 11:12:51 2019 -0400 |
| b |
| b'@@ -0,0 +1,825 @@\n+ENST00000456328.2\tENSG00000223972.5\n+ENST00000450305.2\tENSG00000223972.5\n+ENST00000488147.1\tENSG00000227232.5\n+ENST00000619216.1\tENSG00000278267.1\n+ENST00000473358.1\tENSG00000243485.5\n+ENST00000469289.1\tENSG00000243485.5\n+ENST00000607096.1\tENSG00000284332.1\n+ENST00000417324.1\tENSG00000237613.2\n+ENST00000461467.1\tENSG00000237613.2\n+ENST00000606857.1\tENSG00000268020.3\n+ENST00000642116.1\tENSG00000240361.2\n+ENST00000492842.2\tENSG00000240361.2\n+ENST00000641515.2\tENSG00000186092.6\n+ENST00000335137.4\tENSG00000186092.6\n+ENST00000466430.5\tENSG00000238009.6\n+ENST00000477740.5\tENSG00000238009.6\n+ENST00000471248.1\tENSG00000238009.6\n+ENST00000610542.1\tENSG00000238009.6\n+ENST00000453576.2\tENSG00000238009.6\n+ENST00000495576.1\tENSG00000239945.1\n+ENST00000442987.3\tENSG00000233750.3\n+ENST00000494149.2\tENSG00000268903.1\n+ENST00000595919.1\tENSG00000269981.1\n+ENST00000493797.1\tENSG00000239906.1\n+ENST00000484859.1\tENSG00000241860.7\n+ENST00000490997.5\tENSG00000241860.7\n+ENST00000466557.6\tENSG00000241860.7\n+ENST00000662089.1\tENSG00000241860.7\n+ENST00000491962.1\tENSG00000241860.7\n+ENST00000655252.1\tENSG00000241860.7\n+ENST00000410691.1\tENSG00000222623.1\n+ENST00000496488.1\tENSG00000241599.1\n+ENST00000624431.2\tENSG00000279928.2\n+ENST00000623083.4\tENSG00000279457.4\n+ENST00000612080.1\tENSG00000273874.1\n+ENST00000442116.1\tENSG00000228463.10\n+ENST00000448958.2\tENSG00000228463.10\n+ENST00000441866.2\tENSG00000228463.10\n+ENST00000634344.2\tENSG00000228463.10\n+ENST00000450734.1\tENSG00000228463.10\n+ENST00000424587.7\tENSG00000228463.10\n+ENST00000669836.1\tENSG00000286448.1\n+ENST00000458203.2\tENSG00000236679.2\n+ENST00000450983.1\tENSG00000236601.2\n+ENST00000412666.1\tENSG00000236601.2\n+ENST00000635159.1\tENSG00000236601.2\n+ENST00000431321.2\tENSG00000237094.12\n+ENST00000453935.1\tENSG00000237094.12\n+ENST00000440163.1\tENSG00000237094.12\n+ENST00000455207.5\tENSG00000237094.12\n+ENST00000455464.7\tENSG00000237094.12\n+ENST00000601814.5\tENSG00000237094.12\n+ENST00000445840.2\tENSG00000237094.12\n+ENST00000431812.1\tENSG00000237094.12\n+ENST00000419160.4\tENSG00000237094.12\n+ENST00000440038.7\tENSG00000237094.12\n+ENST00000642074.1\tENSG00000237094.12\n+ENST00000423728.6\tENSG00000237094.12\n+ENST00000616311.5\tENSG00000237094.12\n+ENST00000599771.6\tENSG00000237094.12\n+ENST00000641845.1\tENSG00000237094.12\n+ENST00000641916.1\tENSG00000237094.12\n+ENST00000601486.5\tENSG00000237094.12\n+ENST00000641579.1\tENSG00000237094.12\n+ENST00000616947.2\tENSG00000237094.12\n+ENST00000432964.1\tENSG00000237094.12\n+ENST00000608420.1\tENSG00000237094.12\n+ENST00000641303.1\tENSG00000237094.12\n+ENST00000641063.1\tENSG00000237094.12\n+ENST00000641049.1\tENSG00000237094.12\n+ENST00000642124.1\tENSG00000237094.12\n+ENST00000437905.2\tENSG00000269732.1\n+ENST00000426406.3\tENSG00000284733.1\n+ENST00000432723.3\tENSG00000233653.3\n+ENST00000514436.1\tENSG00000250575.1\n+ENST00000614007.1\tENSG00000278757.1\n+ENST00000634833.2\tENSG00000230021.10\n+ENST00000417636.2\tENSG00000230021.10\n+ENST00000419394