| Previous changeset 9:2c0ca397d302 (2019-07-27) Next changeset 11:666bb48b1007 (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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modified:
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/txpInfo.bin test-data/cached_locally/prebuilt_index/versionInfo.json |
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added:
macros.xml salmonquant.xml test-data/alevin_mat.mtx.gz 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 |
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removed:
salmon.xml test-data/gene_map.tab test-data/reads_1.fastq test-data/reads_1.fastq.bz2 test-data/reads_1.fastq.gz test-data/reads_2.fastq test-data/reads_2.fastq.bz2 test-data/reads_2.fastq.gz test-data/reads_both.fastq test-data/reads_both.fastq.bz2 test-data/reads_both.fastq.gz test-data/salmon_genMap_result1.tab test-data/salmon_quant_result1.tab |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Sep 09 11:11:22 2019 -0400 |
| [ |
| 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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| diff -r 2c0ca397d302 -r 4de6e2e40c7a salmon.xml --- a/salmon.xml Sat Jul 27 12:37:47 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| 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 2c0ca397d302 -r 4de6e2e40c7a salmonquant.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/salmonquant.xml Mon Sep 09 11:11:22 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' |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/alevin_mat.mtx.gz |
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| Binary file test-data/alevin_mat.mtx.gz has changed |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/cached_locally/prebuilt_index/header.json --- a/test-data/cached_locally/prebuilt_index/header.json Sat Jul 27 12:37:47 2019 -0400 +++ b/test-data/cached_locally/prebuilt_index/header.json Mon Sep 09 11:11:22 2019 -0400 |
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| @@ -1,7 +1,7 @@ { "value0": { "IndexType": 1, - "IndexVersion": "q5", + "IndexVersion": "q6", "UsesKmers": true, "KmerLen": 31, "BigSA": false, |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/cached_locally/prebuilt_index/indexing.log --- a/test-data/cached_locally/prebuilt_index/indexing.log Sat Jul 27 12:37:47 2019 -0400 +++ b/test-data/cached_locally/prebuilt_index/indexing.log Mon Sep 09 11:11:22 2019 -0400 |
| [ |
| @@ -1,2 +1,2 @@ -[2019-07-25 13:45:20.599] [jLog] [info] building index -[2019-07-25 13:45:20.654] [jLog] [info] done building index +[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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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/cached_locally/prebuilt_index/quasi_index.log --- a/test-data/cached_locally/prebuilt_index/quasi_index.log Sat Jul 27 12:37:47 2019 -0400 +++ b/test-data/cached_locally/prebuilt_index/quasi_index.log Mon Sep 09 11:11:22 2019 -0400 |
| [ |
| @@ -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 |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/cached_locally/prebuilt_index/refInfo.json --- a/test-data/cached_locally/prebuilt_index/refInfo.json Sat Jul 27 12:37:47 2019 -0400 +++ b/test-data/cached_locally/prebuilt_index/refInfo.json Mon Sep 09 11:11:22 2019 -0400 |
| [ |
| @@ -1,5 +1,5 @@ { "ReferenceFiles": [ - "tools/salmon/test-data/transcripts.fasta" + "test-data/transcripts.fasta" ] } \ No newline at end of file |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/cached_locally/prebuilt_index/txpInfo.bin |
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| Binary file test-data/cached_locally/prebuilt_index/txpInfo.bin has changed |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/cached_locally/prebuilt_index/versionInfo.json --- a/test-data/cached_locally/prebuilt_index/versionInfo.json Sat Jul 27 12:37:47 2019 -0400 +++ b/test-data/cached_locally/prebuilt_index/versionInfo.json Mon Sep 09 11:11:22 2019 -0400 |
| b |
| @@ -1,5 +1,5 @@ { - "indexVersion": 2, + "indexVersion": 4, "hasAuxIndex": false, "auxKmerLength": 31, "indexType": 1 |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/fastqs/moreminifastq1.fastq.gz |
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| Binary file test-data/fastqs/moreminifastq1.fastq.gz has changed |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/fastqs/moreminifastq2.fastq.gz |
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| Binary file test-data/fastqs/moreminifastq2.fastq.gz has changed |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a 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 11:11:22 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' |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/fastqs/reads_1.fastq.gz |
| b |
| Binary file test-data/fastqs/reads_1.fastq.gz has changed |
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| diff -r 2c0ca397d302 -r 4de6e2e40c7a 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 11:11:22 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 2c0ca397d302 -r 4de6e2e40c7a test-data/fastqs/reads_2.fastq.gz |
| b |
| Binary file test-data/fastqs/reads_2.fastq.gz has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/fastqs/reads_both.fastq.bz2 |
| b |
| Binary file test-data/fastqs/reads_both.fastq.bz2 has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/gene_map.tab --- a/test-data/gene_map.tab Sat Jul 27 12:37:47 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ -NM_174914 foo -NM_001168316 bar -NR_003084 baz -NR_031764 foo |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/minitranscript.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minitranscript.fa Mon Sep 09 11:11:22 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 2c0ca397d302 -r 4de6e2e40c7a test-data/minitxp.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/minitxp.tsv Mon Sep 09 11:11:22 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 2c0ca397d302 -r 4de6e2e40c7a test-data/postSample.bam |
| b |
| Binary file test-data/postSample.bam has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/quant1.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quant1.sf Mon Sep 09 11:11:22 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 2c0ca397d302 -r 4de6e2e40c7a test-data/quant2.sf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quant2.sf Mon Sep 09 11:11:22 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 2c0ca397d302 -r 4de6e2e40c7a test-data/quantmergeout.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quantmergeout.tsv Mon Sep 09 11:11:22 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 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_1.fastq --- a/test-data/reads_1.fastq Sat Jul 27 12:37:47 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-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 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_1.fastq.bz2 |
| b |
| Binary file test-data/reads_1.fastq.bz2 has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_1.fastq.gz |
| b |
| Binary file test-data/reads_1.fastq.gz has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_2.fastq --- a/test-data/reads_2.fastq Sat Jul 27 12:37:47 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 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_2.fastq.bz2 |
| b |
| Binary file test-data/reads_2.fastq.bz2 has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_2.fastq.gz |
| b |
| Binary file test-data/reads_2.fastq.gz has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_both.fastq --- a/test-data/reads_both.fastq Sat Jul 27 12:37:47 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 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_both.fastq.bz2 |
| b |
| Binary file test-data/reads_both.fastq.bz2 has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/reads_both.fastq.gz |
| b |
| Binary file test-data/reads_both.fastq.gz has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/salmon_genMap_result1.tab --- a/test-data/salmon_genMap_result1.tab Sat Jul 27 12:37:47 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 2c0ca397d302 -r 4de6e2e40c7a test-data/salmon_quant_result1.tab --- a/test-data/salmon_quant_result1.tab Sat Jul 27 12:37:47 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 2c0ca397d302 -r 4de6e2e40c7a test-data/salmonbam.bam |
| b |
| Binary file test-data/salmonbam.bam has changed |
| b |
| diff -r 2c0ca397d302 -r 4de6e2e40c7a test-data/salquant.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salquant.sam Mon Sep 09 11:11:22 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 2c0ca397d302 -r 4de6e2e40c7a test-data/salquant.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salquant.tsv Mon Sep 09 11:11:22 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 |