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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 9db648ed931f0243c8ce6fe21fff9a06040fcc30-dirty" |
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macros.xml rg_rnaStar.xml test-data/41737_R1_sub240k.fastq.gz test-data/41737_R2_sub240k.fastq.gz test-data/737K-august-2016.small.txt.gz test-data/SNORD83B.22.fa test-data/SNORD83B.22.gtf test-data/rnastar_index2x_versioned.loc test-data/rnastar_test.log test-data/rnastar_test2.log test-data/rnastar_test2_mapped_reads.bam test-data/rnastar_test2_splicejunctions.bed test-data/rnastar_test_mapped_reads.bam test-data/rnastar_test_mapped_reads_twopass.bam test-data/rnastar_test_splicejunctions.bed test-data/rnastar_test_splicejunctions_twopass.bed test-data/rnastar_test_transcriptome_mapped_reads.bam test-data/rnastar_test_twopass.log test-data/test-cache/tophat-test/Genome test-data/test-cache/tophat-test/Log.out test-data/test-cache/tophat-test/SA test-data/test-cache/tophat-test/SAindex test-data/test-cache/tophat-test/chrLength.txt test-data/test-cache/tophat-test/chrName.txt test-data/test-cache/tophat-test/chrNameLength.txt test-data/test-cache/tophat-test/chrStart.txt test-data/test-cache/tophat-test/genomeParameters.txt test-data/test1.gtf test-data/test3.chimjunc.tabular test-data/test3.fastqsanger test-data/test3.fastqsanger.gz test-data/test3.ref.fa test-data/tophat_in2.fastqsanger test-data/tophat_in3.fastqsanger test-data/tophat_test.fa test-data/tophat_test_reads_per_gene.txt tool-data/rnastar_index2x_versioned.loc.sample tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| diff -r 000000000000 -r c4769d5e5c2b macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jul 30 14:36:52 2020 +0000 |
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| b'@@ -0,0 +1,167 @@\n+<macros>\n+ <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager\n+ whenever you make changes to the following two version tokens!\n+ The data manager uses a symlink to this macro file to keep the STAR and\n+ the index versions in sync, but you should manually adjust the +galaxy\n+ version number. -->\n+ <!-- STAR version to be used -->\n+ <token name="@VERSION@">2.7.5a</token>\n+ <!-- STAR index version compatible with this version of STAR\n+ This is the STAR version that introduced the index structure expected\n+ by the current version.\n+ It can be found for any specific version of STAR with:\n+ STAR -h | grep versionGenome\n+ or by looking for the versionGenome parameter in source/parametersDefault\n+ of STAR\'s source code -->\n+ <token name="@IDX_VERSION@">2.7.4a</token>\n+ <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">star</requirement>\n+ <requirement type="package" version="1.9">samtools</requirement>\n+ <yield />\n+ </requirements>\n+ </xml>\n+\n+ <xml name="index_selection" token_with_gene_model="0">\n+ <param argument="--genomeDir" name="genomeDir" type="select"\n+ label="Select reference genome"\n+ help="If your genome of interest is not listed, contact the Galaxy team">\n+ <options from_data_table="@IDX_DATA_TABLE@">\n+ <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />\n+ <filter type="static_value" column="5" value="@IDX_VERSION@" />\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available for the selected input dataset" />\n+ </options>\n+ </param>\n+ </xml>\n+\n+ <token name="@FASTQ_GZ_OPTION@">\n+ --readFilesCommand zcat\n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/bts635</citation>\n+ </citations>\n+ </xml>\n+ <xml name="@SJDBOPTIONS@" token_optional="true">\n+ <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>\n+ <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>\n+ </xml>\n+ <xml name="dbKeyActions">\n+ <actions>\n+ <conditional name="refGenomeSource.geneSource">\n+ <when value="indexed">\n+ <action type="metadata" name="dbkey">\n+ <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">\n+ <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>\n+ <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>\n+ </option>\n+ </action>\n+ </when>\n+ <when value="history">\n+ <action type="metadata" name="dbkey">\n+ <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />\n+ </action>\n+ </when>\n+ </conditional>\n+ </actions>\n+ </xml>\n+ <token name="@TEMPINDEX@"><![CDATA[\n+ ## Create temporary index for custom reference\n+ #if str($refGenomeSource.geneSource) == \'history\':\n+ mkdir -p tempstargenomedir &&\n+ STAR\n+ --runMode genomeGenerate\n+ --genomeDir \'tempstargenomedir\'\n+ --genomeFastaFiles \'${refGenomeSource.genomeFastaFiles}\'\n+ ## Handle di'..b'l.sjdbGTFfile:\n+ --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang\n+ --sjdbGTFfile \'${refGenomeSource.GTFconditional.sjdbGTFfile}\'\n+ #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == \'gff3\':\n+ --sjdbGTFtagExonParentTranscript Parent\n+ #end if\n+ #end if\n+ #end if\n+ #end if\n+ ]]></token>\n+ <xml name="stdio" >\n+ <stdio>\n+ <regex match="FATAL error" source="both" level="fatal"/>\n+ <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>\n+ <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>\n+ <regex match="\\[sam_read1\\] missing header\\? Abort!" source="both" level="fatal"/>\n+ <yield />\n+ </stdio>\n+ </xml>\n+ <xml name="refgenomehandling" >\n+ <conditional name="refGenomeSource">\n+ <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">\n+ <option value="indexed" selected="true">Use a built-in index</option>\n+ <option value="history">Use reference genome from history and create temporary index</option>\n+ </param>\n+ <when value="indexed">\n+ <conditional name="GTFconditional">\n+ <param