| Previous changeset 29:e416daaccd32 (2023-09-01) Next changeset 31:9b7a86a83fce (2024-12-05) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2b3fa63863a366beef057c7f75ccbcaf0c280151 |
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modified:
macros.xml rg_rnaStar.xml test-data/rnastar_test.log |
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added:
test-data/filtered3.vcf test-data/filtered4.bam test-data/rnastar_test_diploid.log test-data/rnastar_test_mapped_reads.vcf test-data/rnastar_test_mapped_reads_diploid.bam test-data/rnastar_test_mapped_reads_test10.bam test-data/rnastar_test_splicejunctions_diploid.bed test-data/rnastar_test_splicejunctions_wasp.bed |
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| diff -r e416daaccd32 -r acd651be2b9c macros.xml --- a/macros.xml Fri Sep 01 13:16:43 2023 +0000 +++ b/macros.xml Tue Aug 27 14:09:53 2024 +0000 |
| [ |
| b'@@ -4,8 +4,8 @@\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 update @IDX_VERSION_SUFFIX@ -->\n <!-- STAR version to be used -->\n- <token name="@TOOL_VERSION@">2.7.10b</token>\n- <token name="@VERSION_SUFFIX@">4</token>\n+ <token name="@TOOL_VERSION@">2.7.11a</token>\n+ <token name="@VERSION_SUFFIX@">1</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@@ -15,18 +15,16 @@\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_VERSION_SUFFIX@">2</token>\n <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>\n-\n <xml name="requirements">\n <requirements>\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+ <requirement type="package" version="1.18">samtools</requirement>\n+ <requirement type="package" version="1.13">gzip</requirement>\n+ <yield/>\n </requirements>\n </xml>\n-\n <xml name="edam">\n <edam_topics>\n <edam_topic>topic_3170</edam_topic>\n@@ -36,20 +34,16 @@\n <edam_operation>operation_0292</edam_operation>\n </edam_operations>\n </xml>\n-\n <xml name="index_selection" token_with_gene_model="0">\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+ <param argument="--genomeDir" type="select" label="Select reference genome" help="If your genome of interest is not listed, contact the Galaxy team">\n <options from_data_table="@IDX_DATA_TABLE@">\n- <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />\n- <filter type="static_value" column="5" value="@IDX_VERSION@" />\n- <filter type="sort_by" column="2" />\n- <validator type="no_options" message="No indexes are available for the selected input dataset" />\n+ <filter type="static_value" column="4" value="@WITH_GENE_MODEL@"/>\n+ <filter type="static_value" column="5" value="@IDX_VERSION@"/>\n+ <filter type="sort_by" column="2"/>\n+ <validator type="no_options" message="No indexes are available for the selected input dataset"/>\n </options>\n </param>\n </xml>\n-\n <token name="@FASTQ_GZ_OPTION@">\n --readFilesCommand zcat\n </token>\n@@ -59,9 +53,9 @@\n </citations>\n </xml>\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="--sjdbGTFfeatureExon" type="text" value="exon" label="Elements to use from the gene model to use for splice junctions" help="By default and for almost all cases: \'exon\', referring to finding junctions at the RNA splice sites. This can optionally be changed to allow splicing at other levels, such as \'gene\', \'transcript\', \'CDS\'."/>\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+ <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="false" help="Exon junction in'..b' <option value="-">No per gene or transcript output as no GTF was provided</option>\n </param>\n- <when value="-" />\n+ <when value="-"/>\n </conditional>\n </xml>\n <xml name="outSAMmapqUnique">\n <!