| Previous changeset 0:8ccfff69dd57 (2017-03-14) Next changeset 2:2cba79e6037e (2017-05-17) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec |
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modified:
README.md customProDB.R customProDB.xml |
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added:
test-data/hg19/cosmic.RData test-data/hg19/dbsnpinCoding.RData test-data/hg19/exon_anno.RData test-data/hg19/ids.RData test-data/hg19/junctions1.bed test-data/hg19/procodingseq.RData test-data/hg19/proseq.RData test-data/hg19/splicemax.RData test-data/hg19/test1.vcf test-data/hg19/test1_sort.bam test-data/hg19/test1_sort.bam.bai test-data/hg19/txdb.sqlite test-data/hg19_dbsnp_snv.fasta test-data/hg19_dbsnp_variant_annotation.rdata test-data/hg19_dbsnp_variant_annotation.sqlite test-data/hg19_genomic_mapping.sqlite test-data/hg19_indel.fasta test-data/hg19_rpkm0.fasta test-data/hg19_rpkm1.fasta test-data/hg19_rpkm1000.fasta test-data/hg19_snv.fasta test-data/hg19_variant_annotation.rdata test-data/hg19_variant_annotation.sqlite |
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removed:
test-data/exon_anno.RData test-data/ids.RData test-data/procodingseq.RData test-data/proseq.RData test-data/test1.vcf test-data/test1_sort.bam test-data/test1_sort.bam.bai test-data/test_indel.fasta test-data/test_rpkm.fasta test-data/test_snv.fasta |
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| diff -r 8ccfff69dd57 -r ad130eaa3a05 README.md --- a/README.md Tue Mar 14 14:14:38 2017 -0400 +++ b/README.md Fri May 12 13:17:40 2017 -0400 |
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| @@ -48,7 +48,6 @@ Authors and contributors: * Matt Chambers <matt.chambers42@gmail.com> - Vanderbilt University Medical Center -* Xiaojing Wang - Vanderbilt University Medical Center +* Xiaojing Wang <xiaojing.wang@bcm.edu> + Baylor Medical College |
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| diff -r 8ccfff69dd57 -r ad130eaa3a05 customProDB.R --- a/customProDB.R Tue Mar 14 14:14:38 2017 -0400 +++ b/customProDB.R Fri May 12 13:17:40 2017 -0400 |
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| b'@@ -27,64 +27,146 @@\n option_list$cosmic <- make_option(\'--cosmic\', type=\'character\')\n option_list$annotationFromHistory <- make_option(\'--annotationFromHistory\', type=\'logical\', action="store_true", default=FALSE)\n option_list$rpkmCutoff <- make_option(\'--rpkmCutoff\', type=\'character\')\n-#option_list$outputIndels <- make_option(\'--outputIndels\', type=\'logical\', action="store_true", default=FALSE)\n+option_list$outputIndels <- make_option(\'--outputIndels\', type=\'logical\', action="store_true", default=FALSE)\n #option_list$outputNovelJunctions <- make_option(\'--outputNovelJunctions\', type=\'logical\', action="store_true", default=FALSE)\n-option_list$outputFile <- make_option(\'--outputFile\', type=\'character\')\n+#option_list$bedFile <- make_option(\'--bedFile\', type=\'character\')\n+#option_list$bsGenome <- make_option(\'--bsGenome\', type=\'character\')\n+option_list$outputRData <- make_option(\'--outputRData\', type=\'logical\', action="store_true", default=FALSE)\n+option_list$outputSQLite <- make_option(\'--outputSQLite\', type=\'logical\', action="store_true", default=FALSE)\n \n \n opt <- parse_args(OptionParser(option_list=option_list))\n \n \n customProDB <- function(\n-\tbam_file = GalaxyInputFile(required=TRUE), \n-\tbai_file = GalaxyInputFile(required=TRUE), \n-\tvcf_file = GalaxyInputFile(required=TRUE), \n-\texon_anno_file = GalaxyInputFile(required=TRUE),\n-\tproteinseq_file = GalaxyInputFile(required=TRUE),\n-\tprocodingseq_file = GalaxyInputFile(required=TRUE),\n-\tids_file = GalaxyInputFile(required=TRUE),\n-\tdbsnpinCoding_file = GalaxyInputFile(required=FALSE),\n-\tcosmic_file = GalaxyInputFile(required=FALSE),\n-\tannotationFromHistory = GalaxyLogicalParam(required=FALSE),\n-\trpkmCutoff = GalaxyNumericParam(required=TRUE),\n-\t#outputIndels = GalaxyLogicalParam(required=FALSE),\n-\t#outputNovelJunctions = GalaxyLogicalParam(required=FALSE),\n-\toutputFile = GalaxyOutput("FASTA","fasta"))\n+ bam_file = GalaxyInputFile(required=TRUE), \n+ bai_file = GalaxyInputFile(required=TRUE), \n+ vcf_file = GalaxyInputFile(required=TRUE), \n+ exon_anno_file = GalaxyInputFile(required=TRUE),\n+ proteinseq_file = GalaxyInputFile(required=TRUE),\n+ procodingseq_file = GalaxyInputFile(required=TRUE),\n+ ids_file = GalaxyInputFile(required=TRUE),\n+ dbsnpinCoding_file = GalaxyInputFile(required=FALSE),\n+ cosmic_file = GalaxyInputFile(required=FALSE),\n+ annotationFromHistory = GalaxyLogicalParam(required=FALSE),\n+ rpkmCutoff = GalaxyNumericParam(required=TRUE),\n+ outputIndels = GalaxyLogicalParam(required=FALSE),\n+ outputRData = GalaxyLogicalParam(required=FALSE),\n+ outputSQLite = GalaxyLogicalParam(required=FALSE)\n+ #,outputNovelJunctions = GalaxyLogicalParam(required=FALSE)\n+ #,bedFile = GalaxyInputFile(required=FALSE)\n+ #,bsGenome = GalaxyCharacterParam(required=FALSE)\n+ )\n {\n+ old <- options(stringsAsFactors = FALSE, gsubfn.engine = "R")\n+ on.exit(options(old), add = TRUE)\n+\n file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/"))\n file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/"))\n file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/"))\n file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/"))\n \n+ load(exon_anno_file)\n+ load(proteinseq_file)\n+ load(procodingseq_file)\n+ load(ids_file)\n+\n if (length(dbsnpinCoding_file) > 0)\n {\n file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))\n- labelrsid = T\n+ labelrsid = TRUE\n+ load(dbsnpinCoding_file)\n }\n else\n {\n- labelrsid = F\n+ dbsnpinCoding = NULL\n+ labelrsid = FALSE\n }\n \n if (length(cosmic_file) > 0)\n {\n file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))\n- cosmic = T\n+ use_cosmic = TRUE\n+ load(cosmic_file)\n }\n else\n {\n- cosmic = F\n+ cosmic = NULL\n+ use_cosmic = FALSE\n }\n \n bamLink = "input.bam"\n file'..b'devtools::install_github)\n+ download.file("https://github.com/chambm/customProDB/archive/master.zip", "customProDB.zip", quiet=TRUE)\n+ unzip("customProDB.zip")\n+ devtools::load_all("customProDB-master")\n \n easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(),\n rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output",\n- nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic)\n+ nov_junction=FALSE, INDEL=outputIndels,\n+ lablersid=labelrsid, COSMIC=use_cosmic)\n+\n+ # save