name="GTFselect" type="select"\n+ label="Reference genome with or without an annotation"\n+ help="Select the \'... with builtin gene-model\' option to select from the list of available indexes that were built with splice junction information. Select the \'... without builtin gene-model\' option to select from the list of available indexes without annotated splice junctions.">\n+ <option value="without-gtf" selected=\'true\'>use genome reference without builtin gene-model</option>\n+ <option value="with-gtf">use genome reference with builtin gene-model</option>\n+ </param>\n+ <when value="with-gtf">\n+ <expand macro="index_selection" with_gene_model="1" />\n+ </when>\n+ <when value="without-gtf">\n+ <expand macro="index_selection" with_gene_model="0" />\n+ <expand macro="@SJDBOPTIONS@" />\n+ </when>\n+ </conditional>\n+ </when>\n+ <when value="history">\n+ <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />\n+ <!-- Currently, this parameter is not exposed in the wrapper,\n+ but used only in the tests to avoid excessive index sizes for\n+ the tiny test genomes. -->\n+ <param name="genomeSAindexNbases" type="hidden" value="" />\n+ <conditional name="GTFconditional">\n+ <param name="GTFselect" type="select"\n+ label="Build index with our without known splice junctions annotation"\n+ help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">\n+ <option value="without-gtf">build index without gene-model</option>\n+ <option value="with-gtf">build index with gene-model</option>\n+ </param>\n+ <when value="with-gtf">\n+ <expand macro="@SJDBOPTIONS@" optional="false"/>\n+ </when>\n+ <when value="without-gtf" />\n+ </conditional>\n+ </when>\n+ </conditional>\n+ </xml>\n+</macros>\n' |
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| diff -r 000000000000 -r c4769d5e5c2b rg_rnaStar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rg_rnaStar.xml Thu Jul 30 14:36:52 2020 +0000 |
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| b'@@ -0,0 +1,895 @@\n+<tool id="rna_star" name="RNA STAR" version="@VERSION@" profile="17.01">\n+ <description>Gapped-read mapper for RNA-seq data</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="stdio" />\n+\n+<!--\n+ important quote (https://groups.google.com/forum/#!topic/rna-star/q4zGzlPgwXY):\n+ Hi Gary,\n+\n+ if you generate the genome with GTF file, and do not specify the value for - -sjdbOverhang, it will be set to the default 100.\n+ If you want to be able to set arbitrary value of - -sjdbOverhang on the fly, you have to generate the genome without annotations (GTF) - then you supply both the - -sjdbOverhang and GTF file at the mapping step.\n+\n+ Cheers\n+ Alex\n+-->\n+ <command><![CDATA[\n+ @TEMPINDEX@\n+ STAR\n+ @REFGENOMEHANDLING@\n+\n+ --readFilesIn\n+ #if str($singlePaired.sPaired) == \'paired_collection\':\n+ \'$singlePaired.input.forward\' \'$singlePaired.input.reverse\'\n+\n+ #if $singlePaired.input.forward.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n+ @FASTQ_GZ_OPTION@\n+ #end if\n+ #else\n+ \'$singlePaired.input1\'\n+ #if str($singlePaired.sPaired) == \'paired\':\n+ \'$singlePaired.input2\'\n+ #end if\n+\n+ #if $singlePaired.input1.is_of_type(\'fastq.gz\', \'fastqsanger.gz\'):\n+ @FASTQ_GZ_OPTION@\n+ #end if\n+ #end if\n+\n+ --outSAMtype BAM SortedByCoordinate\n+\n+ ## Two pass mode\n+ --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset}\n+ #for $sj_input in $twopass.sj_precalculated:\n+ \'$sj_input\'\n+ #end for\n+ #if str($twopass.twopassMode) != \'None\':\n+ #if str($refGenomeSource.GTFconditional.GTFselect) == \'with-gtf\':\n+ #if not $refGenomeSource.GTFconditional.sjdbGTFfile:\n+ ## case of cached index without built-in gene model,\n+ ## when user does not supply the optional gtf, but\n+ ## specifies the splice junction overhang\n+ --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang\n+ #end if\n+ #end if\n+ #end if\n+\n+ --quantMode ${quantmode_output.quantMode}\n+ #if \'TranscriptomeSAM\' in str($quantmode_output.quantMode):\n+ --quantTranscriptomeBan ${quantmode_output.quantTranscriptomeBan}\n+ #end if\n+\n+ ## Output format parameters\n+\n+ ## Read tags\n+ #set read_tags = str($oformat.outSAMattributes).split(\',\')\n+ #if \'XS\' in str($oformat.outSAMattributes):\n+ ## STAR writes XS tag when --outSAMstrandField intronMotif is used\n+ $read_tags.remove(\'XS\')\n+ --outSAMstrandField intronMotif\n+ #end if\n+ #if \'HI\' in str($oformat.outSAMattributes):\n+ --outSAMattrIHstart ${oformat.HI_offset}\n+ #end if\n+ #set $tag_names = \' \'.join($read_tags)\n+ --outSAMattributes $tag_names\n+\n+ ## Read FLAG\n+ --outSAMprimaryFlag ${oformat.outSAMprimaryFlag}\n+\n+ ## Read MAPQ\n+ --outSAMmapqUnique ${oformat.outSAMmapqUnique}\n+\n+ ## Output filter parameters\n+\n+ ## Basic Filters\n+ #if str($filter.basic_filters) != \'None\':\n+ #set $filter_options = str($filter.basic_filters).split(\',\')\n+ #else:\n+ #set filter_options = []\n+ #end if\n+ #if \'exclude_unmapped\' in $filter_options:\n+ $filter_options.remove(\'exclude_unmapped\')\n+ --outSAMunmapped None\n+ #else:\n+ --outSAMunmapped Within\n+ #end if\n+ #if \'--outFilterIntronMotifs RemoveNoncanonical\' in $filter_options:\n+ ## RemoveNoncanonical excludes a superset of the reads excluded\n+ ## with RemoveNoncanonicalUnannotated\n+ #if \'--outFilterIntronMotifs RemoveNoncanonicalUnannotated\' '..b' <conditional name="twopass">\n+ <param name="twopassMode" value="None --sjdbFileChrStartEnd" />\n+ <param name="sj_precalculated" value="rnastar_test_splicejunctions_twopass.bed" />\n+ </conditional>\n+ <section name="oformat">\n+ <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />\n+ <param