-- MAPQ 255 is the default in STAR (coming from tophat behaviour and compatibility for Cufflinks) but it is a problematic value\n - according to SAM/BAM specs it means "undefined".\n - Using 255 as the max mapq causes problem with modern downstream tools like mutect2: https://sites.duke.edu/workblog/2021/08/18/star-rnaseq-gatk-mutect2/ and 60 has become an inofficial replacement for 255. -->\n- <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255"\n- label="MAPQ value for unique mappers"\n- help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is\n-used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2." />\n+ <param argument="--outSAMmapqUnique" type="integer" value="60" min="0" max="255" label="MAPQ value for unique mappers" help="STAR bases the mapping quality scores of alignment records in its BAM output on the number of alternative mappings for the read. If a read maps to multiple locations on the reference genome, the following MAPQ scoring scheme is used: >=5 mappings => MAPQ=0; 3-4 mappings => MAPQ=1; 2 mappings => MAPQ=3. This setting lets you control the MAPQ used for reads mapped to a single location. Set to 255 for compatibility with Cufflink (default in STAR) but keep to 60 for modern downstream tools like mutect2."/>\n+ </xml>\n+ <xml name="wasp">\n+ <!--\n+ This is re-implementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,\n+ Yoav Gilad and Jonathan K Pritchard. Please cite the original WASP paper: Nature Methods 12,\n+ 1061\xe2\x80\x931063 (2015) https://www.nature.com/articles/nmeth.3582. WASP filtering is activated\n+ with "waspOutputMode SAMtag".\n+ -->\n+ <conditional name="wasp_conditional">\n+ <param argument="--waspOutputMode" type="select" label="Actiavte WASP filtering">\n+ <help><![CDATA[This is a reimplementation of the original WASP algorithm by Bryce van de Geijn, Graham McVicker,\n+ Yoav Gilad and Jonathan K Pritchard. https://doi.org/10.1038/nmeth.3582. This option will add the vW tag to the SAM output. vW:i:1 means\n+ alignment passed WASP filtering, and all other values mean it did not:<br/>\n+ - vW:i:2 = multi-mapping read<br/>\n+ - vW:i:3 = variant base in the read is N (non-ACGT)<br/>\n+ - vW:i:4 = remapped read did not map <br/>\n+ - vW:i:5 = remapped read multi-maps <br/>\n+ - vW:i:6 = remapped read maps to a different locus <br/>\n+ - vW:i:7 = read overlaps too many variants <br/>\n+ ]]>\n+ </help>\n+ <option value="" selected="true">No WASP filtering</option>\n+ <option value="wasp_mode">Activate WASP filtering</option>\n+ </param>\n+ <when value="wasp_mode">\n+ <param argument="--varVCFfile" type="data" format="vcf" label="VCF file with personal variants" help="Each variant is expected to have a genotype with two alleles. The VCF file needs to have the 10th column with genotype recorded as 0/1, 1/0, 1/1 (or | instead of /)"/>\n+ </when>\n+ <when value=""/>\n+ </conditional>\n </xml>\n </macros>\n' |
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| diff -r e416daaccd32 -r acd651be2b9c rg_rnaStar.xml --- a/rg_rnaStar.xml Fri Sep 01 13:16:43 2023 +0000 +++ b/rg_rnaStar.xml Tue Aug 27 14:09:53 2024 +0000 |
| [ |