variant annotations to an RData file (needed by proBAMr)\n+ if (outputRData || outputSQLite)\n+ {\n+ variantAnnotation = getVariantAnnotation(vcf_file, ids, exon, proteinseq, procodingseq, dbsnpinCoding, cosmic)\n+ if (outputRData) save(variantAnnotation, file="output.rdata")\n+ }\n+\n+ if (outputSQLite)\n+ {\n+ # create protein-centric variant annotation table (needed by Galaxy-P viewer MVP)\n+ varproseq = unique(rbind(variantAnnotation$snvproseq, variantAnnotation$indelproseq))\n+ ref_vs_var_seq = sqldf::sqldf("SELECT reference.pro_name, variant.pro_name AS var_pro_name, reference.peptide AS ref_seq, variant.peptide AS var_seq\n+ FROM proteinseq reference, varproseq variant\n+ WHERE reference.tx_name=variant.tx_name\n+ GROUP BY variant.pro_name")\n+ getCigarishString = function(ref, var)\n+ {\n+ a = Biostrings::pairwiseAlignment(ref, var)\n+ d = gsub("[A-Z]", "=", Biostrings::compareStrings(a@pattern, a@subject))\n+ r = rle(strsplit(d, "")[[1]])\n+ gsub("-", "D", gsub("\\\\+", "I", gsub("\\\\?", "X", paste0(r$lengths, r$values, collapse=""))))\n+ }\n+ ref_vs_var_seq$cigar = mapply(FUN=getCigarishString, ref_vs_var_seq$ref_seq, ref_vs_var_seq$var_seq, USE.NAMES=FALSE)\n+ ref_vs_var_seq$annotation = substring(ref_vs_var_seq$var_pro_name, stringr::str_length(ref_vs_var_seq$pro_name)+2)\n+\n+ variant_annotation_sqlite = dbConnect(RSQLite::SQLite(), "output_variant_annotation.sqlite")\n+ dbWriteTable(variant_annotation_sqlite,\n+ "variant_annotation",\n+ sqldf::sqldf("SELECT var_pro_name, pro_name, cigar, annotation FROM ref_vs_var_seq"))\n+ DBI::dbExecute(variant_annotation_sqlite, "CREATE INDEX variant_annotation_var_pro_name ON variant_annotation (var_pro_name)")\n+\n+ # save genomic mapping to a SQLite file (needed by Galaxy-P viewer MVP)\n+ exon$cds_start = as.integer(exon$cds_start)\n+ exon$cds_end = as.integer(exon$cds_end)\n+ genomic_mapping_sqlite = dbConnect(RSQLite::SQLite(), "output_genomic_mapping.sqlite")\n+ varprocoding = unique(rbind(variantAnnotation$snvprocoding, variantAnnotation$indelprocoding))\n+ dbWriteTable(genomic_mapping_sqlite,\n+ "genomic_mapping",\n+ sqldf::sqldf("SELECT exon.gene_name, exon.tx_name, varprocoding.pro_name, cds_start, cds_end,\n+ chromosome_name AS chr_name, cds_chr_start, cds_chr_end, exon.strand\n+ FROM exon, varprocoding\n+ WHERE exon.tx_id=varprocoding.tx_id AND cds_chr_start > 0\n+ GROUP BY exon.tx_id, rank\n+ UNION\n+ SELECT gene_name, tx_name, pro_name, cds_start, cds_end,\n+ chromosome_name AS chr_name, cds_chr_start, cds_chr_end, exon.strand\n+ FROM exon\n+ WHERE cds_chr_start > 0\n+ GROUP BY tx_id, rank"))\n+ DBI::dbExecute(genomic_mapping_sqlite, "CREATE INDEX genomic_mapping_pro_name ON genomic_mapping (pro_name)")\n+ }\n+\n+ invisible(NULL)\n }\n \n \n' |
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| diff -r 8ccfff69dd57 -r ad130eaa3a05 customProDB.xml --- a/customProDB.xml Tue Mar 14 14:14:38 2017 -0400 +++ b/customProDB.xml Fri May 12 13:17:40 2017 -0400 |
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| b'@@ -1,8 +1,24 @@\n-<tool id="custom_pro_db" name="CustomProDB" version="1.14.0">\n+<tool id="custom_pro_db" name="CustomProDB" version="1.16.0">\n <description>Generate protein FASTAs from exosome or transcriptome data</description>\n <requirements>\n- <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>\n+ <requirement type="package" version="3.3.1">r-base</requirement>\n+ <!--<requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>-->\n <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>\n+ <requirement type="package" version="1.21.0">bioconductor-biocinstaller</requirement>\n+ <requirement type="package" version="1.20.3">bioconductor-variantannotation</requirement>\n+ <requirement type="package" version="1.11.1">r-devtools</requirement>\n+ <requirement type="package" version="3.98_1.4">r-xml</requirement>\n+ <requirement type="package" version="0.10.11">r-rmysql</requirement>\n+ <requirement type="package" version="1.0.2">r-testthat</requirement>\n+ <requirement type="package" version="0.1.0">r-getoptlong</requirement>\n+ <requirement type="package" version="1.1.2">r-stringi</requirement>\n+ <requirement type="package" version="1.1.0">r-stringr</requirement>\n+ <requirement type="package" version="1.10.0">r-data.table</requirement>\n+ <!--<requirement type="package" version="0.4_10">r-sqldf</requirement>-->\n+ <requirement type="package" version="0.6_6">r-gsubfn</requirement>\n+ <requirement type="package" version="2.3_47">r-chron</requirement>\n+ <requirement type="package" version="0.3.10">r-proto</requirement>\n+ <requirement type="package" version="1.8.4">r-plyr</requirement>\n </requirements>\n <stdio>\n <exit_code range="1:" level="fatal" description="Job Failed" />\n@@ -13,7 +29,9 @@\n --bai=\'${genome_annotation.bamInput.metadata.bam_index}\'\n --vcf=\'$genome_annotation.vcfInput\'\n --rpkmCutoff=$rpkmCutoff\n- --outputFile=\'${output_rpkm}\'\n+ $outputIndels\n+ $outputSQLite\n+ $outputRData\n \n #if str($genome_annotation.source) == \'history\':\n --exon_anno=\'$genome_annotation.exonAnno\'\n@@ -24,7 +42,7 @@\n --dbsnpinCoding=\'$genome_annotation.dbsnpInCoding\'\n #end if\n #if str($genome_annotation.cosmic) != \'None\':\n- --cosmic=\'$genome_annotation.cosmic"\n+ --cosmic=\'$genome_annotation.cosmic\'\n #end if\n #else:\n #set index_path = $genome_annotation.builtin.fields.path\n@@ -87,24 +105,77 @@\n </when>\n </conditional>\n <param name="rpkmCutoff" type="float" value="1" min="0" label="Transcript Expression Cutoff (RPKM)" help="If non-zero, if a transcript does not meet this expression cutoff (based on RPKM) then it will not be included in the output database." />\n+ <param name="outputIndels" type="boolean" truevalue="--outputIndels" falsevalue="" label="Create a variant FASTA for short insertions and deletions" />\n+ <param name="outputSQLite" type="boolean" truevalue="--outputSQLite" falsevalue="" label="Create SQLite files for mapping proteins to genome and summarizing variant proteins" />\n+ <param name="outputRData" type="boolean" truevalue="--outputRData" falsevalue="" label="Create RData file of variant protein coding sequences" help="The PSM2SAM tool needs this to map variant proteins to genomic locations" />\n </inputs>\n <outputs>\n <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit(\'.\',1)[0]}_rpkm.fasta"/>\n <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit(\'.\',1)[0]}_snv.fasta"/>\n- <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit(\'.