Repository 'rna_starsolo'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/rna_starsolo

Changeset 13:9ee34ba73ebf (2023-02-17)
Previous changeset 12:79b885ce78d7 (2022-11-01) Next changeset 14:1cd2511a396e (2023-02-22)
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ae6b59a8e52fd34e2347d1fd8d34129c36779266
modified:
macros.xml
rg_rnaStarSolo.xml
test-data/filtered3.bam
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
b
diff -r 79b885ce78d7 -r 9ee34ba73ebf macros.xml
--- a/macros.xml Tue Nov 01 16:57:42 2022 +0000
+++ b/macros.xml Fri Feb 17 20:04:43 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'
b
diff -r 79b885ce78d7 -r 9ee34ba73ebf rg_rnaStarSolo.xml
--- a/rg_rnaStarSolo.xml Tue Nov 01 16:57:42 2022 +0000
+++ b/rg_rnaStarSolo.xml Fri Feb 17 20:04:43 2023 +0000
b
b'@@ -1,4 +1,4 @@\n-<tool id="rna_starsolo" name="RNA STARSolo" version="@VERSION@" profile="20.01" license="MIT">\n+<tool id="rna_starsolo" name="RNA STARSolo" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">\n     <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description>\n     <macros>\n         <import>macros.xml</import>\n@@ -22,16 +22,20 @@\n \n     #if str($sc.solo_type) == "CB_UMI_Simple":\n     @READSHANDLING@\n-    --soloCBwhitelist \'$sc.soloCBwhitelist\'\n+    #if $sc.soloCBwhitelist:\n+        --soloCBwhitelist \'$sc.soloCBwhitelist\'\n+    #else\n+        --soloCBwhitelist None\n+    #end if\n     ## 1 - check length of barcode, 0 - do not check\n     ## Good for checking custom chemistries\n     --soloBarcodeReadLength $sc.soloBarcodeReadLength\n-    #if str($sc.params.chemistry) == "CR2":\n+    #if str($sc.params.chemistry) == "Cv2":\n     --soloCBstart 1\n     --soloCBlen 16\n     --soloUMIstart 17\n     --soloUMIlen 10\n-    #else if str($sc.params.chemistry) == "CR3":\n+    #else if str($sc.params.chemistry) == "Cv3":\n     --soloCBstart 1\n     --soloCBlen 16\n     --soloUMIstart 17\n@@ -90,12 +94,20 @@\n     --soloCBwhitelist None\n     #end if\n \n-    --soloUMIfiltering $solo.soloUMIfiltering\n     --soloStrand $solo.soloStrand\n     --soloFeatures $solo.soloFeatures\n-    --soloUMIdedup $sc.soloUMIdedup\n-    --quantMode TranscriptomeSAM\n-    --outSAMtype BAM Unsorted\n+    --soloUMIdedup $sc.umidedup.soloUMIdedup\n+    #if str($sc.umidedup.soloUMIdedup) == "1MM_CR":\n+        --soloUMIfiltering $sc.umidedup.soloUMIfiltering\n+    #end if\n+    --quantMode TranscriptomeSAM $solo.quantModeGene\n+    #set $tag_names = str($solo.outSAMattributes).replace(\',\', \' \')\n+    --outSAMattributes $tag_names\n+    #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != \'None\':\n+        --outSAMtype BAM SortedByCoordinate\n+    #else:\n+        --outSAMtype BAM Unsorted\n+    #end if\n \n     #if str($solo.filter.filter_type) == "cellranger2":\n     --soloCellFilter CellRanger2.2 $solo.filter.n_expected $solo.filter.max_perc $solo.filter.max_min_ratio\n@@ -109,24 +121,39 @@\n     ## Splice junctions are always under "raw" directory\n \n     --soloOutFormatFeaturesGeneField3 \'${solo.soloOutFormatFeaturesGeneField3}\'\n+\n+    ## Limits\n+    @LIMITS@\n+\n+    ##outWig:\n+    @OUTWIG@\n     ## Rename the the selected features directory\n     && mv Solo.out/${solo.soloFeatures} Solo.out/soloFeatures\n     ## put the barcodes and features stats into a single file\n     && cat <(echo "Barcodes:") Solo.out/Barcodes.stats <(echo "Genes:") Solo.out/soloFeatures/Features.stats > \'${output_stats}\'\n \n-    ## BAM sorting (logic copied from samtools_sort wrapper)\n-    ## choosing BAM SortedByCoord appeared once to give fewer reads\n-    ## than BAM Unsorted followed by a samtools sort\n-    ## so better go with the latter?\n+\n+    #if "CB" in $tag_names or "UB" in $tag_names or str($outWig.outWigType) != \'None\':\n+        ## recompress BAM output for smaller file size\n+        && samtools view -b -o \'$output_BAM\' Aligned.sortedByCoord.out.bam\n+    #else:\n+        ## BAM sorting (logic copied from samtools_sort wrapper)\n+        ## choosing BAM SortedByCoord appeared once to give fewer reads\n+        ## than BAM Unsorted followed by a samtools sort\n+        ## so better go with the latter?\n \n-    &&\n-    ##compute the number of ADDITIONAL threads to be used by samtools (-@)\n-    addthreads=\\${GALAXY_SLOTS:-2} && (( addthreads-- )) &&\n-    ##compute the number of memory available to samtools sort (-m)\n-    ##use only 75% of available: https://github.com/samtools/samtools/issues/831\n-    addmemory=\\${GALAXY_MEMORY_MB_PER_SLOT:-768} &&\n-    ((addmemory=addmemory*75/100)) &&\n-    samtools sort -@ \\$addthreads -m \\$addmemory"M" -T "\\${TMPDIR:-.}" -O bam -o \'$output_BAM\' Aligned.out.bam\n+        &&\n+        ##compute the number of ADDITIONAL threads to be used by samtools (-@)\n+        addthreads=\\${GALAXY_SLOTS:-2} &&'..b's n="14" />\n+                </assert_contents>\n+            </output>\n+            <output name="output_matrix" >\n+                <assert_contents>\n+                    <has_line_matching expression="14\\s+394\\s+7" />\n+                    <has_line_matching expression="4\\s+381\\s+1" />\n+                    <has_n_lines n="10" />\n+                </assert_contents>\n+            </output>\n+            <output name="output_stats" >\n+                <assert_contents>\n+                    <has_line_matching expression="\\s+noUnmapped\\s+5823" />\n+                    <has_line_matching expression="\\s+yesUMIs\\s+8" />\n+                </assert_contents>\n+            </output>\n+            <output name="output_BAM" >\n+                <assert_contents>\n+                    <has_size value="153108" delta="600" />\n+                </assert_contents>\n+            </output>\n+        </test>\n+        <test expect_num_outputs="6">\n+            <!