| Previous changeset 1:bc685d13b637 (2015-11-19) Next changeset 3:318b2a9d54dd (2017-04-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a89b30e7cbe4e7db22f36773112f7ed833285cb3 |
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modified:
rg_rnaStar.xml |
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added:
README.rst test-data/test3.chimjunc.tabular test-data/test3.fastqsanger test-data/test3.ref.fa |
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| diff -r bc685d13b637 -r ace9f5a2b40f README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 05 11:56:20 2016 -0500 |
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| @@ -0,0 +1,7 @@ + +System Requirements +=================== + +- **Memory**: To run efficiently, RNA-STAR requires enough free memory to + hold the SA-indexed reference genome in RAM. For Human Genome hg19 this is + index about 27GB and running RNA-STAR requires approximately ~30GB of RAM. |
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| diff -r bc685d13b637 -r ace9f5a2b40f rg_rnaStar.xml --- a/rg_rnaStar.xml Thu Nov 19 05:34:06 2015 -0500 +++ b/rg_rnaStar.xml Fri Feb 05 11:56:20 2016 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="rna_star" name="RNA STAR" version="2.4.0d">\n+<tool id="rna_star" name="RNA STAR" version="2.4.0d-2">\n <description>Gapped-read mapper for RNA-seq data</description>\n <requirements>\n <requirement type="package" version="2.4.0d">rnastar</requirement>\n@@ -12,86 +12,160 @@\n </stdio>\n \n <command><![CDATA[\n- ##\n- ## Run STAR.\n- ##\n+ ## Create temporary index for custom reference\n #if str($refGenomeSource.genomeSource) == \'history\':\n- mkdir -p tempstargenomedir; STAR --runMode genomeGenerate --genomeDir "tempstargenomedir" --genomeFastaFiles "$refGenomeSource.ownFile" --runThreadN 2\n+ mkdir -p tempstargenomedir &&\n+ STAR\n+ --runMode genomeGenerate\n+ --genomeDir "tempstargenomedir"\n+ --genomeFastaFiles "$refGenomeSource.ownFile"\n+ --runThreadN \\${GALAXY_SLOTS:-4}\n+ \n #if str($refGenomeSource.geneModel) != \'None\':\n- --sjdbOverhang "100" --sjdbGTFfile "$refGenomeSource.geneModel"\n- #if str($refGenomeSource.geneModel.ext) == \'gff3\':\n- --sjdbGTFtagExonParentTranscript Parent\n- #end if\n+ --sjdbOverhang "$refGenomeSource.overhang"\n+ --sjdbGTFfile "$refGenomeSource.geneModel"\n+ \n+ #if str($refGenomeSource.geneModel.ext) == \'gff3\':\n+ --sjdbGTFtagExonParentTranscript Parent\n+ #end if\n #end if\n ;\n #end if\n+ \n+ \n+ ## Actual alignment\n STAR\n- ## Can adjust this as appropriate for the system.\n- --genomeLoad NoSharedMemory\n+ --runThreadN \\${GALAXY_SLOTS:-4}\n+ --genomeLoad NoSharedMemory \n #if str($refGenomeSource.genomeSource) == \'history\':\n --genomeDir "tempstargenomedir"\n #else\n --genomeDir "$refGenomeSource.index.fields.path"\n #end if\n- --readFilesIn $singlePaired.input1\n- #if str($singlePaired.sPaired) == "paired"\n- $singlePaired.input2\n+ \n+ --readFilesIn\n+ #if str($singlePaired.sPaired) == "paired_collection"\n+ "$singlePaired.input.forward" "$singlePaired.input.reverse"\n+ #else\n+ "$singlePaired.input1"\n+ #if str($singlePaired.sPaired) == "paired"\n+ "$singlePaired.input2"\n+ #end if\n #end if\n- --runThreadN \\${GALAXY_SLOTS:-4}\n- #if str($params.settingsType) == "full":\n- --chimSegmentMin $params.chim_segment_min\n- --chimScoreMin $params.chim_score_min\n- --seedSearchStartLmax $params.seed_search_start_l_max\n- --alignSJDBoverhangMin $params.align_sjdb_overhang_min\n- --outFilterScoreMinOverLread $params.out_filter_score_min_over_l_read\n+\n+ ## Output parameters\n+ #if str( $output_params.output_select ) == "yes":\n+ --outSAMattributes $output_params.outSAMattributes\n+ --outSAMstrandField $output_params.outSAMstrandField\n+ --outFilterIntronMotifs $output_params.outFilterIntronMotifs\n+ #if str( $output_params.output_params2.output_select2 ) == "yes":\n+ --outSAMunmapped $output_params.output_params2.unmapped_opt\n+ --outSAMprimaryFlag $output_params.output_params2.primary_opt\n+ --outSAMmapqUnique "$output_params.output_params2.unique"\n+ --outFilterType $output_params.output_params2.sjfilter_opt\n+ --outFilterMultimapScoreRange "$output_params.output_params2.multiScoreRange"\n+ --outFilterMultimapNmax "$output_params.output_params2.multiNmax"\n+ --outFilterMismatchNmax "$output_params.output_params2.mismatchNmax"\n+ --outFilterMismatchNoverLmax "$output_params.output_params2.mismatchNoverLmax"\n+ --outFilterMismatchNoverReadLmax "$output_params.output_params2.mismatchNoverReadLmax"\n+ --outFilterScoreMin "$output_params.output_params2.scoreMin"\n+ --outFilterScoreMinOverLread "$output_params.output_params2.scoreMinOverLread"\n+ --outFilterMatchNmin "$output_param'..b' />\n+ <param name="outSAMstrandField" value="intronMotif" />\n+ <param name="outFilterIntronMotifs" value="RemoveNoncanonical" />\n+ \n+ <param name="output_select2" value="yes" />\n+ <param name="settingsType" value="full" />\n+ <param name="seed_select" value="yes" />\n+ <param name="align_select" value="yes" />\n+ <param name="chim_select" value="yes" />\n+ \n+ <!-- Uses default settings, should be similar to test1, but tests the parameters -->\n+ <output name="output_log" file="rnastar_test.log" compare="diff" lines_diff="10"/>\n+ <output name="splice_junctions" file="rnastar_test_splicejunctions.bed"/>\n+ <output name="mapped_reads" file="rnastar_test_mapped_reads.bam" compare="sim_size" delta="634" /><!-- header is 434 bytes larger -->\n+ </test>\n \n-If you have un-stranded RNA-seq data, and wish to run Cufflinks/Cuffdiff on STAR alignments, you will\n-need to run STAR with --outSAMstrandField intronMotif option, which will generate the XS\n-strand attribute for all alignments that contain splice junctions. The spliced alignments that have undefined\n-strand (i.e. containing only non-canonical junctions) will be suppressed.\n+ </tests>\n+ <help>\n+**What it does**\n+\n+This tool runs STAR, an ultrafast universal RNA-seq aligner.\n \n-If you have stranded RNA-seq data, you do not need to use any specific STAR options. Instead, you need\n-to run Cufflinks with the library option --library-type options. For example, cufflinks with\n-library-type fr-firststrand should be used for the b\n+**Extra SAM attributes**\n+\n+The Standard option includes the following four attributes::\n \n-It is recommended to remove the non-canonical junctions for Cufflinks runs using b\n+ NH: Number of reported alignments that contain the query in the current record.\n+ HI: Query hit index, indicating the alignment record is the i-th one stored in SAM\n+ AS: Local alignment score (paired for paired-end reads)\n+ nM: Number of mismatches per (paired) alignment\n \n+The All option includes the Standard attributes, plus the following four::\n \n---outFilterIntronMotifs RemoveNoncanonical\n-filter out alignments that contain non-canonical junctions\n-\n-OR\n+ NM: Edit distance to the reference, including ambiguous bases but excluding clipping\n+ MD: String for mismatching positions\n+ jM: Intron motifs for all junctions\n+ jI: Start and end of introns for all junctions\n \n---outFilterIntronMotifs RemoveNoncanonicalUnannotated\n-filter out alignments that contain non-canonical unannotated junctions\n-when using annotated splice junctions database. The annotated non-\n-canonical junctions will be kept.\n+**STAR-Fusion**\n \n+STAR-Fusion_ is used to identify candidate fusion transcripts. The recommended_ parameters for running\n+STAR prior to STAR-Fusion can be pre-selected, with the following exceptions::\n+\n+ --twopassMode Basic # not an option in STAR 2.4.0\n+ --chimSegmentReadGapMax 3 # not an option in STAR 2.4.0\n+ --alignSJstitchMismatchNmax 5 -1 5 5 # not an option in STAR 2.4.0\n \n **Attributions**\n \n@@ -341,13 +520,13 @@\n \n .. _STAR: https://bitbucket.org/jgoecks/jeremys-code/raw/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml\n .. _licensed: http://creativecommons.org/licenses/by-nc-nd/3.0/\n+.. _STAR-Fusion: https://github.com/STAR-Fusion/STAR-Fusion\n+.. _recommended: https://github.com/STAR-Fusion/STAR-Fusion/wiki#alternatively-running-star-yourself-and-then-running-star-fusion-using-the-existing-outputs\n .. _rna_star: https://github.com/alexdobin/STAR\n .. _rna_starMS: http://bioinformatics.oxfordjournals.org/content/29/1/15.full\n .. _Galaxy: http://getgalaxy.org\n-\n </help>\n-<citations>\n- <citation type="doi">10.1093/bioinformatics/bts635</citation>\n-</citations>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/bts635</citation>\n+ </citations>\n </tool>\n-\n' |