\',1)[0]}_indel.fasta"/>\n+ <data format="fasta" name="output_indel" fro'..b' name="source" value="history" />\n+ <param name="exonAnno" value="hg19/exon_anno.RData" />\n+ <param name="proteinSeq" value="hg19/proseq.RData" />\n+ <param name="proCodingSeq" value="hg19/procodingseq.RData" />\n+ <param name="ids" value="hg19/ids.RData" />\n+ <param name="rpkmCutoff" value="1" />\n+ <param name="outputIndels" value="" />\n+ <param name="outputRData" value="--outputRData" />\n+ <param name="outputSQLite" value="--outputSQLite" />\n+ <output name="output_rpkm" file="hg19_rpkm1.fasta" />\n+ <output name="output_snv" file="hg19_snv.fasta" />\n+ <output name="output_variant_annotation_rdata" file="hg19_variant_annotation.rdata" />\n+ <output name="output_genomic_mapping_sqlite" file="hg19_genomic_mapping.sqlite" />\n+ <output name="output_variant_annotation_sqlite" file="hg19_variant_annotation.sqlite" />\n+ </test>\n+ <test expect_num_outputs="5">\n+ <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />\n+ <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />\n <param name="source" value="history" />\n- <param name="exonAnno" value="exon_anno.RData" />\n- <param name="proteinSeq" value="proseq.RData" />\n- <param name="proCodingSeq" value="procodingseq.RData" />\n- <param name="ids" value="ids.RData" />\n- <output name="output_rpkm" file="test_rpkm.fasta" />\n- <output name="output_snv" file="test_snv.fasta" />\n- <output name="output_indel" file="test_indel.fasta" />\n+ <param name="exonAnno" value="hg19/exon_anno.RData" />\n+ <param name="proteinSeq" value="hg19/proseq.RData" />\n+ <param name="proCodingSeq" value="hg19/procodingseq.RData" />\n+ <param name="ids" value="hg19/ids.RData" />\n+ <param name="dbsnpInCoding" value="hg19/dbsnpinCoding.RData" />\n+ <param name="cosmic" value="hg19/cosmic.RData" />\n+ <param name="rpkmCutoff" value="0" />\n+ <param name="outputIndels" value="--outputIndels" />\n+ <param name="outputSQLite" value="--outputSQLite" />\n+ <output name="output_rpkm" file="hg19_rpkm0.fasta" />\n+ <output name="output_snv" file="hg19_dbsnp_snv.fasta" />\n+ <output name="output_indel" file="hg19_indel.fasta" />\n+ <output name="output_variant_annotation_rdata" file="hg19_dbsnp_variant_annotation.rdata" />\n+ <output name="output_variant_annotation_sqlite" file="hg19_dbsnp_variant_annotation.sqlite" />\n+ </test>\n+ <test expect_num_outputs="3">\n+ <param name="bamInput" value="hg19/test1_sort.bam" dbkey="hg19" />\n+ <param name="vcfInput" value="hg19/test1.vcf" dbkey="hg19" />\n+ <param name="source" value="history" />\n+ <param name="exonAnno" value="hg19/exon_anno.RData" />\n+ <param name="proteinSeq" value="hg19/proseq.RData" />\n+ <param name="proCodingSeq" value="hg19/procodingseq.RData" />\n+ <param name="ids" value="hg19/ids.RData" />\n+ <param name="rpkmCutoff" value="1000" />\n+ <param name="outputIndels" value="--outputIndels" />\n+ <output name="output_rpkm" file="hg19_rpkm1000.fasta" />\n+ <output name="output_snv" file="hg19_snv.fasta" />\n+ <output name="output_indel" file="hg19_indel.fasta" />\n </test>\n </tests>\n <help>\n@@ -113,8 +184,7 @@\n Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help>\n <citations>\n <citation type="doi">10.1093/bioinformatics/btt543</citation>\n- <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub \n-repository},\n+ <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository},\n year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = \n {$sha1$}" -->\n </citations>\n' |
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| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19/junctions1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19/junctions1.bed Fri May 12 13:17:40 2017 -0400 |
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| @@ -0,0 +1,76 @@ +track name=junctions description="TopHat junctions" +chr1 32479909 32495942 JUNC00002865 8 + 32479909 32495942 255,0,0 2 69,44 0,15989 +chr1 32495950 32497196 JUNC00002866 13 + 32495950 32497196 255,0,0 2 73,72 0,1174 +chr1 32496010 32498851 JUNC00002867 3 + 32496010 32498851 255,0,0 2 13,63 0,2778 +chr1 32497175 32498854 JUNC00002868 20 + 32497175 32498854 255,0,0 2 66,66 0,1613 +chr1 32498867 32502584 JUNC00002869 29 + 32498867 32502584 255,0,0 2 68,74 0,3643 +chr1 32502572 32503560 JUNC00002870 1 + 32502572 32503560 255,0,0 2 22,54 0,934 +chr1 32502571 32503507 JUNC00002871 48 + 32502571 32503507 255,0,0 2 73,72 0,864 +chr1 32503572 32504220 JUNC00002872 45 + 32503572 32504220 255,0,0 2 65,68 0,580 +chr1 32503695 32504219 JUNC00002873 3 + 32503695 32504219 255,0,0 2 25,67 0,457 +chr1 32504152 32505174 JUNC00002874 41 + 32504152 32505174 255,0,0 2 68,59 0,963 +chr1 32505115 32508202 JUNC00002875 43 + 32505115 32508202 255,0,0 2 59,75 0,3012 +chr1 32508245 32510977 JUNC00002876 4 + 32508245 32510977 255,0,0 2 75,46 0,2686 +chr2 48010576 48018138 JUNC00057360 5 + 48010576 48018138 255,0,0 2 56,73 0,7489 +chr2 48028222 48030628 JUNC00057361 15 + 48028222 48030628 255,0,0 2 72,70 0,2336 +chr2 48030789 48032107 JUNC00057362 5 + 48030789 48032107 255,0,0 2 35,59 0,1259 +chr2 48032104 48032810 JUNC00057363 3 + 48032104 48032810 255,0,0 2 62,54 0,652 +chr2 48032781 48033370 JUNC00057364 12 + 48032781 48033370 255,0,0 2 65,28 0,561 +chr2 48033454 48033654 JUNC00057365 10 + 48033454 48033654 255,0,0 2 43,64 0,136 +chr2 48033733 48033987 JUNC00057366 2 + 48033733 48033987 255,0,0 2 57,70 0,184 +chr2 48035311 48035520 JUNC00057367 9 - 48035311 48035520 255,0,0 2 75,53 0,156 +chr5 112197081 112198267 JUNC00080003 4 + 112197081 112198267 255,0,0 2 33,63 0,1123 +chr5 112198248 112200197 JUNC00080004 1 + 112198248 112200197 255,0,0 2 32,44 0,1905 +chr5 112200165 112200377 JUNC00080005 3 + 112200165 112200377 255,0,0 2 60,60 0,152 +chr5 112200186 112227336 JUNC00080006 1 + 112200186 112227336 255,0,0 2 39,37 0,27113 +chr5 112200355 112203167 JUNC00080007 23 + 112200355 112203167 255,0,0 2 74,67 0,2745 +chr7 140439692 140449108 JUNC00096155 1 - 140439692 140449108 255,0,0 2 54,22 0,9394 +chr7 140482938 140487384 JUNC00096156 2 - 140482938 140487384 255,0,0 2 19,37 0,4409 +chr7 140487347 140494120 JUNC00096157 2 - 140487347 140494120 255,0,0 2 37,13 0,6760 +chr7 140494238 140500208 JUNC00096158 1 - 140494238 140500208 255,0,0 2 29,47 0,5923 +chr7 140706282 140710284 JUNC00096159 15 - 140706282 140710284 255,0,0 2 53,66 0,3936 +chr9 86584235 86585148 JUNC00101237 14 - 86584235 86585148 255,0,0 2 60,72 0,841 +chr9 86584288 86585148 