| Previous changeset 22:980d2a2e1180 (2022-11-01) Next changeset 24:4df95e2d7f61 (2023-02-22) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266 |
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modified:
macros.xml rg_rnaStar.xml test-data/filtered3.bam |
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added:
test-data/Signal.Unique.str1.out.bg test-data/Signal.Unique.str2.out.bg test-data/Signal.UniqueMultiple.str1.out.bg test-data/Signal.UniqueMultiple.str2.out.bg test-data/rnastar_test_mapped_reads_PE.bam test-data/rnastar_test_splicejunctions_PE.bed test-data/tophat_Signal.Unique.both.read2.out.wig test-data/tophat_rev_Signal.Unique.str1.out.bg test-data/tophat_rev_Signal.Unique.str2.out.bg test-data/tophat_revlib_R1.fastqsanger test-data/tophat_revlib_R2.fastqsanger test-data/tophat_test.fa.gz test-data/tophat_test_reads_per_gene_PE.txt test-data/tophat_test_reads_per_gene_PE_rev.txt |
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| diff -r 980d2a2e1180 -r a2b0feda6933 macros.xml --- a/macros.xml Tue Nov 01 16:56:55 2022 +0000 +++ b/macros.xml Fri Feb 17 20:03:27 2023 +0000 |
| [ |
| b'@@ -1,11 +1,12 @@\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+ <!-- REMEMBER to bump the version of @IDX_VERSION_SUFFIX@\n+ whenever you make changes to the @TOOL_VERSION@ token!\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+ the index versions in sync, but you should manually update @IDX_VERSION_SUFFIX@ -->\n <!-- STAR version to be used -->\n- <token name="@VERSION@">2.7.8a</token>\n+ <token name="@TOOL_VERSION@">2.7.10b</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n+ <token name="@PROFILE@">21.01</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@@ -14,12 +15,14 @@\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_VERSION_SUFFIX@">1</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+ <requirement type="package" version="@TOOL_VERSION@">star</requirement>\n+ <requirement type="package" version="1.16.1">samtools</requirement>\n+ <requirement type="package" version="1.12">gzip</requirement>\n <yield />\n </requirements>\n </xml>\n@@ -35,7 +38,7 @@\n </xml>\n \n <xml name="index_selection" token_with_gene_model="0">\n- <param argument="--genomeDir" name="genomeDir" type="select"\n+ <param argument="--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@@ -55,8 +58,8 @@\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+ <xml name="SJDBOPTIONS">\n+ <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" 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@@ -81,11 +84,16 @@\n <token name="@TEMPINDEX@"><![CDATA[\n ## Create temporary index for custom reference\n #if str($refGenomeSource.geneSource) == \'history\':\n+ #if $refGenomeSource.genomeFastaFiles.ext == "fasta"\n+ ln -s \'$refGenomeSource.genomeFastaFiles\' refgenome.fa &&\n+ #else\n+ gunzip -c \'$refGenomeSource.genomeFastaFiles\' > refgenome.fa &&\n+ #end if\n mkdir -p tempstargenomedir &&\n STAR\n --runMode genomeGenerate\n --genomeDir \'tempstargenomedir\'\n- --genomeFastaFiles \'${refGenomeSource.genomeFastaFiles}\'\n+ --genomeFastaFiles refgenome.fa\n ## Handle difference between indices with/without annotations\n #if \'GTFconditional\' in $refGenomeSource:\n ## GTFconditional exists only in STAR, but not STARsolo\n@@ -109,6 +117,8 @@\n --genomeSAindexNbases ${refGenomeSource'..b' <expand macro="dbKeyActions" />\n+ <change_format>\n+ <when input="outWig.outWigType" value="wiggle" format="wig" />\n+ </change_format>\n+ </data>\n+ <data format="bedgraph" name="signal_unique_str2" label="${tool.name} on ${on_string}: Coverage Uniquely mapped strand 2" from_work_dir="Signal.Unique.str2.out">\n+ <filter>outWig[\'outWigType\'] != "None" and outWig[\'outWigStrand\']</filter>\n+ <expand macro="dbKeyActions" />\n+ <change_format>\n+ <when input="outWig.outWigType" value="wiggle" format="wig" />\n+ </change_format>\n+ </data>\n+ <data format="bedgraph" name="signal_uniquemultiple_str2" label="${tool.name} on ${on_string}: Coverage Uniquely + Multiple mapped strand 2" from_work_dir="Signal.UniqueMultiple.str2.out">\n+ <filter>outWig[\'outWigType\'] != "None" and outWig[\'outWigStrand\']</filter>\n+ <expand macro="dbKeyActions" />\n+ <change_format>\n+ <when input="outWig.outWigType" value="wiggle" format="wig" />\n+ </change_format>\n+ </data>\n+ </xml>\n+ <xml name="quantMode">\n+ <conditional name="quantmode_output">\n+ <param argument="--quantMode" type="select"\n+ label="Per gene/transcript output"\n+ help="STAR can provide