.2\tENSG00000230021.10\n+ENST00000440196.3\tENSG00000230021.10\n+ENST00000641296.1\tENSG00000230021.10\n+ENST00000357876.6\tENSG00000230021.10\n+ENST00000635509.2\tENSG00000230021.10\n+ENST00000634337.2\tENSG00000230021.10\n+ENST00000648019.1\tENSG00000230021.10\n+ENST00000440200.5\tENSG00000230021.10\n+ENST00000452176.2\tENSG00000230021.10\n+ENST00000441245.5\tENSG00000230021.10\n+ENST00000414688.6\tENSG00000230021.10\n+ENST00000636676.1\tENSG00000230021.10\n+ENST00000447954.2\tENSG00000230021.10\n+ENST00000423796.1\tENSG00000235146.2\n+ENST00000450696.1\tENSG00000235146.2\n+ENST00000416931.1\tENSG00000225972.1\n+ENST00000457540.1\tENSG00000225630.1\n+ENST00000414273.1\tENSG00000237973.1\n+ENST00000621981.1\tENSG00000278791.1\n+ENST00000427426.1\tENSG00000229344.1\n+ENST00000467115.1\tENSG00000240409.1\n+ENST00000514057.1\tENSG00000248527.1\n+ENST00000416718.2\tENSG00000198744.5\n+ENST00000438434.2\tENSG00000268663.1\n+ENST00000332831.4\tENSG00000284662.1\n+ENST00000440782.3\tENSG00000229376.3\n+ENST00000506640.2\tENSG00000228327.3\n+ENST00000428504.2\tENSG00000228327.3\n+ENST00000411'..b'378543.2\tENSG00000162585.17\n+ENST00000378546.9\tENSG00000162585.17\n+ENST00000401813.7\tENSG00000162585.17\n+ENST00000487186.5\tENSG00000162585.17\n+ENST00000476803.1\tENSG00000162585.17\n+ENST00000440825.6\tENSG00000162585.17\n+ENST00000420515.1\tENSG00000162585.17\n+ENST00000514625.1\tENSG00000162585.17\n+ENST00000420964.1\tENSG00000162585.17\n+ENST00000442483.2\tENSG00000234396.3\n+ENST00000378536.5\tENSG00000157933.10\n+ENST00000508416.1\tENSG00000157933.10\n+ENST00000478223.2\tENSG00000157933.10\n+ENST00000507179.1\tENSG00000157933.10\n+ENST00000659232.1\tENSG00000287356.1\n+ENST00000661319.1\tENSG00000287356.1\n+ENST00000378531.8\tENSG00000116151.14\n+ENST00000606372.5\tENSG00000116151.14\n+ENST00000378529.7\tENSG00000116151.14\n+ENST00000607342.5\tENSG00000116151.14\n+ENST000004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|
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/postSample.bam |
| b |
| Binary file test-data/postSample.bam has changed |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/quant1.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quant1.sf Mon Sep 09 11:12:51 2019 -0400 |
| b |
| @@ -0,0 +1,17 @@ +Name Length EffectiveLength TPM NumReads +NM_001168316 2283 2105.822 16885.110678 109.344 +NM_174914 2385 2207.822 105635.334105 717.204 +NR_031764 1853 1675.822 4938.752774 25.452 +NM_004503 1681 1503.822 40278.221177 186.267 +NM_006897 1541 1363.822 80591.523840 338.000 +NM_014212 2037 1859.822 4720.877567 27.000 +NM_014620 2300 2122.822 45264.801180 295.491 +NM_017409 1959 1781.822 3832.527965 21.000 +NM_017410 2396 2218.822 3370.821260 23.000 +NM_018953 1612 1434.822 25610.070535 113.000 +NM_022658 2288 2110.822 385910.389229 2505.000 +NM_153633 1666 1488.822 40912.516458 187.313 +NM_153693 2072 1894.822 3420.132589 19.929 +NM_173860 849 671.822 238628.920644 493.000 +NR_003086 1641 1461.823 0.000000 0.000 +NM_014621 2300 1111.822 452.801180 29.491 |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/quant2.