JUNC00101238 5 - 86584288 86585148 255,0,0 2 67,72 0,788 +chr9 86585177 86585724 JUNC00101239 171 - 86585177 86585724 255,0,0 2 69,73 0,474 +chr9 86585666 86585827 JUNC00101240 80 - 86585666 86585827 255,0,0 2 68,16 0,145 +chr9 86585811 86586262 JUNC00101241 121 - 86585811 86586262 255,0,0 2 16,75 0,376 +chr17 37856490 37863316 JUNC00043382 57 + 37856490 37863316 255,0,0 2 74,74 0,6752 +chr17 37863341 37864648 JUNC00043383 28 + 37863341 37864648 255,0,0 2 53,75 0,1232 +chr17 37864380 37864622 JUNC00043384 1 + 37864380 37864622 255,0,0 2 27,49 0,193 +chr17 37864713 37865643 JUNC00043385 20 + 37864713 37865643 255,0,0 2 74,73 0,857 +chr17 37865631 37866134 JUNC00043386 29 + 37865631 37866134 255,0,0 2 74,69 0,434 +chr17 37866065 37866413 JUNC00043387 29 + 37866065 37866413 255,0,0 2 69,75 0,273 +chr17 37866380 37866667 JUNC00043388 56 + 37866380 37866667 255,0,0 2 74,75 0,212 +chr17 37866659 37868249 JUNC00043389 68 + 37866659 37868249 255,0,0 2 75,69 0,1521 +chr17 37868237 37868649 JUNC00043390 36 + 37868237 37868649 255,0,0 2 63,75 0,337 +chr17 37868627 37871602 JUNC00043391 24 + 37868627 37871602 255,0,0 2 74,64 0,2911 +chr17 37871542 37871773 JUNC00043392 76 + 37871542 37871773 255,0,0 2 70,75 0,156 +chr17 37871718 37872065 JUNC00043393 56 + 37871718 37872065 255,0,0 2 71,73 0,274 +chr17 37872121 37872628 JUNC00043394 51 + 37872121 37872628 255,0,0 2 71,75 0,432 +chr17 37872629 37872839 JUNC00043395 38 + 37872629 37872839 255,0,0 2 57,72 0,138 +chr17 37872783 37873647 JUNC00043396 93 + 37872783 37873647 255,0,0 2 75,75 0,789 +chr17 37873658 37876087 JUNC00043397 55 + 37873658 37876087 255,0,0 2 75,48 0,2381 +chr17 37876039 37879645 JUNC00043398 31 + 37876039 37879645 255,0,0 2 48,74 0,3532 +chr17 37879639 37879863 JUNC00043399 72 + 37879639 37879863 255,0,0 2 71,73 0,151 +chr17 37879822 37880201 JUNC00043400 5 + 37879822 37880201 255,0,0 2 49,37 0,342 +chr17 37879841 37880239 JUNC00043401 37 + 37879841 37880239 255,0,0 2 72,75 0,323 +chr17 37880190 37881051 JUNC00043402 94 + 37880190 37881051 255,0,0 2 73,73 0,788 +chr17 37881089 37881375 JUNC00043403 50 + 37881089 37881375 255,0,0 2 75,74 0,212 +chr17 37881384 37881651 JUNC00043404 101 + 37881384 37881651 255,0,0 2 73,72 0,195 +chr17 37881584 37882026 JUNC00043405 117 + 37881584 37882026 255,0,0 2 71,67 0,375 +chr17 37882031 37882885 JUNC00043406 117 + 37882031 37882885 255,0,0 2 75,71 0,783 +chr17 37882838 37883141 JUNC00043407 80 + 37882838 37883141 255,0,0 2 74,74 0,229 +chr17 37883186 37883619 JUNC00043408 43 + 37883186 37883619 255,0,0 2 70,72 0,361 +chr17 37883725 37884015 JUNC00043409 279 + 37883725 37884015 255,0,0 2 75,74 0,216 +chr17 37885789 37885996 JUNC00043410 16 - 37885789 37885996 255,0,0 2 69,59 0,148 +chr17 7572938 7573998 JUNC00041578 29 - 7572938 7573998 255,0,0 2 70,72 0,988 +chr17 7573960 7576926 JUNC00041579 28 - 7573960 7576926 255,0,0 2 73,74 0,2892 +chr17 7576852 7577086 JUNC00041580 35 - 7576852 7577086 255,0,0 2 74,68 0,166 +chr17 7577084 7577572 JUNC00041581 49 - 7577084 7577572 255,0,0 2 71,74 0,414 +chr17 7577534 7578239 JUNC00041582 30 - 7577534 7578239 255,0,0 2 74,63 0,642 +chr17 7578221 7578441 JUNC00041583 18 - 7578221 7578441 255,0,0 2 68,71 0,149 +chr17 7578480 7579369 JUNC00041584 19 - 7578480 7579369 255,0,0 2 74,58 0,831 +chr17 7579515 7579724 JUNC00041585 35 - 7579515 7579724 255,0,0 2 75,25 0,184 +chr17 7579699 7579894 JUNC00041586 25 - 7579699 7579894 255,0,0 2 22,56 0,139 +chr17 7579874 7590761 JUNC00041587 29 - 7579874 7590761 255,0,0 2 66,67 0,10820 +chr17 7591825 7592027 JUNC00041588 6 + 7591825 7592027 255,0,0 2 54,62 0,140 |
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| Binary file test-data/hg19/proseq.RData has changed |
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| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19/test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19/test1.vcf Fri May 12 13:17:40 2017 -0400 |
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| b'@@ -0,0 +1,87 @@\n+##fileformat=VCFv4.1\n+##samtoolsVersion=0.1.17 (r973:277)\n+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">\n+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">\n+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">\n+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">\n+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">\n+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">\n+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">\n+##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">\n+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">\n+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">\n+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">\n+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">\n+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">\n+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">\n+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">\n+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">\n+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">\n+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">\n+##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">\n+#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest\n+chr1\t32386425\t.\tT\tC\t24\t.\tDP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36\tGT:PL:GQ\t1/1:56,9,0:15\n+chr1\t32507666\t.\tG\tT\t6.2\t.\tDP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36\tGT:PL:GQ\t0/1:35,0,78:36\n+chr1\t32524459\t.\tA\tC\t3.54\t.\tDP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1\tGT:PL:GQ\t0/1:31,0,98:30\n+chr1\t32622505\t.\tG\tA\t101\t.\tDP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075\tGT:PL:GQ\t0/1:131,0,162:99\n+chr12\t25357574\t.\tCAA\tC\t109\t.\tINDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5\tGT:PL:GQ\t1/1:149,12,0:21\n+chr12\t25357628\t.\tTA\tT\t53.4\t.\tINDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5\tGT:PL:GQ\t1/1:93,9,0:16\n+chr12\t25358650\t.\tA\tT\t73\t.\tDP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72\tGT:PL:GQ\t1/1:106,45,0:87\n+chr12\t25358662\t.\tCTTTTTTTT\tCTTTTTT,CTTTTTTT\t31.6\t.\tINDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5\tGT:PL:GQ\t1/1:96,42,24,91,0,64:33\n+chr12\t25358943\t.\tT\tC\t67.1\t.\tDP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48\tGT:PL:GQ\t1/1:100,21,0:39\n+chr12\t25358969\t.\tT\tG\t36.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:69,12,0:21\n+chr12\t25359352\t.\tG\tA\t172\t.