analysis results not only with respect to the reference genome, but also with respect to genes and transcripts described by a gene model. Note: This functionality requires either the selection above of a cached index with a gene model, or a gene model provided alongside the index/reference genome in GTF or GFF3 format!">\n+ <option value="-">No per gene or transcript output</option>\n+ <option value="GeneCounts">Per gene read counts (GeneCounts)</option>\n+ <option value="TranscriptomeSAM">Transcript-based BAM output (TranscriptomeSAM)</option>\n+ <option value="TranscriptomeSAM GeneCounts">Both per gene read counts and transcript-based BAM output (TranscriptomeSAM GeneCounts)</option>\n+ </param>\n+ <when value="-" />\n+ <when value="GeneCounts" />\n+ <when value="TranscriptomeSAM">\n+ <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"\n+ label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"\n+ help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />\n+ </when>\n+ <when value="TranscriptomeSAM GeneCounts">\n+ <param argument="--quantTranscriptomeBan" type="boolean" truevalue="IndelSoftclipSingleend" falsevalue="Singleend"\n+ label="Exclude alignments with indels or soft clipping from the transcriptome BAM output?"\n+ help="You will need to exclude alignments with indels and soft-clipped bases from the transcriptome BAM output for compatibility with certain transcript quantification tools, most notably RSEM. If you are using a tool, like eXpress, that can deal with indels and soft-clipped bases, you can achieve better results by leaving this option disabled." />\n+ </when>\n+ </conditional>\n+ </xml>\n+ <xml name="quantModeNoGTF">\n+ <conditional name="quantmode_output">\n+ <param argument="--quantMode" type="select"\n+ label="Per gene/transcript output">\n+ <option value="-">No per gene or transcript output as no GTF was provided</option>\n+ </param>\n+ <when value="-" />\n+ </conditional>\n+ </xml>\n </macros>\n' |
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| diff -r 980d2a2e1180 -r a2b0feda6933 rg_rnaStar.xml --- a/rg_rnaStar.xml Tue Nov 01 16:56:55 2022 +0000 +++ b/rg_rnaStar.xml Fri Feb 17 20:03:27 2023 +0000 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="rna_star" name="RNA STAR" version="@VERSION@+galaxy1" profile="20.01" license="MIT">\n+<tool id="rna_star" name="RNA STAR" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">\n <description>Gapped-read mapper for RNA-seq data</description>\n <macros>\n <import>macros.xml</import>\n@@ -65,9 +65,9 @@\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+ --quantMode ${refGenomeSource.GTFconditional.quantmode_output.quantMode}\n+ #if \'TranscriptomeSAM\' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):\n+ --quantTranscriptomeBan ${refGenomeSource.GTFconditional.quantmode_output.quantTranscriptomeBan}\n #end if\n \n ## Output format parameters\n@@ -206,9 +206,7 @@\n #end if\n \n ## Limits\n- --limitOutSJoneRead $algo.params.limits.limitOutSJoneRead\n- --limitOutSJcollapsed $algo.params.limits.limitOutSJcollapsed\n- --limitSjdbInsertNsj $algo.params.limits.limitSjdbInsertNsj\n+ @LIMITS@\n #else:\n ## Go with STAR\'s default algorithmic settings,\n ## but we need to provide a reasonable default\n@@ -238,14 +236,19 @@\n --chimOutJunctionFormat 1\n #end if\n #end if\n+\n+ ##outWig:\n+ @OUTWIG@\n &&\n ## recompress BAM output for smaller file size\n samtools view -b -o \'$mapped_reads\' Aligned.sortedByCoord.out.bam\n- #if \'TranscriptomeSAM\' in str($quantmode_output.quantMode):\n+ #if \'TranscriptomeSAM\' in str($refGenomeSource.GTFconditional.quantmode_output.quantMode):\n ## same recompression for optional transcriptome BM\n &&\n samtools view -b -o \'$transcriptome_mapped_reads\' Aligned.toTranscriptome.out.bam\n #end if\n+ ##outWig:\n+ @OUTWIGOUTPUTS@\n ]]></command>\n \n <inputs>\n@@ -279,15 +282,22 @@\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, and, optionally, provide your own splice-junction annonations.">\n- <option value="without-gtf" selected=\'true\'>use genome reference without builtin gene-model</option>\n+ <option value="without-gtf-with-gtf" selected=\'true\'>use genome reference without builtin gene-model but provide a gtf</option>\n+ <option value="without-gtf">use genome reference without builtin gene-model and do not provide a gtf</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+ <expand macro="quantMode" />\n+ </when>\n+ <when value="without-gtf-with-gtf">\n+ <expand macro="index_selection" with_gene_model="0" />\n+ <expand macro="SJDBOPTIONS"/>\n+ <expand macro="quantMode" />\n </when>\n <when value="without-gtf">\n <expand macro="index_selection" with_gene_model="0" />\n- <expand macro="@SJDBOPTIONS@" />\n+ <expand macro="quantModeNoGTF" />\n </when>\n </conditi'..b'ompare="sim_size" delta="634" />\n+ <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE.txt" />\n+ <output name="signal_unique_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig"/>\n+ <output name="signal_uniquemultiple_str1" file="tophat_Signal.Unique.both.read2.out.wig" ftype="wig" />\n+ </test>\n+ <!