| b'@@ -47,9 +47,11 @@\n \n ## Two pass mode\n --twopassMode ${twopass.twopassMode} ${twopass.twopass_read_subset}\n- #for $sj_input in $twopass.sj_precalculated:\n- \'$sj_input\'\n- #end for\n+ #if str($twopass.sj_precalculated).strip():\n+ #for $sj_input in $twopass.sj_precalculated:\n+ \'$sj_input\'\n+ #end for\n+ #end if\n #if str($twopass.twopassMode) != \'None\':\n #if str($refGenomeSource.GTFconditional.GTFselect) == \'with-gtf\':\n ## need to check first if its a cached index or from history\n@@ -91,6 +93,15 @@\n ## Read MAPQ\n --outSAMmapqUnique ${oformat.outSAMmapqUnique}\n \n+ ## Transform diploid mode output to reference coordinates\n+ #if str($refGenomeSource.geneSource) == \'history\':\n+ #if \'diploidconditional\' in $refGenomeSource:\n+ #if str($refGenomeSource.diploidconditional.diploid) == \'Yes\':\n+ \'${refGenomeSource.diploidconditional.genomeTransformOutput}\'\n+ #end if \n+ #end if\n+ #end if\n+\n ## Output filter parameters\n \n ## Basic Filters\n@@ -206,7 +217,7 @@\n #end if\n \n ## Limits\n- @LIMITS@\n+ @LIMITS@\n #else:\n ## Go with STAR\'s default algorithmic settings,\n ## but we need to provide a reasonable default\n@@ -223,12 +234,16 @@\n #end if\n #end if\n #end if\n-\n --outBAMsortingThreadN \\${GALAXY_SLOTS:-4}\n --outBAMsortingBinsN $perf.outBAMsortingBinsN\n --winAnchorMultimapNmax $perf.winAnchorMultimapNmax\n --limitBAMsortRAM \\$((\\${GALAXY_MEMORY_MB:-0}*1000000))\n \n+ #if $oformat.wasp_conditional.waspOutputMode == "wasp_mode":\n+ --waspOutputMode SAMtag\n+ --varVCFfile \'$oformat.wasp_conditional.varVCFfile\'\n+ #end if\n+\n ## Handle chimeric options and output\n #if str($chimOutType):\n --chimOutType $chimOutType\n@@ -318,6 +333,18 @@\n <expand macro="quantModeNoGTF" />\n </when>\n </conditional>\n+ <conditional name="diploidconditional">\n+ <param name="diploid" type="select" label="Diploid mode" help="Map RNA-seq reads to a diploid genome">\n+ <option value="No" selected="True">No</option>\n+ <option value="Yes">Yes</option>\n+ </param>\n+ <when value="Yes">\n+ <param argument="--genomeTransformVCF" type="data" format="vcf" label="VCF file with diploid SNVs and InDels" help="The homozygous and heterozygous alleles from this VCF will be inserted into the reference genome to create a transformed genome with two haplotypes"/>\n+ <param argument="--genomeTransformOutput" type="boolean" checked="false" truevalue="--genomeTransformOutput SAM SJ Quant" falsevalue="--genomeTransformOutput None" label="Transform alignments, spliced junctions and quantifications back to the reference coordinates" help="Use this if downstream processing relies on reference coordinates"/>\n+ </when>\n+ <when value="No">\n+ </when>\n+ </conditional>\n </when>\n </conditional>\n \n@@ -387,6 +414,7 @@\n primary?"/> -->\n <param name="outSAMprimaryFlag" type="hidden" value="OneBestScore" />\n <expand macro="outSAMmapqUnique"/>\n+ <expand macro="wasp"/>\n </section>\n <section name="filter" title="Output filter criteria" expanded="true">\n <param name="basic_filters" type="select" display="checkboxes" multiple="true" optional="true"\n@@ -544,20 +572,24 @@\n </data>\n <expand macro="outWigOutputs"/>\n </outputs>\n-\n <tests>\n <tes'..b'ype="fastqsanger.gz" />\n </conditional>\n <conditional name="refGenomeSource">\n <param name="geneSource" value="history" />\n- <param name="genomeFastaFiles" value="tophat_test.fa.gz" />\n+ <param name="genomeFastaFiles" value="filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa.gz" />\n <param name="genomeSAindexNbases" value="5" />\n </conditional>\n <section name="oformat">\n <param name="outSAMattributes" value="NH,HI,AS,nM,NM,MD,jM,jI,MC,ch" />\n+ <conditional name="wasp_conditional">\n+ <param name="waspOutputMode" value="wasp_mode"/>\n+ <param name="varVCFfile" value="filtered3.vcf" ftype="vcf" />\n+ </conditional>\n </section>\n <section name="algo">\n <conditional name="params">\n@@ -565,8 +597,7 @@\n </conditional>\n </section>\n <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />\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" />\n+ <output name="splice_junctions" file="rnastar_test_splicejunctions_wasp.bed"/>\n </test>\n <!