\tDP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69\tGT:PL:GQ\t1/1:205,42,0:81\n+chr12\t25359464\t.\tTAA\tTA\t123\t.\tINDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113\tGT:PL:GQ\t1/1:164,78,0:99\n+chr12\t25360138\t.\tT\tC\t169\t.\tDP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84\tGT:PL:GQ\t1/1:202,57,0:99\n+chr12\t25361091\t.\tT\tC\t93\t.\tDP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69\tGT:PL:GQ'..b'1e-06,1,1\tGT:PL:GQ\t0/1:173,0,238:99\n+chr17\t7572657\t.\tG\tT\t225\t.\tDP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27\tGT:PL:GQ\t0/1:255,0,190:99\n+chr17\t7591866\t.\tG\tT\t45\t.\tDP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01\tGT:PL:GQ\t0/1:75,0,162:78\n+chr17\t7606153\t.\tC\tT\t74\t.\tDP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1\tGT:PL:GQ\t0/1:104,0,165:99\n+chr2\t48010558\t.\tC\tA\t12.3\t.\tDP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1\tGT:PL:GQ\t0/1:42,0,31:34\n+chr2\t48016554\t.\tT\tC\t32\t.\tDP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21\tGT:PL:GQ\t0/1:62,0,48:51\n+chr2\t48018081\t.\tA\tG\t77\t.\tDP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34\tGT:PL:GQ\t0/1:107,0,24:27\n+chr2\t48018221\t.\tC\tT\t22\t.\tDP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1\tGT:PL:GQ\t0/1:52,0,116:55\n+chr2\t48027990\t.\tG\tT\t122\t.\tDP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039\tGT:PL:GQ\t0/1:152,0,131:99\n+chr2\t48030458\t.\tG\tC\t105\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:137,12,0:21\n+chr5\t112154737\t.\tCT\tC\t29\t.\tINDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012\tGT:PL:GQ\t0/1:59,0,85:62\n+chr5\t112162854\t.\tT\tC\t60\t.\tDP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36\tGT:PL:GQ\t1/1:92,9,0:16\n+chr5\t112164561\t.\tG\tA\t87.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:120,12,0:21\n+chr5\t112175639\t.\tC\tT\t31\t.\tDP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1\tGT:PL:GQ\t0/1:61,0,62:61\n+chr5\t112175897\t.\tGAA\tGA\t7.8\t.\tINDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33\tGT:PL:GQ\t0/1:37,0,97:39\n+chr5\t112176559\t.\tT\tG\t72\t.\tDP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51\tGT:PL:GQ\t1/1:105,24,0:45\n+chr5\t112176756\t.\tT\tA\t143\t.\tDP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54\tGT:PL:GQ\t1/1:176,27,0:51\n+chr5\t112180015\t.\tC\tA\t123\t.\tDP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1\tGT:PL:GQ\t0/1:153,0,67:70\n+chr5\t112204170\t.\tG\tA\t112\t.\tDP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:144,12,0:21\n+chr7\t140043303\t.\tC\tT\t88\t.\tDP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42\tGT:PL:GQ\t0/1:118,0,167:99\n+chr7\t140065806\t.\tT\tC\t38.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:71,12,0:21\n+chr7\t140065845\t.\tC\tA\t44.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:77,12,0:21\n+chr7\t140152904\t.\tCAAAA\tCAAAAA\t41.5\t.\tINDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1\tGT:PL:GQ\t0/1:79,0,91:82\n+chr7\t140153495\t.\tG\tT\t140\t.\tDP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038\tGT:PL:GQ\t0/1:170,0,184:99\n+chr7\t140158851\t.\tC\tG\t153\t.\tDP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1\tGT:PL:GQ\t1/1:186,75,0:99\n+chr7\t140244560\t.\tC\tT\t78\t.\tDP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1\tGT:PL:GQ\t0/1:108,0,23:26\n+chr7\t140406430\t.\tT\tA\t8.64\t.\tDP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021\tGT:PL:GQ\t0/1:38,0,167:40\n+chr7\t140406436\t.\tA\tG\t4.77\t.\tDP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08\tGT:PL:GQ\t0/1:33,0,170:33\n+chr7\t140424582\t.\tG\tC\t18.1\t.\tDP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1\tGT:PL:GQ\t0/1:48,0,56:50\n+chr7\t140426098\t.\tG\tA\t10.2\t.\tDP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33\tGT:PL:GQ\t1/1:41,6,0:8\n+chr7\t140702871\t.\tG\tA\t77.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:110,12,0:21\n+chr7\t140706061\t.\tG\tT\t119\t.\tDP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1\tGT:PL:GQ\t0/1:149,0,178:99\n+chr7\t140706157\t.\tG\tT\t42\t.\tDP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013\tGT:PL:GQ\t0/1:72,0,170:75\n+chr9\t86583076\t.\tC\tT\t64\t.\tDP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1\tGT:PL:GQ\t0/1:94,0,100:96\n+chr9\t86593314\t.\tG\tC\t186\t.\tDP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072\tGT:PL:GQ\t0/1:216,0,216:99\n+chr9\t86595070\t.\tC\tT\t140\t.\tDP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1\tGT:PL:GQ\t0/1:170,0,188:99\n+chr9\t86595498\t.\tG\tA\t66\t.\tDP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1\tGT:PL:GQ\t0/1:96,0,225:99\n' |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19/test1_sort.bam |
| b |
| Binary file test-data/hg19/test1_sort.bam has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19/test1_sort.bam.bai |
| b |
| Binary file test-data/hg19/test1_sort.bam.bai has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19/txdb.sqlite |
| b |
| Binary file test-data/hg19/txdb.sqlite has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_dbsnp_snv.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_dbsnp_snv.fasta Fri May 12 13:17:40 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>NP_000170_T139I,E956D |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPIRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLDKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL +>NP_001120983_rs121913332:R1432*,rs459552:V1804D |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTK |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_dbsnp_variant_annotation.rdata --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_dbsnp_variant_annotation.rdata Fri May 12 13:17:40 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>NP_000170_T139I,E956D |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPIRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLDKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL +>NP_001120983_rs121913332:R1432*,rs459552:V1804D |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTK |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_dbsnp_variant_annotation.sqlite |
| b |
| Binary file test-data/hg19_dbsnp_variant_annotation.sqlite has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_genomic_mapping.sqlite |
| b |