-- test paired-end input as collection and outWig stranded -->\n+ <test expect_num_outputs="8">\n+ <conditional name="singlePaired">\n+ <param name="sPaired" value="paired_collection" />\n+ <param name="input" >\n+ <collection type="paired">\n+ <element name="forward" value="tophat_revlib_R1.fastqsanger" ftype="fastq"/>\n+ <element name="reverse" value="tophat_revlib_R2.fastqsanger" ftype="fastq"/>\n+ </collection>\n+ </param>\n+ </conditional>\n+ <conditional name="refGenomeSource">\n+ <param name="geneSource" value="history" />\n+ <param name="genomeFastaFiles" value="tophat_test.fa" />\n+ <param name="genomeSAindexNbases" value="5" />\n+ <conditional name="GTFconditional">\n+ <param name="GTFselect" value="with-gtf" />\n+ <param name="sjdbOverhang" value="75"/>\n+ <param name="sjdbGTFfile" value="test1.gtf" ftype="gtf"/>\n+ <conditional name="quantmode_output">\n+ <param name="quantMode" value="GeneCounts"/>\n+ </conditional>\n+ </conditional>\n+ </conditional>\n+ <section name="oformat">\n+ <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />\n+ </section>\n+ <section name="algo">\n+ <conditional name="params">\n+ <param name="settingsType" value="default" />\n+ </conditional>\n+ </section>\n+ <conditional name="outWig">\n+ <param name="outWigType" value="bedGraph" />\n+ </conditional>\n+\n+ <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />\n+ <output name="splice_junctions">\n+ <assert_contents>\n+ <has_n_lines n="2"/>\n+ <has_line_matching expression="test_chromosome\\s+251\\s+350\\s+1\\s+1\\s+0\\s+24\\s+0\\s+33"/>\n+ <has_line_matching expression="test_chromosome\\s+401\\s+500\\s+1\\s+1\\s+0\\s+25\\s+0\\s+36"/>\n+ </assert_contents>\n+ </output>\n+ <output name="mapped_reads" >\n+ <assert_contents>\n+ <has_size value="4711" delta="800"/>\n+ </assert_contents>\n+ </output>\n+ <output name="reads_per_gene" file="tophat_test_reads_per_gene_PE_rev.txt" />\n+ <output name="signal_unique_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>\n+ <output name="signal_uniquemultiple_str1" file="tophat_rev_Signal.Unique.str1.out.bg" ftype="bedgraph"/>\n+ <output name="signal_unique_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />\n+ <output name="signal_uniquemultiple_str2" file="tophat_rev_Signal.Unique.str2.out.bg" ftype="bedgraph" />\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n@@ -1024,7 +1128,7 @@\n In addition, the following parameters_ related to chimeric alignment are recommended for improved sensitivity\n \n - under *Output filter criteria*,\n- **Would you like to set additional output filters?**: select `Yes\' to set \n+ **Would you like to set additional output filters?**: select `Yes` to set \n **Maximum number of alignments to output a read\'s alignment results, plus 1** to 50 \n \n - under *Algorithmic settings*, **Configure seed, alignment and limits options**:\n' |
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| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/Signal.Unique.str1.out.bg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Signal.Unique.str1.out.bg Fri Feb 17 20:03:27 2023 +0000 |
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|
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/Signal.Unique.str2.out.bg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Signal.Unique.str2.out.bg Fri Feb 17 20:03:27 2023 +0000 |
| b |
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|
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/Signal.UniqueMultiple.str1.out.bg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Signal.UniqueMultiple.str1.out.bg Fri Feb 17 20:03:27 2023 +0000 |
| b |
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|
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/Signal.UniqueMultiple.str2.out.bg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Signal.UniqueMultiple.str2.out.bg Fri Feb 17 20:03:27 2023 +0000 |
| b |
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|