name="outSAMmapqUnique" value="255" />\n+ </section>\n+ <section name="filter">\n+ <param name="basic_filters" value="exclude_unmapped,--outFilterIntronMotifs RemoveNoncanonicalUnannotated,--outFilterIntronMotifs RemoveNoncanonical" />\n+ <conditional name="output_params2">\n+ <param name="output_select2" value="yes" />\n+ </conditional>\n+ </section>\n+ <section name="algo">\n+ <conditional name="params">\n+ <param name="settingsType" value="full" />\n+ </conditional>\n+ </section>\n+\n+ <output name="output_log" file="rnastar_test_twopass.log" compare="re_match_multiline" />\n+ <output name="splice_junctions" file="rnastar_test_splicejunctions_twopass.bed"/>\n+ <output name="mapped_reads" file="rnastar_test_mapped_reads_twopass.bam" compare="sim_size" delta="634" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+STAR_ is an ultrafast universal RNA-seq aligner.\n+\n+**Compatibility Notes**\n+\n+STAR has a huge amount of options to filter alignments and to configure the\n+exact format of its output.\n+\n+Some tools you may plan to use in your downstream analysis of the results are known to be sensitive to these settings or combinations of them.\n+\n+*STAR-Fusion*\n+\n+STAR-Fusion_ can use the chimeric junctions output of STAR as input, but you\n+need to enable **chimeric alignment detection** by STAR for that dataset to be\n+generated. Hence, be sure to select:\n+\n+**Report chimeric alignments?**: `As separate tabular "Junctions" output (Junctions)`.\n+\n+In addition, for best results it is recommended_ that you\n+\n+- use **2-pass mapping** for more sensitive novel splice junction discovery\n+\n+- under *BAM output format specification*,\n+ **Read alignment tags to include in the BAM output**: select `XS` as an\n+ additional tag to generate (this is the equivalent of using\n+ `--outSAMstrandField intronMotif` on the command line)\n+\n+- under *Algorithmic settings*, **Configure seed, alignment and limits options**:\n+ `use parameters suggested for STAR-Fusion`.\n+\n+*Cufflinks*\n+\n+.. class:: infomark\n+\n+ Cufflinks is not considered to be the best tool for use downstream of STAR\n+ anymore. Consider using *Stringtie* instead, which also should pose no\n+ compatibility issues.\n+\n+To avoid compatibility issues with Cufflinks you should:\n+\n+- select **XS** as a *Read alignment tag to include in the BAM output* if (and\n+ only if) your sequenced reads come from an unstranded library prep\n+- *not* select the *jM* and *jI* tags for inclusion\n+- keep the **HI** tag selected and\n+- select *HI tag values should be* **zero-based**\n+- exclude **All alignments across non-canonical junctions** under *Output\n+ filter criteria -> Exclude the following records from the BAM output*\n+\n+-----\n+\n+Attribution\n+\n+Minor tweaks to output names to suit downstream purposes, toolshed automated\n+dependencies and odds and ends of other code and documentation comprising\n+this tool were originally written by Ross Lazarus and have been licensed under\n+the creative commons\n+`BY-NC_ND 3.0 license <http://creativecommons.org/licenses/by-nc-nd/3.0/>`__.\n+\n+.. _STAR: https://github.com/alexdobin/STAR\n+.. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion\n+.. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-kickstart-mode-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs\n+ ]]></help>\n+ <expand macro="citations"/>\n+</tool>\n' |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/41737_R1_sub240k.fastq.gz |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/SNORD83B.22.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD83B.22.fa Thu Jul 30 14:36:52 2020 +0000 |
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| @@ -0,0 +1,17 @@ +>22 dna:chromosome chromosome:GRCh38:22:39313740:50818468:1 REF +CACACTCAAAGCAGCAAACAGCCCAGCAAGGCCAGACTGGGAATTTCCTCATCTCAGGAC +TTCAAAGCCAGTGTGAAAGGACTGCCAACACCCTCTCCTTCCTTTCCTCTCCCACCACAG +GGCCACCAGCGTCTGTGGCCTTGGATCCTCCCTCTACAAGAGCCCCCCCATGACAAGTCA +GGACCTGCCTCACCTTGCGGAGGGTGAGCACCCGCTTCTTGGTTCCCACCACACAGCCTT +TCAGCATGACAAAGTCATTGGTCACTTCACCATAGTGGACAAAGCCACCCTGGAAAACGA +GCATCGGATCAGCACAGGCCCAGGAGGGGATTGTCGTGCAGATGACCCCTCCAGGTTCAG +GCCCTCCCTGACCACAGGGCTGTTCTCAGAAGGAAGGCAACAAGGAACGGTTCCGCAGTC +TGTCTCGGGCGCTGTGCCCAGCGCACATTCCAGGCCTCATCACTGAACAGCTGAGCCTGA +GACCCCACTTCTCACCAGCCAACCCCGACGAGTGGACTCAGATGACAACATGCCACTTAC +AAGGGACACAGCTAGGTGTTGTGTTGGCTTCAGTTAACGATCCTGCTAGCAGCCCCTAGG +AAGCAGCCTATCCCCAAAAGCACGAGGCCTGGGATGGCCTCACAGAGCAGAACACCCATT +ACTTACCAGAGGGTTGATGCTCTTGTCAGATAGGTCATAGTCAGTGGAGGCATTGTTCTT +GATCAGCTTGCCGTCCTTGATAAGGTAGCCCTGGCCAATCTTATAAATCTGAATGAACAA +GAAGGGTGTAAGGCTGGGGCATTAGGGACAAATAACCCAGACATGCCAGTGTGCTGACCT +GCAAAGCACGCTAGAAGGCAGCTGAGGCCTCAGTCCCAGTCACAGCGTATCCCAAGGTCA +GAGCAAAAAGCTGGCTGGCCCTCCAGGTTCCTTTCTGTAAGGCGGCTGGGCTAAAACTAA \ No newline at end of file |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/SNORD83B.22.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SNORD83B.22.gtf Thu Jul 30 14:36:52 2020 +0000 |
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| @@ -0,0 +1,8 @@ +#!genome-build GRCh38.p12 +#!genome-version GRCh38 +#!genome-date 2013-12 +#!genome-build-accession NCBI:GCA_000001405.27 +#!genebuild-last-updated 2018-11 +22 ensembl gene 39313819 39313911 . - . gene_id "ENSG00000209480"; gene_version "1"; gene_name "SNORD83B"; gene_source "ensembl"; gene_biotype "snoRNA"; +22 ensembl transcript 39313819 39313911 . - . gene_id "ENSG00000209480"; gene_version "1"; transcript_id "ENST00000386745"; transcript_version "1"; gene_name "SNORD83B"; gene_source "ensembl"; gene_biotype "snoRNA"; transcript_name "SNORD83B-201"; transcript_source "ensembl"; transcript_biotype "snoRNA"; tag "basic"; transcript_support_level "NA"; +22 ensembl exon 39313819 39313911 . - . gene_id "ENSG00000209480"; gene_version "1"; transcript_id "ENST00000386745"; transcript_version "1"; exon_number "1"; gene_name "SNORD83B"; gene_source "ensembl"; gene_biotype "snoRNA"; transcript_name "SNORD83B-201"; transcript_source "ensembl"; transcript_biotype "snoRNA"; exon_id "ENSE00001501751"; exon_version "1"; tag "basic"; transcript_support_level "NA"; |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_index2x_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_index2x_versioned.loc Thu Jul 30 14:36:52 2020 +0000 |