| Binary file test-data/hg19_genomic_mapping.sqlite has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_indel.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_indel.fasta Fri May 12 13:17:40 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>NP_001120983_954:CT>C |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a| +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLACLAPKTAVYPCDSLDVFLSSSSFYMAMTKTLYCWEIPGAVKRLGPGPVQHSTTSFTHSLMTREAGVKSESFIFWNRYALTVKPVGSGRKLMNQAWTRTKIQCQLLLNIRSVLLCVF +>NP_001120983_4552:GAA>GA |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a| +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNEQNQSSLKNQMKTKRKRQKKLLILKRTY |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_rpkm0.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_rpkm0.fasta Fri May 12 13:17:40 2017 -0400 |
| b |
| @@ -0,0 +1,12 @@ +>NP_004439 |121102.4845|NM_004448|ERBB2|receptor tyrosine-protein kinase erbB-2 isoform a precursor +MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV +>NP_000170 |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPTRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL +>NP_001120983 |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQEKEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASKLPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPINFSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEAQGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLNAERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIEGTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTELTSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEKLQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPSKPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKKKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFDWKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHLTPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLITGKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKGPPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPSRSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSSPSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKGLNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSPTLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQAGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKREHSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQSKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPAVSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDNQAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSETNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSARPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV +>NP_001119584 |0|NM_001126112|TP53|cellular tumor antigen p53 isoform a +MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKTCPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRNTFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVRVCACPGRDRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALELKDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD +>NP_004324 |0|NM_004333|BRAF|serine/threonine-protein kinase B-raf +MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDSLKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRKTFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPIPQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQRDRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSPGPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDVAVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHHLHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATVKSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNINNRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARSLPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH +>NP_203524 |0|NM_033360|KRAS|GTPase KRas isoform a precursor +MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQRVEDAFYTLVREIRQYRLKKISKEEKTPGCVKIKKCIIM |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_rpkm1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_rpkm1.fasta Fri May 12 13:17:40 2017 -0400 |
| b |
| @@ -0,0 +1,6 @@ +>NP_004439 |121102.4845|NM_004448|ERBB2|receptor tyrosine-protein kinase erbB-2 isoform a precursor +MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV +>NP_000170 |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPTRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL +>NP_001120983 |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQEKEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASKLPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPINFSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEAQGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLNAERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIEGTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTELTSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEKLQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPSKPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKKKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFDWKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHLTPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLITGKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKGPPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPSRSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSSPSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKGLNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSPTLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQAGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKREHSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQSKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPAVSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDNQAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSETNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSARPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_rpkm1000.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_rpkm1000.fasta Fri May 12 13:17:40 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>NP_004439 |121102.48|NM_004448|ERBB2|receptor tyrosine-protein kinase erbB-2 isoform a precursor +MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV +>NP_000170 |18647.78|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPTRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_snv.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_snv.fasta Fri May 12 13:17:40 2017 -0400 |
| b |
| @@ -0,0 +1,4 @@ +>NP_000170_T139I,E956D |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 +MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPIRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLDKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL +>NP_001120983_R1432*,V1804D |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a +MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTK |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_variant_annotation.rdata |