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/filtered3.bam |
| b |
| Binary file test-data/filtered3.bam has changed |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/rnastar_test_mapped_reads_PE.bam |
| b |
| Binary file test-data/rnastar_test_mapped_reads_PE.bam has changed |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/rnastar_test_splicejunctions_PE.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions_PE.bed Fri Feb 17 20:03:27 2023 +0000 |
| b |
| @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 51 0 37 +test_chromosome 401 500 1 1 0 41 0 36 |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/tophat_Signal.Unique.both.read2.out.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_Signal.Unique.both.read2.out.wig Fri Feb 17 20:03:27 2023 +0000 |
| b |
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+540 10526.31579 +541 10526.31579 +542 10526.31579 +543 10526.31579 +544 10526.31579 +545 5263.15789 +546 5263.15789 +547 5263.15789 |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/tophat_rev_Signal.Unique.str2.out.bg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_rev_Signal.Unique.str2.out.bg Fri Feb 17 20:03:27 2023 +0000 |
| b |
| @@ -0,0 +1,124 @@ +test_chromosome 58 59 10416.66667 +test_chromosome 59 65 20833.33333 +test_chromosome 65 70 31250.00000 +test_chromosome 70 72 41666.66667 +test_chromosome 72 75 52083.33333 +test_chromosome 75 79 62500.00000 +test_chromosome 79 87 72916.66667 +test_chromosome 87 93 83333.33333 +test_chromosome 93 95 93750.00000 +test_chromosome 95 97 104166.66667 +test_chromosome 97 99 114583.33333 +test_chromosome 99 100 125000.00000 +test_chromosome 100 102 135416.66667 +test_chromosome 102 107 145833.33333 +test_chromosome 107 112 177083.33333 +test_chromosome 112 118 187500.00000 +test_chromosome 118 121 197916.66667 +test_chromosome 121 128 218750.00000 +test_chromosome 128 130 229166.66667 +test_chromosome 130 131 260416.66667 +test_chromosome 131 132 270833.33333 +test_chromosome 132 133 260416.66667 +test_chromosome 133 136 250000.00000 +test_chromosome 136 137 270833.33333 +test_chromosome 137 138 281250.00000 +test_chromosome 138 140 302083.33333 +test_chromosome 140 145 291666.66667 +test_chromosome 145 147 281250.00000 +test_chromosome 147 150 270833.33333 +test_chromosome 150 152 260416.66667 +test_chromosome 152 153 270833.33333 +test_chromosome 153 154 291666.66667 +test_chromosome 154 155 312500.00000 +test_chromosome 155 156 322916.66667 +test_chromosome 156 159 333333.33333 +test_chromosome 159 160 343750.00000 +test_chromosome 160 161 354166.66667 +test_chromosome 161 163 364583.33333 +test_chromosome 163 164 375000.00000 +test_chromosome 164 165 385416.66667 +test_chromosome 165 167 406250.00000 +test_chromosome 167 168 416666.66667 +test_chromosome 168 169 406250.00000 +test_chromosome 169 171 427083.33333 +test_chromosome 171 172 437500.00000 +test_chromosome 172 177 427083.33333 +test_chromosome 177 182 416666.66667 +test_chromosome 182 183 385416.66667 +test_chromosome 183 187 395833.33333 +test_chromosome 187 194 385416.66667 +test_chromosome 194 196 395833.33333 +test_chromosome 196 199 385416.66667 +test_chromosome 199 200 406250.00000 +test_chromosome 200 204 416666.66667 +test_chromosome 204 205 427083.33333 +test_chromosome 205 207 406250.00000 +test_chromosome 207 209 416666.66667 +test_chromosome 209 211 427083.33333 +test_chromosome 211 212 406250.00000 +test_chromosome 212 213 385416.66667 +test_chromosome 213 220 375000.00000 +test_chromosome 220 224 385416.66667 +test_chromosome 224 226 395833.33333 +test_chromosome 226 227 406250.00000 +test_chromosome 227 228 395833.33333 +test_chromosome 228 229 385416.66667 +test_chromosome 229 232 354166.66667 +test_chromosome 232 233 364583.33333 +test_chromosome 233 234 375000.00000 +test_chromosome 234 235 364583.33333 +test_chromosome 235 236 343750.00000 +test_chromosome 236 238 333333.33333 +test_chromosome 238 239 322916.66667 +test_chromosome 239 240 312500.00000 +test_chromosome 240 242 291666.66667 +test_chromosome 242 243 302083.33333 +test_chromosome 243 244 312500.00000 +test_chromosome 244 245 291666.66667 +test_chromosome 245 246 281250.00000 +test_chromosome 246 249 270833.33333 +test_chromosome 249 250 260416.66667 +test_chromosome 350 351 291666.66667 +test_chromosome 351 352 302083.33333 +test_chromosome 352 353 312500.00000 +test_chromosome 353 354 322916.66667 +test_chromosome 354 357 333333.33333 +test_chromosome 357 358 343750.00000 +test_chromosome 