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| diff -r bc685d13b637 -r ace9f5a2b40f test-data/test3.chimjunc.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.chimjunc.tabular Fri Feb 05 11:56:20 2016 -0500 |
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| @@ -0,0 +1,24 @@ +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_60 181 60M15S 241 60S15M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_62 183 58M17S 241 58S17M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_64 185 56M19S 241 56S19M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_66 187 54M21S 241 54S21M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_68 189 52M23S 241 52S23M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_70 191 50M25S 241 50S25M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_72 193 48M27S 241 48S27M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_74 195 46M29S 241 46S29M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_76 197 44M31S 241 44S31M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_78 199 42M33S 241 42S33M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_80 201 40M35S 241 40S35M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_82 203 38M37S 241 38S37M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_84 205 36M39S 241 36S39M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_86 207 34M41S 241 34S41M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_88 209 32M43S 241 32S43M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_90 211 30M45S 241 30S45M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_92 213 28M47S 241 28S47M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_94 215 26M49S 241 26S49M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_96 217 24M51S 241 24S51M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_98 219 22M53S 241 22S53M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_100 221 20M55S 241 20S55M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_102 223 18M57S 241 18S57M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_104 225 16M59S 241 16S59M +chr1 241 + chr2 240 + 0 0 0 test_chimeric_mRNA_106 227 14M61S 241 14S61M |
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| diff -r bc685d13b637 -r ace9f5a2b40f test-data/test3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.fastqsanger Fri Feb 05 11:56:20 2016 -0500 |
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| 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' 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| diff -r bc685d13b637 -r ace9f5a2b40f test-data/test3.ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test3.ref.fa Fri Feb 05 11:56:20 2016 -0500 |
| b |
| @@ -0,0 +1,18 @@ +>chr1 +GACGGACGTATTCCTCTGGCCTCAACGGTTCCTGCTTTCGCTGGGATCCAAGATTGGCAG +CTGAAACCGCCTTTCCAAAGTGAGTCCTTCGTCTGTGACTAACTGTGCCAAATCGTCTTG +CAAACTCCTGATCCAGTTTAACTCACCAAATTATAGCCATACAGACCCAAATTTTAAATC +ATATCACGCGACTAGCCTCTGCTTAATTTCTGTGCTCAAGGGTTTTGGTCCGCCCGAGCG +GTGCAGCCGATTAGGACCATCTAATGCACTTGTTACAAGACTTCTTTTAAATACTTTCTT +CCTGCCCAGTAGCGGATGATAATGGTTGTTGCCAGCCGGTGTGGAAGGTAACAGCACCGG +TGCGAGCCTAATGTGCCGTCTCCACCAACACAAGGCTATCCGGTCGTATAATAGGATTCC +GCAATGGGGTTAGCAAATGGCAGCCTAAACGATATCGGGGACTTGCGATGTACATGCTTT +>chr2 +TCAACAATAAGCGCTTTTTGTAGGCAGGGGCACCCCCTATCAGTGGCTGCGCCAAAACAT +CTTCGGATCCCCTTGTCCAATCAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGA +CATCATTAGTGATTAAATGCCACTCCCAAAATTCTGCCTAGAAATGTTTAAGTTCGCTCC +ACTAAAGTTGTTTAAAACGACTACTAAATCCGCGTGATAGGGGATTTCATATTTAATCTT +TTATCGTAAGGAACAGCCGATCTTAATGGATGGCCGCAGGTGGTATGGAAGCTATAAGCG +CGGGTGAGAGGGTAATTAGGCGTGTTCACCTACACTACGCTAACGGGCGATTCTATAAGA +TTGCACATTGCGTCTACTTATAAGATGTCTCAACGGCATGCGCAACTTGTGAAGTGCCTA +CTATCCTTAAACGCATATCTCGCACAGTAACTCCCCAATATGTGAGCATCTGATGTTGCC |