| b |
| Binary file test-data/hg19_variant_annotation.rdata has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/hg19_variant_annotation.sqlite |
| b |
| Binary file test-data/hg19_variant_annotation.sqlite has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/ids.RData |
| b |
| Binary file test-data/ids.RData has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/procodingseq.RData |
| b |
| Binary file test-data/procodingseq.RData has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/proseq.RData |
| b |
| Binary file test-data/proseq.RData has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/test1.vcf --- a/test-data/test1.vcf Tue Mar 14 14:14:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,87 +0,0 @@\n-##fileformat=VCFv4.1\n-##samtoolsVersion=0.1.17 (r973:277)\n-##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">\n-##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">\n-##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">\n-##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">\n-##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">\n-##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">\n-##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">\n-##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">\n-##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">\n-##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">\n-##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">\n-##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">\n-##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">\n-##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">\n-##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">\n-##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">\n-##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">\n-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">\n-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">\n-##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">\n-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">\n-##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">\n-##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">\n-#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\ttest\n-chr1\t32386425\t.\tT\tC\t24\t.\tDP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36\tGT:PL:GQ\t1/1:56,9,0:15\n-chr1\t32507666\t.\tG\tT\t6.2\t.\tDP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36\tGT:PL:GQ\t0/1:35,0,78:36\n-chr1\t32524459\t.\tA\tC\t3.54\t.\tDP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1\tGT:PL:GQ\t0/1:31,0,98:30\n-chr1\t32622505\t.\tG\tA\t101\t.\tDP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075\tGT:PL:GQ\t0/1:131,0,162:99\n-chr12\t25357574\t.\tCAA\tC\t109\t.\tINDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5\tGT:PL:GQ\t1/1:149,12,0:21\n-chr12\t25357628\t.\tTA\tT\t53.4\t.\tINDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5\tGT:PL:GQ\t1/1:93,9,0:16\n-chr12\t25358650\t.\tA\tT\t73\t.\tDP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72\tGT:PL:GQ\t1/1:106,45,0:87\n-chr12\t25358662\t.\tCTTTTTTTT\tCTTTTTT,CTTTTTTT\t31.6\t.\tINDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5\tGT:PL:GQ\t1/1:96,42,24,91,0,64:33\n-chr12\t25358943\t.\tT\tC\t67.1\t.\tDP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48\tGT:PL:GQ\t1/1:100,21,0:39\n-chr12\t25358969\t.\tT\tG\t36.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:69,12,0:21\n-chr12\t25359352\t.\tG\tA\t172\t.\tDP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69\tGT:PL:GQ\t1/1:205,42,0:81\n-chr12\t25359464\t.\tTAA\tTA\t123\t.\tINDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113\tGT:PL:GQ\t1/1:164,78,0:99\n-chr12\t25360138\t.\tT\tC\t169\t.\tDP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84\tGT:PL:GQ\t1/1:202,57,0:99\n-chr12\t25361091\t.\tT\tC\t93\t.\tDP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69\tGT:PL:GQ'..b'1e-06,1,1\tGT:PL:GQ\t0/1:173,0,238:99\n-chr17\t7572657\t.\tG\tT\t225\t.\tDP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27\tGT:PL:GQ\t0/1:255,0,190:99\n-chr17\t7591866\t.\tG\tT\t45\t.\tDP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01\tGT:PL:GQ\t0/1:75,0,162:78\n-chr17\t7606153\t.\tC\tT\t74\t.\tDP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1\tGT:PL:GQ\t0/1:104,0,165:99\n-chr2\t48010558\t.\tC\tA\t12.3\t.\tDP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1\tGT:PL:GQ\t0/1:42,0,31:34\n-chr2\t48016554\t.\tT\tC\t32\t.\tDP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21\tGT:PL:GQ\t0/1:62,0,48:51\n-chr2\t48018081\t.\tA\tG\t77\t.\tDP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34\tGT:PL:GQ\t0/1:107,0,24:27\n-chr2\t48018221\t.\tC\tT\t22\t.\tDP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1\tGT:PL:GQ\t0/1:52,0,116:55\n-chr2\t48027990\t.\tG\tT\t122\t.\tDP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039\tGT:PL:GQ\t0/1:152,0,131:99\n-chr2\t48030458\t.\tG\tC\t105\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:137,12,0:21\n-chr5\t112154737\t.\tCT\tC\t29\t.\tINDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012\tGT:PL:GQ\t0/1:59,0,85:62\n-chr5\t112162854\t.\tT\tC\t60\t.\tDP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36\tGT:PL:GQ\t1/1:92,9,0:16\n-chr5\t112164561\t.\tG\tA\t87.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:120,12,0:21\n-chr5\t112175639\t.\tC\tT\t31\t.\tDP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1\tGT:PL:GQ\t0/1:61,0,62:61\n-chr5\t112175897\t.\tGAA\tGA\t7.8\t.\tINDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33\tGT:PL:GQ\t0/1:37,0,97:39\n-chr5\t112176559\t.\tT\tG\t72\t.\tDP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51\tGT:PL:GQ\t1/1:105,24,0:45\n-chr5\t112176756\t.\tT\tA\t143\t.\tDP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54\tGT:PL:GQ\t1/1:176,27,0:51\n-chr5\t112180015\t.\tC\tA\t123\t.\tDP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1\tGT:PL:GQ\t0/1:153,0,67:70\n-chr5\t112204170\t.\tG\tA\t112\t.\tDP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:144,12,0:21\n-chr7\t140043303\t.\tC\tT\t88\t.\tDP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42\tGT:PL:GQ\t0/1:118,0,167:99\n-chr7\t140065806\t.\tT\tC\t38.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:71,12,0:21\n-chr7\t140065845\t.