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quant2.sf Mon Sep 09 11:12:51 2019 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_001168316 2283 2105.822 16885.110678 109.344 +NM_174914 2385 2207.822 105635.334105 717.204 +NR_031764 1853 1675.822 4938.752774 25.452 +NM_004503 1681 1503.822 40278.221177 186.267 +NM_006897 1541 1363.822 80591.523840 338.000 +NM_014212 2037 1859.822 4720.877567 27.000 +NM_014620 2300 2122.822 45264.801180 295.491 +NM_017409 1959 1781.822 3832.527965 21.000 +NM_017410 2396 2218.822 3370.821260 23.000 +NM_018953 1612 1434.822 25610.070535 113.000 +NM_022658 2288 2110.822 385910.389229 2505.000 +NM_153633 1666 1488.822 40912.516458 187.313 +NM_153693 2072 1894.822 3420.132589 19.929 +NM_173860 849 671.822 238628.920644 493.000 +NR_003084 1640 1462.822 0.000000 0.000 |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/quantmergeout.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quantmergeout.tsv Mon Sep 09 11:12:51 2019 -0400 |
| b |
| @@ -0,0 +1,18 @@ +Name qwerty asdf +NR_003084 1640 NA +NM_153633 1666 1666 +NM_174914 2385 2385 +NM_017410 2396 2396 +NM_018953 1612 1612 +NR_031764 1853 1853 +NM_014620 2300 2300 +NM_017409 1959 1959 +NM_153693 2072 2072 +NM_014212 2037 2037 +NM_004503 1681 1681 +NM_014621 NA 2300 +NR_003086 NA 1641 +NM_022658 2288 2288 +NM_173860 849 849 +NM_006897 1541 1541 +NM_001168316 2283 2283 |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/salmonbam.bam |
| b |
| Binary file test-data/salmonbam.bam has changed |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/salquant.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salquant.sam Mon Sep 09 11:12:51 2019 -0400 |
| b |
| b'@@ -0,0 +1,28523 @@\n+@HD\tVN:1.0\tSO:unknown\n+@SQ\tSN:NM_001168316\tLN:2283\n+@SQ\tSN:NM_174914\tLN:2385\n+@SQ\tSN:NR_031764\tLN:1853\n+@SQ\tSN:NM_004503\tLN:1681\n+@SQ\tSN:NM_006897\tLN:1541\n+@SQ\tSN:NM_014212\tLN:2037\n+@SQ\tSN:NM_014620\tLN:2300\n+@SQ\tSN:NM_017409\tLN:1959\n+@SQ\tSN:NM_017410\tLN:2396\n+@SQ\tSN:NM_018953\tLN:1612\n+@SQ\tSN:NM_022658\tLN:2288\n+@SQ\tSN:NM_153633\tLN:1666\n+@SQ\tSN:NM_153693\tLN:2072\n+@SQ\tSN:NM_173860\tLN:849\n+@SQ\tSN:NR_003084\tLN:1640\n+@PG\tID:rapmap\tPN:rapmap\tVN:0.6.0\n+1:NM_014620:16:182\t99\tNM_014620\t17\t1\t50M\t=\t149\t182\tGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+1:NM_014620:16:182\t147\tNM_014620\t149\t1\t50M\t=\t17\t-182\tTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGAAGCTGGGGGCAGCTGGGG\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+1:NM_014620:16:182\t355\tNM_153693\t17\t1\t50M\t=\t149\t182\tGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\t*\tNH:i:3\tHI:i:2\tAS:i:0\n+1:NM_014620:16:182\t403\tNM_153693\t149\t1\t50M\t=\t17\t-182\tTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGAAGCTGGGGGCAGCTGGGG\t*\tNH:i:3\tHI:i:2\tAS:i:0\n+1:NM_014620:16:182\t355\tNR_003084\t17\t1\t50M\t=\t149\t182\tGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\t*\tNH:i:3\tHI:i:3\tAS:i:0\n+1:NM_014620:16:182\t403\tNR_003084\t149\t1\t50M\t=\t17\t-182\tTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGAAGCTGGGGGCAGCTGGGG\t*\tNH:i:3\tHI:i:3\tAS:i:0\n+2:NM_014620:1094:172\t99\tNM_014620\t1095\t1\t50