358 359 333333.33333 +test_chromosome 359 361 343750.00000 +test_chromosome 361 365 354166.66667 +test_chromosome 365 369 364583.33333 +test_chromosome 369 370 343750.00000 +test_chromosome 370 372 354166.66667 +test_chromosome 372 374 375000.00000 +test_chromosome 374 379 354166.66667 +test_chromosome 379 380 333333.33333 +test_chromosome 380 381 322916.66667 +test_chromosome 381 383 312500.00000 +test_chromosome 383 395 302083.33333 +test_chromosome 395 399 291666.66667 +test_chromosome 399 400 281250.00000 +test_chromosome 500 505 260416.66667 +test_chromosome 505 506 250000.00000 +test_chromosome 506 507 239583.33333 +test_chromosome 507 508 229166.66667 +test_chromosome 508 516 218750.00000 +test_chromosome 516 517 208333.33333 +test_chromosome 517 518 187500.00000 +test_chromosome 518 521 177083.33333 +test_chromosome 521 522 166666.66667 +test_chromosome 522 524 156250.00000 +test_chromosome 524 526 145833.33333 +test_chromosome 526 527 135416.66667 +test_chromosome 527 528 125000.00000 +test_chromosome 528 529 114583.33333 +test_chromosome 529 532 104166.66667 +test_chromosome 532 534 93750.00000 +test_chromosome 534 536 83333.33333 +test_chromosome 536 540 72916.66667 +test_chromosome 540 543 62500.00000 +test_chromosome 543 545 52083.33333 +test_chromosome 545 547 41666.66667 +test_chromosome 547 549 20833.33333 +test_chromosome 549 550 10416.66667 |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/tophat_revlib_R1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_revlib_R1.fastqsanger Fri Feb 17 20:03:27 2023 +0000 |
| b |
| b'@@ -0,0 +1,192 @@\n+@test_mRNA_150_290_0/1\n+TCCTAAAAAGTCCGCCTCGGTCTCAGTCTCAAGTAGAAAAAGTCCCGTTGGCGATCCGTCTACGTCCGAGTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/1\n+GAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAATATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACG\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_8_155_9/1\n+TACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATAGTACAGTCGCTGCATCTGACGCTCGAAGTCC\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_118_297_f/1\n+AGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/1\n+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/1\n+AGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGGATCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_218_16/1\n+AGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_46_195_17/1\n+ATCCCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGACAAATATGTAGCGTCCTACTGCCCTCCTCAGTCCAATCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_126_282_18/1\n+AGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_104_274_1c/1\n+TCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_44_225_1e/1\n+CCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCATATACGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_48_249_20/1\n+GTCCCGTTGCCGATCCGTCTCCGTCCGAGTAAGATAGTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_110_267_22/1\n+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_69_229_23/1\n+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTAGACGCTCAGCCGTAGGGCCGCGCGCCAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_21_208_24/1\n+GTAATAGTGGCGTATCGCAAGCTCGACGCTCAGGCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+'..b'IIIIIIIIII\n+@test_mRNA_26_189_30/1\n+AGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTACCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_79_256_31/1\n+AGAAAAAGTCCCGTTGCCGATCCGGCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATGGCAAGCTCGAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_267_32/1\n+CAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGAAAGATAATAAAGTAATAGTGCCGTATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_145_300_37/1\n+GCAAGTCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTTCCGATCCGTCTACGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_81_228_3a/1\n+CCTACGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAGCCATAGGGCCGCGCGCCAAATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_30_231_3c/1\n+CTACGTGCGAGTAAGATATTAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTTAGCCGTAGGGCCGCGCGCCAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_220_3d/1\n+GAAGATAATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_104_278_3e/1\n+CGCCTCGATTCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_23_186_42/1\n+TCGACGCTCAGTCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTTCTGCCCTCCTCCGTCCGATCGTCCTAAATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_106_253_45/1\n