-- test with cached genome index -->\n <test expect_num_outputs="3">\n@@ -810,6 +841,7 @@\n \n <output name="chimeric_junctions" file="test3.chimjunc.tabular" compare="diff" lines_diff="2"/>\n </test>\n+ <!-- test 10 -->\n <test expect_num_outputs="3">\n <conditional name="singlePaired">\n <param name="sPaired" value="single" />\n@@ -837,7 +869,7 @@\n \n <output name="output_log" file="rnastar_test.log" compare="re_match_multiline" />\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" />\n+ <output name="mapped_reads" file="rnastar_test_mapped_reads_test10.bam" compare="sim_size" delta="634" />\n </test>\n <!-- twopass mode tests -->\n <!-- test Basic twopass -->\n@@ -1117,6 +1149,28 @@\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+ <!-- test diploid mode -->\n+ <test expect_num_outputs="3">\n+ <conditional name="singlePaired">\n+ <param name="sPaired" value="single" />\n+ <param name="input1" value="tophat_in2.fastqsanger" ftype="fastqsanger" />\n+ </conditional>\n+ <conditional name="refGenomeSource">\n+ <param name="geneSource" value="history" />\n+ <param name="genomeFastaFiles" value="tophat_test.fa.gz" />\n+ <param name="genomeSAindexNbases" value="5" />\n+ </conditional>\n+ <conditional name="diploidconditional">\n+ <param name="diploid" value="Yes" />\n+ <!-- generated from rnastar_test_mapped_reads.bam with\n+ bcftools mpileup and bcftools call -->\n+ <param name="genomeTransformVCF" value="rnastar_test_mapped_reads.vcf" ftype="vcf" />\n+ <param name="genomeTransformOutput" value="true" />\n+ </conditional>\n+ <output name="output_log" file="rnastar_test_diploid.log" compare="re_match_multiline" />\n+ <output name="splice_junctions" file="rnastar_test_splicejunctions_diploid.bed"/>\n+ <output name="mapped_reads" file="rnastar_test_mapped_reads_diploid.bam" compare="sim_size" delta="634" />\n+ </test>\n </tests>\n <help><![CDATA[\n **What it does**\n' |
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| diff -r e416daaccd32 -r acd651be2b9c test-data/filtered3.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/filtered3.vcf Tue Aug 27 14:09:53 2024 +0000 |
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| b'@@ -0,0 +1,175 @@\n+##fileformat=VCFv4.2\n+##FILTER=<ID=PASS,Description="All filters passed">\n+##bcftoolsVersion=1.15.1+htslib-1.15.1\n+##bcftoolsCommand=mpileup -f filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa filtered3.bam\n+##reference=file://filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa\n+##contig=<ID=21,length=697740>\n+##ALT=<ID=*,Description="Represents allele(s) other than observed.">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel">\n+##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel">\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3">\n+##INFO=<ID=RPBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)">\n+##INFO=<ID=MQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)">\n+##INFO=<ID=BQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)">\n+##INFO=<ID=MQSBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)">\n+##INFO=<ID=SCBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)">\n+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher\'s