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| @@ -0,0 +1,4 @@ +##STAR versioned indexes +#build_id dbkey display_name path with_gene_model version +000 ? test_index ${__HERE__}/test-cache/tophat-test 0 2.7.4a +001 ? test_index_with_gene_model ${__HERE__}/test-cache/tophat-test 1 2.7.4a |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_test.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test.log Thu Jul 30 14:36:52 2020 +0000 |
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| @@ -0,0 +1,34 @@ + Started job on | .* + Started mapping on | .* + Finished on | .* + Mapping speed, Million of reads per hour | .* + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 99 + Uniquely mapped reads % | 99.00% + Average mapped length | 74.65 + Number of splices: Total | 52 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 52 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 2.00% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 0.00% + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_test2.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test2.log Thu Jul 30 14:36:52 2020 +0000 |
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| @@ -0,0 +1,34 @@ + Started job on | .* + Started mapping on | .* + Finished on | .* + Mapping speed, Million of reads per hour | .* + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 89 + Uniquely mapped reads % | 89.00% + Average mapped length | 74.80 + Number of splices: Total | 47 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 47 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 1.73% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 10.00% + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_test2_splicejunctions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test2_splicejunctions.bed Thu Jul 30 14:36:52 2020 +0000 |
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| @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 23 0 33 +test_chromosome 401 500 1 1 0 24 0 36 |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_test_splicejunctions.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions.bed Thu Jul 30 14:36:52 2020 +0000 |
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| @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 27 0 37 +test_chromosome 401 500 1 1 0 25 0 36 |
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| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_test_splicejunctions_twopass.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions_twopass.bed Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 1 30 0 37 +test_chromosome 401 500 1 1 1 26 0 36 |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_test_transcriptome_mapped_reads.bam |
| b |
| Binary file test-data/rnastar_test_transcriptome_mapped_reads.bam has changed |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/rnastar_test_twopass.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_twopass.log Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,34 @@ + Started job on | .* + Started mapping on | .* + Finished on | .* + Mapping speed, Million of reads per hour | .* + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 99 + Uniquely mapped reads % | 99.00% + Average mapped length | 74.84 + Number of splices: Total | 56 + Number of splices: Annotated (sjdb) | 56 + Number of splices: GT/AG | 56 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 2.01% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 0.00% + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/Genome |
| b |
| Binary file test-data/test-cache/tophat-test/Genome has changed |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/Log.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/tophat-test/Log.out Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,50 @@ +STAR version=2.7.5a +STAR compilation time,server,dir=Tue Jun 16 12:17:16 EDT 2020 vega:/home/dobin/data/STAR/STARcode/STAR.master/source +##### Command Line: +STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5 +##### Initial USER parameters from Command Line: +###### All USER parameters from Command Line: +runMode genomeGenerate ~RE-DEFINED +genomeDir tempstargenomedir ~RE-DEFINED +genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa ~RE-DEFINED +genomeSAindexNbases 5 ~RE-DEFINED +##### Finished reading parameters from all sources + +##### Final user re-defined parameters-----------------: +runMode genomeGenerate +genomeDir tempstargenomedir +genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa +genomeSAindexNbases 5 + +------------------------------- +##### Final effective command line: +STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5 +---------------------------------------- + +Number of fastq files for each mate = 1 +Finished loading and checking parameters +--genomeDir directory created: tempstargenomedir/ +Jul 29 17:04:16 ... starting to generate Genome files +tools/rgrnastar/test-data/tophat_test.fa : chr # 0 "test_chromosome" chrStart: 0 +Estimated genome size=201262144 = 262144 + 201000000 +GstrandBit=32 +Number of SA indices: 1300 +Jul 29 17:04:16 ... starting to sort Suffix Array. This may take a long time... +Number of chunks: 1; chunks size limit: 18599685304 bytes +Jul 29 17:04:16 ... sorting Suffix Array chunks and saving them to disk... +Writing 10400 bytes into tempstargenomedir//SA_0 ; empty space on disk = 66320359424 bytes ... done +Jul 29 17:04:16 ... loading chunks from disk, packing SA... +Jul 29 17:04:16 ... finished generating suffix array +Jul 29 17:04:16 ... generating Suffix Array index +Jul 29 17:04:16 ... completed Suffix Array index +Jul 29 17:04:16 ... writing Genome to disk ... +Writing 262144 bytes into tempstargenomedir//Genome ; empty space on disk = 66320355328 bytes ... done +SA size in bytes: 5366 +Jul 29 17:04:16 ... writing Suffix Array to disk ... +Writing 5366 bytes into tempstargenomedir//SA ; empty space on disk = 66320093184 bytes ... done +Jul 29 17:04:16 ... writing SAindex to disk +Writing 8 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done +Writing 48 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done +Writing 5971 bytes into tempstargenomedir//SAindex ; empty space on disk = 66320084992 bytes ... done +Jul 29 17:04:16 ..... finished successfully +DONE: Genome generation, EXITING |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/SA |
| b |
| Binary file test-data/test-cache/tophat-test/SA has changed |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/SAindex |
| b |
| Binary file test-data/test-cache/tophat-test/SAindex has changed |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/chrLength.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/tophat-test/chrLength.txt Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ +650 |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/chrName.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/tophat-test/chrName.txt Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ +test_chromosome |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/chrNameLength.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/tophat-test/chrNameLength.txt Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,1 @@ +test_chromosome 650 |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/chrStart.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/tophat-test/chrStart.txt Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,2 @@ +0 +262144 |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test-cache/tophat-test/genomeParameters.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test-cache/tophat-test/genomeParameters.txt Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,19 @@ +### STAR --runMode genomeGenerate --genomeDir tempstargenomedir --genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa --genomeSAindexNbases 5 +### GstrandBit 32 +versionGenome 2.7.4a +genomeType Full +genomeFastaFiles tools/rgrnastar/test-data/tophat_test.fa +genomeSAindexNbases 5 +genomeChrBinNbits 18 +genomeSAsparseD 1 +genomeTransformType None +genomeTransformVCF - +sjdbOverhang 0 +sjdbFileChrStartEnd - +sjdbGTFfile - +sjdbGTFchrPrefix - +sjdbGTFfeatureExon exon +sjdbGTFtagExonParentTranscript transcript_id +sjdbGTFtagExonParentGene gene_id +sjdbInsertSave Basic +genomeFileSizes 262144 5366 |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test1.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test1.gtf Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,4 @@ +test_chromosome test gene 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test transcript 1 650 . + . gene_id "GENE1"; gene_name "GENE1"; transcript_id "GENE1_t1"; +test_chromosome test exon 1 650 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; +test_chromosome test CDS 100 550 . + . gene_id "GENE1"; transcript_id "GENE1_t1"; exon_number "1"; gene_name "GENE1"; |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test3.chimjunc.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.chimjunc.tabular Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,27 @@ +chr_donorA brkpt_donorA strand_donorA chr_acceptorB brkpt_acceptorB strand_acceptorB junction_type repeat_left_lenA repeat_right_lenB read_name start_alnA cigar_alnA start_alnB cigar_alnB num_chim_aln max_poss_aln_score non_chim_aln_score this_chim_aln_score bestall_chim_aln_score PEmerged_bool readgrp +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_60 181 60M15S 241 60S15M 1 75 59 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_62 183 58M17S 241 58S17M 1 75 57 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_64 185 56M19S 241 56S19M 1 75 55 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_66 187 54M21S 241 54S21M 1 75 53 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_68 189 52M23S 241 52S23M 1 75 51 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_70 191 50M25S 241 50S25M 1 75 49 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_72 193 48M27S 241 48S27M 1 75 47 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_74 195 46M29S 241 46S29M 1 75 45 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_76 197 44M31S 241 44S31M 1 75 43 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_78 199 42M33S 241 42S33M 1 75 41 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_80 201 40M35S 241 40S35M 1 75 39 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_82 203 38M37S 241 38S37M 1 75 37 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_84 205 36M39S 241 36S39M 1 75 38 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_86 207 34M41S 241 34S41M 1 75 40 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_88 209 32M43S 241 32S43M 1 75 