-- test 10 -->\n+            <!-- Test soloFeatures -->\n+            <conditional name="refGenomeSource">\n+                <param name="geneSource" value="history" />\n+                <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />\n+                <param name="genomeSAindexNbases" value="4" />\n+                <param name="sjdbOverhang" value="100" />\n+                <param name="sjdbGTFfile" value="filtered3.Homo_sapiens.GRCh38.100.chr21.gtf" ftype="gtf"/>\n+            </conditional>\n+            <conditional name="sc" >\n+                <param name="solo_type" value="CB_UMI_Simple" />\n+                <conditional name="input_types">\n+                    <param name="use" value="repeat" />\n+                    <param name="input1" value="pbmc_1k_v2_L001.R1.10k.fastq.gz" ftype="fastqsanger.gz" />\n+                    <param name="input2" value="pbmc_1k_v2_L001.R2.10k.fastq.gz" ftype="fastqsanger.gz" />\n+                </conditional>\n+                <param name="soloCBwhitelist" value="filtered.barcodes.txt" />\n+                <param name="soloCBmatchWLtype" value="1MM_multi_pseudocounts" />\n+                <conditional name="params">\n+                    <param name="chemistry" value="Cv3" />\n+                </conditional>\n+                <conditional name="umidedup">\n+                    <param name="soloUMIdedup" value="1MM_CR" />\n+                    <param name="soloUMIfiltering" value="MultiGeneUMI" />\n+                </conditional>\n+            </conditional>\n+            <section name="solo" >\n+                <param name="soloStrand" value="Forward" />\n+                <param name="soloFeatures" value="GeneFull_ExonOverIntron" />\n+                <conditional name="filter">\n+                    <param name="filter_type" value="no_filter" />\n+                </conditional>\n+                <param name="soloOutFormatFeaturesGeneField3" value="Dummy Text" />\n+            </section>\n+            <output name="output_barcodes" >\n+                <assert_contents>\n+                    <!-- first and last line -->\n+                    <has_line line="AAACCTGAGCGCTCCA" />\n+                    <has_line line="TTTGGTTAGTGGGCTA" />\n+                    <has_n_lines n="394" />\n+                </assert_contents>\n+            </output>\n+            <output name="output_genes" >\n+                <assert_contents>\n+                    <has_line_matching expression="ENSG00000279493\\s+FP565260\\.4\\s+Dummy\\s+Text" />\n+                    <has_line_matching expression="ENSG00000279064\\s+FP236315\\.1\\s+Dummy\\s+Text" />\n+                    <has_n_lines n="14" />\n+                </assert_contents>\n+            </output>\n+            <output name="output_matrixGeneFull" >\n+                <assert_contents>\n+                    <has_line_matching expression="14\\s+394\\s+104" />\n+                    <has_line_matching expression="10\\s+2\\s+1" />\n+                    <has_n_lines n="107" />\n                 </assert_contents>\n             </output>\n         </test>\n'
b
diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 2023 +0000
b
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b
diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 2023 +0000
b
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b
diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 2023 +0000
b
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b
diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 2023 +0000
b
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diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/filtered3.bam
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Binary file test-data/filtered3.bam has changed
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diff -r 79b885ce78d7 -r 9ee34ba73ebf test-data/rnastar_test_mapped_reads_PE.bam
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Binary file test-data/rnastar_test_mapped_reads_PE.bam has changed
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diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 2023 +0000
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@@ -0,0 +1,2 @@
+test_chromosome 251 350 1 1 0 51 0 37
+test_chromosome 401 500 1 1 0 41 0 36
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diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 2023 +0000
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@@ -0,0 +1,290 @@
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b
diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 2023 +0000
b
@@ -0,0 +1,124 @@
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b
diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 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 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 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 79b885ce78d7 -r 9ee34ba73ebf test-data/tophat_test.fa.gz
b
Binary file test-data/tophat_test.fa.gz has changed
b
diff -r 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 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 79b885ce78d7 -r 9ee34ba73ebf 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 20:04:43 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