exact test to detect strand bias">\n+##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric.">\n+##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)">\n+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed">\n+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">\n+##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases">\n+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality">\n+##bcftools_callVersion=1.15.1+htslib-1.15.1\n+##bcftools_callCommand=call -mv -Ob -o filtered3.bcf; Date=Tue Aug 27 14:09:53 2024\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tfiltered3.bam\n+21\t13871\t.\tG\tA\t8.19139\t.\tDP=16;VDB=0.163924;SGB=-0.651104;RPBZ=-1.26304;MQBZ=1.7272;BQBZ=1;SCBZ=-0.447396;FS=0;MQ0F=0.0625;AC=1;AN=2;DP4=8,0,8,0;MQ=9\tGT:PL\t0/1:38,0,6\n+21\t13918\t.\tA\tG\t8.05611\t.\tDP=9;VDB=0.12166;SGB=-0.616816;RPBZ=1.03713;MQBZ=-0.154303;BQBZ=0;SCBZ=0.707107;FS=0;MQ0F=0.111111;AC=1;AN=2;DP4=3,0,6,0;MQ=14\tGT:PL\t0/1:40,0,15\n+21\t13924\t.\tG\tA\t27.0767\t.\tDP=11;VDB=0.0108096;SGB=-0.651104;RPBZ=-0.261911;MQBZ=0.968246;BQBZ=-0.745356;SCBZ=-0.931695;FS=0;MQ0F=0.0909091;AC=2;AN=2;DP4=2,0,8,0;MQ=14\tGT:PL\t1/1:54,3,0\n+21\t13928\t.\tG\tC\t34.42\t.\tDP=11;VDB=0.0257451;SGB=-0.670168;FS=0;MQ0F=0.0909091;AC=2;AN=2;DP4=0,0,10,0;MQ=14\tGT:PL\t1/1:64,24,0\n+21\t13962\t.\tA\tG\t3.21856\t.\tDP=13;VDB=0.00595258;SGB=-0.616816;RPBZ=2.14581;MQBZ=0.245201;BQBZ=-0.113961;SCBZ=-1.73888;FS=0;MQ0F=0.0769231;AC=1;AN=2;DP4=7,0,6,0;MQ=12\tGT:PL\t0/1:33,0,34\n+21\t15349\t.\tG\tC\t3.74242\t.\tDP=33;VDB=3.28209e-07;SGB=-0.689466;RPBZ=-1.0584;MQBZ=1.31911;MQSBZ=-1.01601;BQBZ=-1.40181;SCBZ=0.601646;FS=0;MQ0F=0.0606061;AC=1;AN=2;DP4=1,15,1,15;MQ=13\tGT:PL\t0/1:34,0,49\n+21\t15425\t.\tT\tC\t15.3182\t.\tDP=21;VDB=0.739317;SGB=-0.686358;RPBZ=-1.79168;MQBZ=0.125524;BQBZ=1.41022;SCBZ=0.514874;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,7,0,14;MQ=12\tGT:PL\t0/1:47,0,9\n+21\t15431\t.\tG\tA\t6.81655\t.\tDP=18;VDB=0.777008;SGB=-0.683931;RPBZ=-0.93741;MQBZ=-1.01859;BQBZ=1.61245;SCBZ=-1.53815;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,5,0,13;MQ=10\tGT:PL\t0/1:38,0,11\n+21\t19605\t.\tA\t'..b';FS=0;MQ0F=0;AC=2;AN=2;DP4=4,0,5,0;MQ=11\tGT:PL\t1/1:37,3,0\n+21\t152547\t.\tA\tG\t8.54666\t.\tDP=8;VDB=0.00477428;SGB=-0.636426;RPBZ=0.223607;MQBZ=-0.774597;BQBZ=-0.377964;SCBZ=0.377964;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,7,0;MQ=12\tGT:PL\t1/1:35,4,0\n+21\t221789\t.\tT\tC\t19.4636\t.\tDP=5;VDB=0.300397;SGB=-0.590765;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=0,0,5,0;MQ=12\tGT:PL\t1/1:49,15,0\n+21\t221824\t.\tA\tG\t17.2912\t.\tDP=5;VDB=0.446842;SGB=-0.556411;RPBZ=0;MQBZ=0.790569;BQBZ=0;SCBZ=0;FS=0;MQ0F=0.2;AC=2;AN=2;DP4=1,0,4,0;MQ=12\tGT:PL\t1/1:44,8,0\n+21\t236291\t.\tA\tG\t3.21958\t.\tDP=7;VDB=0.535497;SGB=-0.556411;RPBZ=0.707107;MQBZ=-0.866025;BQBZ=0;SCBZ=-0.585142;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,3,0,4;MQ=17\tGT:PL\t0/1:33,0,31\n+21\t236294\t.\tC\tT\t4.32521\t.\tDP=6;VDB=0.176409;SGB=-0.556411;RPBZ=1.38873;MQBZ=-0.707107;BQBZ=0;SCBZ=0.491869;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,2,0,4;MQ=16\tGT:PL\t0/1:35,0,19\n+21\t236295\t.\tA\tG\t4.32521\t.\tDP=6;VDB=0.522837;SGB=-0.556411;RPBZ=0;MQBZ=-0.707107;BQBZ=0;SCBZ=-1.47561;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,2,0,4;MQ=16\tGT:PL\t0/1:35,0,19\n+21\t236320\t.