42 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_90 211 30M45S 241 30S45M 1 75 44 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_92 213 28M47S 241 28S47M 1 75 46 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_94 215 26M49S 241 26S49M 1 75 48 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_96 217 24M51S 241 24S51M 1 75 50 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_98 219 22M53S 241 22S53M 1 75 52 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_100 221 20M55S 241 20S55M 1 75 54 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_102 223 18M57S 241 18S57M 1 75 56 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_104 225 16M59S 241 16S59M 1 75 58 72 72 0 +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_106 227 14M61S 241 14S61M 1 75 60 72 72 0 +# 2.7.2a STAR --runThreadN 1 --genomeLoad NoSharedMemory --genomeDir tempstargenomedir @ --readFilesIn /tmp/tmpTNNe38/files/2/7/0/dataset_2700161e-e03d-4a50-9bc8-1508ff059881.dat --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --twopassMode None --quantMode - --outSAMstrandField intronMotif --outSAMattrIHstart 1 --outSAMattributes NH HI AS nM NM MD jM jI MC ch --outSAMprimaryFlag OneBestScore --outSAMmapqUnique 255 --outSAMunmapped Within --chimSegmentMin 12 --chimJunctionOverhangMin 12 --alignSJDBoverhangMin 10 --alignMatesGapMax 100000 --alignIntronMax 100000 --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --chimMultimapScoreRange 10 --chimMultimapNmax 10 --chimNonchimScoreDropMin 10 --outBAMsortingThreadN 1 --outBAMsortingBinsN 50 --limitBAMsortRAM 0 --chimOutType Junctions --chimOutJunctionFormat 1 +# Nreads 83 NreadsUnique 72 NreadsMulti 0 |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.fastqsanger Thu Jul 30 14:36:52 2020 +0000 |
| b |
| b'@@ -0,0 +1,332 @@\n+@test_chimeric_mRNA_0\n+CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_2\n+AACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_4\n+CTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_6\n+CCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_8\n+TGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_10\n+ATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_12\n+CCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_14\n+AGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_16\n+TTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_18\n+TAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_20\n+ACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_22\n+TCACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_24\n+ACCAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_26\n+CAAATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_28\n+AATTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_30\n+TTATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_32\n+ATAGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_34\n+AGCCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_36\n+CCATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_38\n+ATACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_40\n+ACAGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_42\n+AGACCCAAATTTTAAATCATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@te'..b't_chimeric_mRNA_122\n+ATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_124\n+CGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_126\n+TAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_128\n+AGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_130\n+GAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_132\n+ACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_134\n+AGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_136\n+CCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_138\n+GATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_140\n+TCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_142\n+TTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_144\n+AATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_146\n+TGGATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_148\n+GATGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_150\n+TGGCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_152\n+GCCGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_154\n+CGCAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_156\n+CAGGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_158\n+GGTGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_160\n+TGGTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_162\n+GTATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_chimeric_mRNA_164\n+ATGGAAGCTATAAGCGCGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test3.fastqsanger.gz |
| b |
| Binary file test-data/test3.fastqsanger.gz has changed |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/test3.ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.ref.fa Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,18 @@ +>chr1 +GACGGACGTATTCCTCTGGCCTCAACGGTTCCTGCTTTCGCTGGGATCCAAGATTGGCAG +CTGAAACCGCCTTTCCAAAGTGAGTCCTTCGTCTGTGACTAACTGTGCCAAATCGTCTTG +CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATC +ATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCG +GTGCAGCCGATTAGGACCATCTAATGCACTTGTTACAAGACTTCTTTTAAATACTTTCTT +CCTGCCCAGTAGCGGATGATAATGGTTGTTGCCAGCCGGTGTGGAAGGTAACAGCACCGG +TGCGAGCCTAATGTGCCGTCTCCACCAACACAAGGCTATCCGGTCGTATAATAGGATTCC +GCAATGGGGTTAGCAAATGGCAGCCTAAACGATATCGGGGACTTGCGATGTACATGCTTT +>chr2 +TCAACAATAAGCGCTTTTTGTAGGCAGGGGCACCCCCTATCAGTGGCTGCGCCAAAACAT +CTTCGGATCCCCTTGTCCAATCAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGA +CATCATTAGTGATTAAATGCCACTCCCAAAATTCTGCCTAGAAATGTTTAAGTTCGCTCC +ACTAAAGTTGTTTAAAACGACTACTAAATCCGCGTGATAGGGGATTTCATATTTAATCTT +TTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCG +CGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAGA +TTGCACATTGCGTCTACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTGCCTA +CTATCCTTAAACGCATATCTCGCACAGTAACTCCCCAATATGTGAGCATCTGATGTTGCC |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/tophat_in2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_in2.fastqsanger Thu Jul 30 14:36:52 2020 +0000 |