M\t=\t1217\t172\tATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+2:NM_014620:1094:172\t147\tNM_014620\t1217\t1\t50M\t=\t1095\t-172\tCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCT\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+2:NM_014620:1094:172\t355\tNM_153633\t461\t1\t50M\t=\t583\t172\tATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+2:NM_014620:1094:172\t403\tNM_153633\t583\t1\t50M\t=\t461\t-172\tCTACCTGACCCGAAGGAGAAGGATCGAGATCGCCCACTCGCTGTGCCTCT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+3:NM_022658:294:172\t99\tNM_022658\t295\t1\t50M\t=\t417\t172\tTGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+3:NM_022658:294:172\t147\tNM_022658\t417\t1\t50M\t=\t295\t-172\tAGCTGCCACGGAGACGCCTCCAAATTCTATGGCTACGAGGCGCTCCCCAG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+4:NM_022658:1362:195\t99\tNM_022658\t1363\t1\t50M\t=\t1508\t195\tACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+4:NM_022658:1362:195\t147\tNM_022658\t1508\t1\t50M\t=\t1363\t-195\tCCCCTTGACTTTCTCTAGGAACCTGATGGAAACCTGAAGGAGATGTGGGT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+5:NM_173860:323:180\t99\tNM_173860\t324\t1\t50M\t=\t454\t180\tGCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+5:NM_173860:323:180\t147\tNM_173860\t454\t1\t50M\t=\t324\t-180\tGGCGGCGCAGGACCTCCGCACGACCCGCCCTCCTGCCAGTCGCTGGAATC\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+6:NM_022658:1062:146\t83\tNM_022658\t1159\t1\t50M\t=\t1063\t-146\tTCCTTGCCCCACACACACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCC\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+6:NM_022658:1062:146\t163\tNM_022658\t1063\t1\t50M\t=\t1159\t146\tGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+7:NM_022658:1912:184\t99\tNM_022658\t1913\t1\t50M\t=\t2047\t184\tCTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+7:NM_022658:1912:184\t147\tNM_022658\t2047\t1\t50M\t=\t1913\t-184\tCTTCTAACCCCAGTAGAGTAGAACTAAATTGCACTGAATGTATAGTTAAC\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+8:NM_022658:304:172\t83\tNM_022658\t427\t1\t50M\t=\t305\t-172\tGAGACGCCTCCAAATTCTATGGCTACGAGGCGCTCCCCAGACAGTCCCTT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+8:NM_022658:304:172\t163\tNM_022658\t305\t1\t50M\t=\t427\t172\tCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9:NM_174914:46:212\t83\tNM_001168316\t209\t1\t50M\t=\t47\t-212\tAACAAAACAGAAACTGAAAGAATATGCAAGGTGTCTTTCTTGGATGTTAT\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+9:NM_174914:46:212\t163\tNM_001168316\t47\t1\t50M\t=\t209\t212\tGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\t*\tNH:i:3\tHI:i:1\tAS:i:0\n+9:NM_174914:46:212\t339\tNM_174914\t209\t1\t50M\t=\t47\t-212\tAACAAAACAGAAACTGAAAGAATATGCAAGGTGTCTTTCTTGGATGTTAT\t*\tNH:i:3\tHI:i:2\tAS:i:0\n+9:NM_174914:46:212\t419\tNM_174914\t47\t1\t50M\t=\t209\t212\tGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\t*\tNH:i:3\tHI:i:2\tAS:i:0\n+9:NM_174914:46:212\t339\tNR_031764\t209\t1\t50M\t=\t47\t-212\tAACAAAACAGAAACTGAAAGAATATGCAAGGTGTCTTTCTTGGATGTTAT\t*\tNH:i:3\tHI:i:3\tAS:i:0\n+9:NM_174914:46:212\t419\tNR_03176'..b'66\t99\tNM_022658\t1204\t1\t50M\t=\t1320\t166\tCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9989:NM_022658:1203:166\t147\tNM_022658\t1320\t1\t50M\t=\t1204\t-166\tCAGAAAAGGACTTGTGGTTTTGTTTTTATGCTAAGGCTAGTGTACTAGAT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9990:NM_006897:430:179\t83\tNM_006897\t560\t1\t50M\t=\t431\t-179\tAGACACTGCCCTCGCCCGAGGCGGACGCGCTCGCCGGCAGCAAGCACAAA\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9990:NM_006897:430:179\t163\tNM_006897\t431\t1\t50M\t=\t560\t179\tGGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9991:NM_173860:200:188\t83\tNM_173860\t339\t1\t50M\t=\t201\t-188\tGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGCTCCCGCTGGAGCCGT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9991:NM_173860:200:188\t163\tNM_173860\t201\t1\t50M\t=\t339\t188\tCTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9992:NM_022658:826:161\t83\tNM_022658\t938\t1\t50M\t=\t827\t-161\tCAACTCCCTTGAAGTTTCGTTTTATGGTAGCAGATAAATTGAGAAGTTTA\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9992:NM_022658:826:161\t163\tNM_022658\t827\t1\t50M\t=\t938\t161\tCCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9993:NM_014620:1162:157\t99\tNM_014620\t1163\t1\t50M\t=\t1270\t157\tAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+9993:NM_014620:1162:157\t147\tNM_014620\t1270\t1\t50M\t=\t1163\t-157\tAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAG\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+9993:NM_014620:1162:157\t355\tNM_153633\t529\t1\t50M\t=\t636\t157\tAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9993:NM_014620:1162:157\t403\tNM_153633\t636\t1\t50M\t=\t529\t-157\tAGAGGCAGATCAAAATCTGGTTCCAAAACCGTCGCATGAAATGGAAGAAG\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9994:NM_022658:752:194\t83\tNM_022658\t897\t1\t50M\t=\t753\t-194\tAACAAGGACTAAGCAAAAAAGAAAGACCCCCCCCCCCTTAGCAACTCCCT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9994:NM_022658:752:194\t163\tNM_022658\t753\t1\t50M\t=\t897\t194\tCAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9995:NM_022658:1888:191\t99\tNM_022658\t1889\t1\t50M\t=\t2030\t191\tAGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9995:NM_022658:1888:191\t147\tNM_022658\t2030\t1\t50M\t=\t1889\t-191\tTGTGCGCTTTTATTGTGCTTCTAACCCCAGTAGAGTAGAACTAAATTGCA\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9996:NM_014620:1559:191\t99\tNM_014620\t1560\t1\t50M\t=\t1701\t191\tATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+9996:NM_014620:1559:191\t147\tNM_014620\t1701\t1\t50M\t=\t1560\t-191\tGTGATGTTGTCTTAGCATGGTACCTGCTGGGTGTTTTTTTTTAAAAGGCC\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+9996:NM_014620:1559:191\t355\tNM_153633\t926\t1\t50M\t=\t1067\t191\tATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9996:NM_014620:1559:191\t403\tNM_153633\t1067\t1\t50M\t=\t926\t-191\tGTGATGTTGTCTTAGCATGGTACCTGCTGGGTGTTTTTTTTTAAAAGGCC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+9997:NM_006897:223:164\t83\tNM_006897\t338\t1\t50M\t=\t224\t-164\tGCCCCCAGCCCCACCTCGGCGCCGACACGCGCTACATGCGGACTTGGCTC\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9997:NM_006897:223:164\t163\tNM_006897\t224\t1\t50M\t=\t338\t164\tTGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9998:NM_022658:1995:180\t99\tNM_022658\t1996\t1\t50M\t=\t2126\t180\tACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9998:NM_022658:1995:180\t147\tNM_022658\t2126\t1\t50M\t=\t1996\t-180\tTGCTCGAAAGAAAAAAATGTTAAAAATATATCTATAATAATAATTTTTTG\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9999:NM_022658:1773:182\t83\tNM_022658\t1906\t1\t50M\t=\t1774\t-182\tTTTATCACTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGC\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+9999:NM_022658:1773:182\t163\tNM_022658\t1774\t1\t50M\t=\t1906\t182\tTACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\t*\tNH:i:1\tHI:i:1\tAS:i:0\n+10000:NM_014620:1728:181\t83\tNM_014620\t1860\t1\t50M\t=\t1729\t-181\tAGGAAAGAAATTTTAAAGCCAATTCTCATCCTTCTCCTCCTCCTCCTTCC\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+10000:NM_014620:1728:181\t163\tNM_014620\t1729\t1\t50M\t=\t1860\t181\tGGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\t*\tNH:i:2\tHI:i:1\tAS:i:0\n+10000:NM_014620:1728:181\t339\tNM_153633\t1226\t1\t50M\t=\t1095\t-181\tAGGAAAGAAATTTTAAAGCCAATTCTCATCCTTCTCCTCCTCCTCCTTCC\t*\tNH:i:2\tHI:i:2\tAS:i:0\n+10000:NM_014620:1728:181\t419\tNM_153633\t1095\t1\t50M\t=\t1226\t181\tGGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\t*\tNH:i:2\tHI:i:2\tAS:i:0\n' |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/salquant.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salquant.tsv Mon Sep 09 11:12:51 2019 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_001168316 2283 2106.176 12692.856724 162.035 +NM_174914 2385 2208.176 111754.512113 1495.728 +NR_031764 1853 1676.176 10456.920006 106.237 +NM_004503 1681 1504.176 36544.042209 333.172 +NM_006897 1541 1364.176 80305.227838 664.000 +NM_014212 2037 1860.176 4878.145933 55.000 +NM_014620 2300 2123.176 46101.401998 593.272 +NM_017409 1959 1782.176 4351.043285 47.000 +NM_017410 2396 2219.176 3122.508832 42.000 +NM_018953 1612 1435.176 26210.531410 228.000 +NM_022658 2288 2111.176 381443.747511 4881.000 +NM_153633 1666 1489.176 39835.312759 359.557 +NM_153693 2072 1895.176 6180.774683 70.998 +NM_173860 849 672.176 236122.974699 962.000 +NR_003084 1640 1463.176 0.000000 0.000 |
| b |
| diff -r 000000000000 -r 908a8d400fa2 test-data/transcripts.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.fasta Mon Sep 09 11:12:51 2019 -0400 |
| b |
| b'@@ -0,0 +1,498 @@\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 000000000000 -r 908a8d400fa2 tool-data/salmon_indexes_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/salmon_indexes_versioned.loc.sample Mon Sep 09 11:12:51 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +# 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 000000000000 -r 908a8d400fa2 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Mon Sep 09 11:12:51 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<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 000000000000 -r 908a8d400fa2 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Mon Sep 09 11:12:51 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<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> |