\tG\tA\t3.20067\t.\tDP=8;VDB=0.220638;SGB=-0.556411;RPBZ=1.76777;MQBZ=0;BQBZ=-0.866025;SCBZ=0.866025;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,3,0,4;MQ=14\tGT:PL\t0/1:33,0,20\n+21\t236327\t.\tA\tG\t6.77159\t.\tDP=6;VDB=0.673544;SGB=-0.590765;RPBZ=-0.29277;MQBZ=-0.69282;BQBZ=-0.447214;SCBZ=0.69282;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,5;MQ=14\tGT:PL\t1/1:34,0,2\n+21\t236359\t.\tA\tT\t8.99921\t.\tDP=4;VDB=0.160409;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,4;MQ=11\tGT:PL\t1/1:38,12,0\n+21\t248947\t.\tT\tC\t4.85359\t.\tDP=4;VDB=0.38;SGB=-0.453602;RPBZ=-0.774597;MQBZ=1.73205;MQSBZ=-1;BQBZ=0;SCBZ=1;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,2,1,1;MQ=11\tGT:PL\t1/1:30,2,0\n+21\t248966\t.\tG\tA\t12.6566\t.\tDP=4;VDB=0.112085;SGB=-0.556411;MQSBZ=-1;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,1,3;MQ=11\tGT:PL\t1/1:42,12,0\n+21\t251560\t.\tC\tT\t11.7172\t.\tDP=3;VDB=0.137328;SGB=-0.511536;MQSBZ=0.707107;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,1;MQ=14\tGT:PL\t1/1:41,9,0\n+21\t289446\t.\tT\tC\t49.4146\t.\tDP=22;VDB=1.4824e-07;SGB=-0.692562;FS=0;MQ0F=0.0454545;AC=2;AN=2;DP4=0,0,22,0;MQ=12\tGT:PL\t1/1:79,66,0\n+21\t289481\t.\tT\tC\t3.73429\t.\tDP=48;VDB=0.22406;SGB=-0.692976;RPBZ=0.341551;MQBZ=-1.11595;BQBZ=-1.2128;SCBZ=-1.70538;FS=0;MQ0F=0.0208333;AC=1;AN=2;DP4=22,0,26,0;MQ=11\tGT:PL\t0/1:34,0,44\n+21\t289488\t.\tT\tC\t6.50824\t.\tDP=50;VDB=0.518994;SGB=-0.693021;RPBZ=0.545171;MQBZ=-1.485;BQBZ=2.489;SCBZ=-1.74235;FS=0;MQ0F=0.04;AC=1;AN=2;DP4=23,0,27,0;MQ=11\tGT:PL\t0/1:38,0,40\n+21\t289520\t.\tA\tC\t21.7432\t.\tDP=41;VDB=4.57336e-05;SGB=-0.69312;RPBZ=-0.393988;MQBZ=0.311388;BQBZ=2.69313;SCBZ=1.10119;FS=0;MQ0F=0.0243902;AC=2;AN=2;DP4=9,0,32,0;MQ=10\tGT:PL\t1/1:49,21,0\n+21\t289647\t.\tG\tA\t3.22451\t.\tDP=3;VDB=0.873285;SGB=-0.511536;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,0;MQ=14\tGT:PL\t1/1:30,9,0\n+21\t339923\t.\tC\tT\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t355659\t.\tC\tT\t6.32811\t.\tDP=4;VDB=0.868052;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1;BQBZ=0;SCBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,3;MQ=11\tGT:PL\t1/1:32,5,0\n+21\t553515\t.\tC\tG\t7.30814\t.\tDP=2;VDB=0.68;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t602273\t.\tA\tC\t6.32811\t.\tDP=4;VDB=0.131948;SGB=-0.511536;RPBZ=-1.34164;MQBZ=1;BQBZ=-0.57735;SCBZ=-1.73205;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,1,0,3;MQ=11\tGT:PL\t1/1:32,5,0\n+21\t682407\t.\tG\tT\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682421\t.\tT\tG\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682423\t.\tC\tG\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682426\t.\tG\tA\t7.30814\t.\tDP=2;VDB=0.56;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20\tGT:PL\t1/1:36,6,0\n+21\t682568\t.\tA\tG\t8.13869\t.\tDP=5;VDB=0.133161;SGB=-0.590765;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,5;MQ=9\tGT:PL\t1/1:37,15,0\n+21\t694476\t.\tC\tG\t18.4764\t.\tDP=6;VDB=0.0341101;SGB=-0.616816;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,6,0;MQ=11\tGT:PL\t1/1:48,18,0\n+21\t694482\t.\tT\tC\t19.4636\t.\tDP=4;VDB=0.131345;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,4,0;MQ=15\tGT:PL\t1/1:49,12,0\n' |
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| diff -r e416daaccd32 -r acd651be2b9c test-data/filtered4.bam |
| b |
| Binary file test-data/filtered4.bam has changed |
| b |