+AAAAGTCCCGTTGCCGATCCGTTTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_194_47/1\n+TCGCAAGCTCGACGCTCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_63_229_4c/1\n+ACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACACTCAGCCGTAGGGCCGCGCGCCAAAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_81_245_4d/1\n+CGTTGCCGATCCGTCTACGTCCGAGTAAGATTATAAAGTAATAGTGGCGTATCGCAACCTCGACGCTCAGCCGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/1\n+TAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/1\n+TCAGCCGTAGGGCCGCGCGCCAAATACGTAGCGTCCTACTGCCCTCCTCAGTCCGATCGTCCTAAATGGTCCAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/1\n+AGTCCCGTTGCCGATCCGTCTACGTCCGAGTAAGATAATAAAGTAATAGTGGCGTATCGCAAGCTCGACGCTCAT\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_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_116_295_63/1\n+TCCCGTCCTAAAAAGTCCGCCTCGATCCCAGTCTCAAGTAGAAAAAGTCCCGTTGCCGATCCGTCTACGTCCGAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/tophat_revlib_R2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_revlib_R2.fastqsanger Fri Feb 17 20:03:27 2023 +0000 |
| b |
| b'@@ -0,0 +1,192 @@\n+@test_mRNA_150_290_0/2\n+TACGTATTTGTCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATCCGCCACTATTACTTTATTATCTTACTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_82_255_2/2\n+GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT\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_8_155_9/2\n+TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG\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_118_297_f/2\n+GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_16_194_10/2\n+GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_105_266_13/2\n+ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_218_16/2\n+GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_46_195_17/2\n+GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_126_282_18/2\n+GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_104_274_1c/2\n+GAGTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATGTGCCGCGCGGCCCTACGGCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_44_225_1e/2\n+ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_48_249_20/2\n+GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_110_267_22/2\n+ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_69_229_23/2\n+AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_21_208_24/2\n+GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+'..b'IIIIIIIIII\n+@test_mRNA_26_189_30/2\n+GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_79_256_31/2\n+ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_89_267_32/2\n+AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_145_300_37/2\n+GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_81_228_3a/2\n+GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_30_231_3c/2\n+GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_58_220_3d/2\n+GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_104_278_3e/2\n+GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_23_186_42/2\n+GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_106_253_45/2\n+CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_51_194_47/2\n+ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_63_229_4c/2\n+ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_81_245_4d/2\n+GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_88_257_50/2\n+GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_9_179_52/2\n+CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@test_mRNA_87_250_57/2\n+AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC\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_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_116_295_63/2\n+TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/tophat_test.fa.gz |
| b |
| Binary file test-data/tophat_test.fa.gz has changed |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/tophat_test_reads_per_gene_PE.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_test_reads_per_gene_PE.txt Fri Feb 17 20:03:27 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +N_unmapped 5 5 5 +N_multimapping 0 0 0 +N_noFeature 0 48 47 +N_ambiguous 0 0 0 +GENE1 95 47 48 |
| b |
| diff -r 980d2a2e1180 -r a2b0feda6933 test-data/tophat_test_reads_per_gene_PE_rev.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_test_reads_per_gene_PE_rev.txt Fri Feb 17 20:03:27 2023 +0000 |
| b |
| @@ -0,0 +1,5 @@ +N_unmapped 0 0 0 +N_multimapping 0 0 0 +N_noFeature 0 48 0 +N_ambiguous 0 0 0 +GENE1 48 0 48 |