| b |
| b'@@ -0,0 +1,400 @@\n+@test_mRNA_150_290_0/1\n+TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_197_1/1\n+TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/1\n+GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_96_238_3/1\n+GATCCGTCTACGTCCGCGTAAGATAATAAAGTACTAGTAGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_72_258_4/1\n+GTAGAAAAAGTCCCGTTGCCCATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_107_286_5/1\n+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_122_299_6/1\n+CAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGCTCCGTCTACGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_234_7/1\n+AGTCTACGTCCGAGTCAGATAATAAACTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_57_231_8/1\n+GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_155_9/1\n+TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_237_a/1\n+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_230_b/1\n+TACGTCCGAGTGAGTTAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_276_c/1\n+CCTCGATCCCAGTCTCAAGTAGAAAAAGCCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_268_d/1\n+CCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAATAATAGTGGCGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_151_286_e/1\n+ACGTATTTGGCGCGCGGCCGTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_118_297_f/1\n+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/1\n+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_28_188_11/1\n+TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_36_218_12/1\n+GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/1\n+AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_248_14/1\n+ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_245_15/1\n+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mR'..b'IIIIIIIIIIIIIII\n+@test_mRNA_33_223_4e/1\n+ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_172_294_4f/1\n+ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/1\n+TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_3_187_51/1\n+TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/1\n+TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_85_268_53/1\n+TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_75_204_54/1\n+ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_41_236_55/1\n+AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_56_183_56/1\n+GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/1\n+AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_271_58/1\n+GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_6_182_59/1\n+TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_53_272_5a/1\n+GATCCCAGTGTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_114_277_5b/1\n+GCCTCGATCCCAGTCTCAAGCAGAAAAAGTCCCGTTGCCGTTCCGTCTACCTCCGAGTAAGATAATAAAGTAATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_39_219_5c/1\n+CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_4_191_5d/1\n+CAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGTGTCCTACTGCCCTACTCAGTCCGATCGTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_73_259_5e/1\n+CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_279_5f/1\n+CCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_125_293_60/1\n+CCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_297_61/1\n+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCGGATCCGTCTACGTCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_22_173_62/1\n+AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_116_295_63/1\n+TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/tophat_in3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_in3.fastqsanger Thu Jul 30 14:36:52 2020 +0000 |
| b |
| b'@@ -0,0 +1,400 @@\n+@test_mRNA_150_290_0/2\n+TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_197_1/2\n+GTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/2\n+GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_96_238_3/2\n+GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_72_258_4/2\n+ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_107_286_5/2\n+TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_122_299_6/2\n+GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_234_7/2\n+GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_57_231_8/2\n+CTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCCTAGGGCCGCGCGCCAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_8_155_9/2\n+TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_237_a/2\n+ATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_230_b/2\n+AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_276_c/2\n+ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_268_d/2\n+CTATTTAAGACGTTCCGCCTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_151_286_e/2\n+AAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGATAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_118_297_f/2\n+GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/2\n+GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_28_188_11/2\n+GCTCGACGCTCAGCCGTAGGGCCTCGCGCCAAATACGAAGCGTCCTACTGCCTTCCTCAGTCCGATCGTCCTAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_36_218_12/2\n+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/2\n+