| diff -r e416daaccd32 -r acd651be2b9c test-data/rnastar_test.log --- a/test-data/rnastar_test.log Fri Sep 01 13:16:43 2023 +0000 +++ b/test-data/rnastar_test.log Tue Aug 27 14:09:53 2024 +0000 |
| b |
| @@ -3,32 +3,35 @@ Finished on | .* Mapping speed, Million of reads per hour | .* - Number of input reads | 100 - Average input read length | 75 + Number of input reads | 15447 + Average input read length | 119 UNIQUE READS: - Uniquely mapped reads number | 99 - Uniquely mapped reads % | 99.00% - Average mapped length | 74.65 - Number of splices: Total | 52 + Uniquely mapped reads number | 150 + Uniquely mapped reads % | 0.97% + Average mapped length | 105.11 + Number of splices: Total | 131 Number of splices: Annotated (sjdb) | 0 - Number of splices: GT/AG | 52 - Number of splices: GC/AG | 0 - Number of splices: AT/AC | 0 - Number of splices: Non-canonical | 0 - Mismatch rate per base, % | 2.00% - Deletion rate per base | 0.00% - Deletion average length | 0.00 - Insertion rate per base | 0.00% - Insertion average length | 0.00 + Number of splices: GT/AG | 100 + Number of splices: GC/AG | 6 + Number of splices: AT/AC | 1 + Number of splices: Non-canonical | 24 + Mismatch rate per base, % | 6.68% + Deletion rate per base | 0.04% + Deletion average length | 1.17 + Insertion rate per base | 0.04% + Insertion average length | 1.50 MULTI-MAPPING READS: - Number of reads mapped to multiple loci | 1 - % of reads mapped to multiple loci | 1.00% - Number of reads mapped to too many loci | 0 - % of reads mapped to too many loci | 0.00% + Number of reads mapped to multiple loci | 451 + % of reads mapped to multiple loci | 2.92% + Number of reads mapped to too many loci | 58 + % of reads mapped to too many loci | 0.38% UNMAPPED READS: + Number of reads unmapped: too many mismatches | 0 % of reads unmapped: too many mismatches | 0.00% - % of reads unmapped: too short | 0.00% - % of reads unmapped: other | 0.00% + Number of reads unmapped: too short | 7912 + % of reads unmapped: too short | 51.22% + Number of reads unmapped: other | 6876 + % of reads unmapped: other | 44.51% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% |
| b |
| diff -r e416daaccd32 -r acd651be2b9c test-data/rnastar_test_diploid.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_diploid.log Tue Aug 27 14:09:53 2024 +0000 |
| b |
| @@ -0,0 +1,37 @@ + Started job on | .* + Started mapping on | .* + Finished on | .* + Mapping speed, Million of reads per hour | inf + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 100 + Uniquely mapped reads % | 100.00% + Average mapped length | 74.65 + Number of splices: Total | 53 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 53 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 1.63% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 0 + % of reads mapped to multiple loci | 0.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + Number of reads unmapped: too many mismatches | 0 + % of reads unmapped: too many mismatches | 0.00% + Number of reads unmapped: too short | 0 + % of reads unmapped: too short | 0.00% + Number of reads unmapped: other | 0 + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% |
| b |
| diff -r e416daaccd32 -r acd651be2b9c test-data/rnastar_test_mapped_reads.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_mapped_reads.vcf Tue Aug 27 14:09:53 2024 +0000 |
| b |
| @@ -0,0 +1,30 @@ +##fileformat=VCFv4.2 +##FILTER=<ID=PASS,Description="All filters passed"> +##bcftoolsVersion=1.13+htslib-1.13+ds +##bcftoolsCommand=mpileup -Ob -o rnastar_test_mapped_reads.bcf -f tophat_test.fa rnastar_test_mapped_reads.bam +##reference=file://tophat_test.fa +##contig=<ID=test_chromosome,length=650> +##ALT=<ID=*,Description="Represents allele(s) other than observed."> +##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> +##INFO=<ID=IDV,Number=1,Type=Integer,Description="Maximum number of raw reads supporting an indel"> +##INFO=<ID=IMF,Number=1,Type=Float,Description="Maximum fraction of raw reads supporting an indel"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth"> +##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias for filtering splice-site artefacts in RNA-seq data (bigger is better)",Version="3"> +##INFO=<ID=RPBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Read Position Bias (closer to 0 is better)"> +##INFO=<ID=MQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality Bias (closer to 0 is better)"> +##INFO=<ID=BQBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Base Quality Bias (closer to 0 is better)"> +##INFO=<ID=MQSBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Mapping Quality vs Strand Bias (closer to 0 is better)"> +##INFO=<ID=SCBZ,Number=1,Type=Float,Description="Mann-Whitney U-z test of Soft-Clip Length Bias (closer to 0 is better)"> +##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> +##INFO=<ID=SGB,Number=1,Type=Float,Description="Segregation based metric."> +##INFO=<ID=MQ0F,Number=1,Type=Float,Description="Fraction of MQ0 reads (smaller is better)"> +##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes for each ALT allele, in the same order as listed"> +##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> +##INFO=<ID=DP4,Number=4,Type=Integer,Description="Number of high-quality ref-forward , ref-reverse, alt-forward and alt-reverse bases"> +##INFO=<ID=MQ,Number=1,Type=Integer,Description="Average mapping quality"> +##bcftools_callVersion=1.13+htslib-1.13+ds +##bcftools_callCommand=call -vmO z -o rnastar_test_mapped_reads.vcf.gz rnastar_test_mapped_reads.bcf; Date=Tue Jan 2 11:53:57 2024 +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT rnastar_test_mapped_reads.bam +test_chromosome 219 . G C 170.416 . DP=27;VDB=0.505999;SGB=-0.693021;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,7,20;MQ=20 GT:PL 1/1:200,81,0 |
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| diff -r e416daaccd32 -r acd651be2b9c test-data/rnastar_test_mapped_reads_diploid.bam |
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| Binary file test-data/rnastar_test_mapped_reads_diploid.bam has changed |
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| diff -r e416daaccd32 -r acd651be2b9c test-data/rnastar_test_mapped_reads_test10.bam |
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| Binary file test-data/rnastar_test_mapped_reads_test10.bam has changed |
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| diff -r e416daaccd32 -r acd651be2b9c test-data/rnastar_test_splicejunctions_diploid.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions_diploid.bed Tue Aug 27 14:09:53 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +test_chromosome 251 350 1 1 0 27 0 37 +test_chromosome 401 500 1 1 0 25 0 36 |
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| diff -r e416daaccd32 -r acd651be2b9c test-data/rnastar_test_splicejunctions_wasp.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rnastar_test_splicejunctions_wasp.bed Tue Aug 27 14:09:53 2024 +0000 |
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