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_248_14/2\n+TCCCGTTGCCGTTCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_245_15/2\n+CGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAGAGAAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mR'..b'IIIIIIIIIIIIIII\n+@test_mRNA_33_223_4e/2\n+GAGTTAGATAATAAAGTAATAGTGGCTTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACCTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_172_294_4f/2\n+CCCGTCCTAAAACGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGCTGCCGACCCGTCTACGTCCGAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/2\n+GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_3_187_51/2\n+CTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/2\n+CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_85_268_53/2\n+CCAGTCTCAAGTAGAAAAAGTCCCGTTGACGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_75_204_54/2\n+TCGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_41_236_55/2\n+TCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_56_183_56/2\n+ACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/2\n+AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_271_58/2\n+ATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATGCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_6_182_59/2\n+CGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_53_272_5a/2\n+TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_114_277_5b/2\n+TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_39_219_5c/2\n+AAGATAATAAAGTAATAGTGGCGTATCGCAAGCTGGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_4_191_5d/2\n+ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_73_259_5e/2\n+AGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATACAGTAATAGTGGCGTATCGCAAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_279_5f/2\n+AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_125_293_60/2\n+CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_111_297_61/2\n+CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_22_173_62/2\n+GTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTCCAGTCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_116_295_63/2\n+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/tophat_test.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_test.fa Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,14 @@ +>test_chromosome +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +ACTACTATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCC +ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC +AGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCT +ACGTATTTGGCGCGCGGCGCTACGGCTGAGCGTCGAGCTTGCGATACGCC +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +ACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT +GTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAG +TTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA +AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA |
| b |
| diff -r 000000000000 -r c4769d5e5c2b test-data/tophat_test_reads_per_gene.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_test_reads_per_gene.txt Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,5 @@ +N_unmapped 0 0 0 +N_multimapping 1 1 1 +N_noFeature 0 51 48 +N_ambiguous 0 0 0 +GENE1 99 48 51 |
| b |
| diff -r 000000000000 -r c4769d5e5c2b tool-data/rnastar_index2x_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/rnastar_index2x_versioned.loc.sample Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,27 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of rna-star indexed sequences data files. +#You will need to create these data files and then create a +#rnastar_index2x_versioned.loc file similar to this one (store it in this +directory) that points to the directories in which those files are stored. +#The rnastar_index2x_versioned.loc file has this format (longer white space +#characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> <with_gene_model> <version> +# +#The <with_gene_model> column should be 1 or 0, indicating whether the index +#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used) +#or not. +# +#The <version> column indicates the STAR version that introduced the format of +#the index, i.e., the oldest STAR version that could make use of the index. +# +#Note that STAR indices can become quite large. Consequently, it is only +#advisable to create indices with annotations if it's known ahead of time that +#(A) the annotations won't be frequently updated and (B) the read lengths used +#will also rarely vary. If either of these is not the case, it's advisable to +#create indices without annotations and then specify an annotation file and +#maximum read length (minus 1) when running STAR. +# +#hg19 hg19 hg19 full /mnt/galaxyIndices/genomes/hg19/rnastar 0 2.7.1a +#hg19Ensembl hg19Ensembl hg19 full with Ensembl annotation /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar 1 2.7.1a + |
| b |
| diff -r 000000000000 -r c4769d5e5c2b tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,6 @@ +<tables> + <table name="rnastar_index2x_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path, with_gene_model, version</columns> + <file path="tool-data/rnastar_index2x_versioned.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r c4769d5e5c2b tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Jul 30 14:36:52 2020 +0000 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Location of rnastar indexes for testing --> + <table name="rnastar_index2x_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path, with_gene_model, version</columns> + <file path="${__HERE__}/test-data/rnastar_index2x_versioned.loc" /> + </table> +</tables> |