\tC\tA\t44.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:77,12,0:21\n-chr7\t140152904\t.\tCAAAA\tCAAAAA\t41.5\t.\tINDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1\tGT:PL:GQ\t0/1:79,0,91:82\n-chr7\t140153495\t.\tG\tT\t140\t.\tDP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038\tGT:PL:GQ\t0/1:170,0,184:99\n-chr7\t140158851\t.\tC\tG\t153\t.\tDP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1\tGT:PL:GQ\t1/1:186,75,0:99\n-chr7\t140244560\t.\tC\tT\t78\t.\tDP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1\tGT:PL:GQ\t0/1:108,0,23:26\n-chr7\t140406430\t.\tT\tA\t8.64\t.\tDP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021\tGT:PL:GQ\t0/1:38,0,167:40\n-chr7\t140406436\t.\tA\tG\t4.77\t.\tDP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08\tGT:PL:GQ\t0/1:33,0,170:33\n-chr7\t140424582\t.\tG\tC\t18.1\t.\tDP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1\tGT:PL:GQ\t0/1:48,0,56:50\n-chr7\t140426098\t.\tG\tA\t10.2\t.\tDP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33\tGT:PL:GQ\t1/1:41,6,0:8\n-chr7\t140702871\t.\tG\tA\t77.5\t.\tDP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39\tGT:PL:GQ\t1/1:110,12,0:21\n-chr7\t140706061\t.\tG\tT\t119\t.\tDP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1\tGT:PL:GQ\t0/1:149,0,178:99\n-chr7\t140706157\t.\tG\tT\t42\t.\tDP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013\tGT:PL:GQ\t0/1:72,0,170:75\n-chr9\t86583076\t.\tC\tT\t64\t.\tDP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1\tGT:PL:GQ\t0/1:94,0,100:96\n-chr9\t86593314\t.\tG\tC\t186\t.\tDP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072\tGT:PL:GQ\t0/1:216,0,216:99\n-chr9\t86595070\t.\tC\tT\t140\t.\tDP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1\tGT:PL:GQ\t0/1:170,0,188:99\n-chr9\t86595498\t.\tG\tA\t66\t.\tDP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1\tGT:PL:GQ\t0/1:96,0,225:99\n' |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/test1_sort.bam |
| b |
| Binary file test-data/test1_sort.bam has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/test1_sort.bam.bai |
| b |
| Binary file test-data/test1_sort.bam.bai has changed |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/test_indel.fasta --- a/test-data/test_indel.fasta Tue Mar 14 14:14:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->NP_001120983_954:CT>C |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a| -MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLACLAPKTAVYPCDSLDVFLSSSSFYMAMTKTLYCWEIPGAVKRLGPGPVQHSTTSFTHSLMTREAGVKSESFIFWNRYALTVKPVGSGRKLMNQAWTRTKIQCQLLLNIRSVLLCVF ->NP_001120983_4552:GAA>GA |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a| -MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNEQNQSSLKNQMKTKRKRQKKLLILKRTY |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/test_rpkm.fasta --- a/test-data/test_rpkm.fasta Tue Mar 14 14:14:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,6 +0,0 @@ ->NP_004439 |121102.4845|NM_004448|ERBB2|receptor tyrosine-protein kinase erbB-2 isoform a precursor -MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGASPGGLRELQLRSLTEILKGGVLIQRNPQLCYQDTILWKDIFHKNNQLALTLIDTNRSRACHPCSPMCKGSRCWGESSEDCQSLTRTVCAGGCARCKGPLPTDCCHEQCAAGCTGPKHSDCLACLHFNHSGICELHCPALVTYNTDTFESMPNPEGRYTFGASCVTACPYNYLSTDVGSCTLVCPLHNQEVTAEDGTQRCEKCSKPCARVCYGLGMEHLREVRAVTSANIQEFAGCKKIFGSLAFLPESFDGDPASNTAPLQPEQLQVFETLEEITGYLYISAWPDSLPDLSVFQNLQVIRGRILHNGAYSLTLQGLGISWLGLRSLRELGSGLALIHHNTHLCFVHTVPWDQLFRNPHQALLHTANRPEDECVGEGLACHQLCARGHCWGPGPTQCVNCSQFLRGQECVEECRVLQGLPREYVNARHCLPCHPECQPQNGSVTCFGPEADQCVACAHYKDPPFCVARCPSGVKPDLSYMPIWKFPDEEGACQPCPINCTHSCVDLDDKGCPAEQRASPLTSIISAVVGILLVVVLGVVFGILIKRRQQKIRKYTMRRLLQETELVEPLTPSGAMPNQAQMRILKETELRKVKVLGSGAFGTVYKGIWIPDGENVKIPVAIKVLRENTSPKANKEILDEAYVMAGVGSPYVSRLLGICLTSTVQLVTQLMPYGCLLDHVRENRGRLGSQDLLNWCMQIAKGMSYLEDVRLVHRDLAARNVLVKSPNHVKITDFGLARLLDIDETEYHADGGKVPIKWMALESILRRRFTHQSDVWSYGVTVWELMTFGAKPYDGIPAREIPDLLEKGERLPQPPICTIDVYMIMVKCWMIDSECRPRFRELVSEFSRMARDPQRFVVIQNEDLGPASPLDSTFYRSLLEDDDMGDLVDAEEYLVPQQGFFCPDPAPGAGGMVHHRHRSSSTRSGGGDLTLGLEPSEEEAPRSPLAPSEGAGSDVFDGDLGMGAAKGLQSLPTHDPSPLQRYSEDPTVPLPSETDGYVAPLTCSPQPEYVNQPDVRPQPPSPREGPLPAARPAGATLERPKTLSPGKNGVVKDVFAFGGAVENPEYLTPQGGAAPQPHPPPAFSPAFDNLYYWDQDPPERGAPPSTFKGTPTAENPEYLGLDVPV ->NP_000170 |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 -MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPTRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL ->NP_001120983 |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a -MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKREVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGFSCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQEKEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASKLPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPINFSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEAQGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLNAERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIEGTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTELTSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEKLQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPSKPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKKKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFDWKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHLTPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLITGKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKGPPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPSRSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSSPSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKGLNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSPTLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQAGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKREHSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQSKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPAVSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDNQAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSETNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSARPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV |
| b |
| diff -r 8ccfff69dd57 -r ad130eaa3a05 test-data/test_snv.fasta --- a/test-data/test_snv.fasta Tue Mar 14 14:14:38 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,4 +0,0 @@ ->NP_000170_T139I,E956D |18647.7757|NM_000179|MSH6|DNA mismatch repair protein Msh6 -MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFFDDSPIRGWVSKRLLKPYTGSKSKEAQKGGHFYSAKPEILRAMQRADEALNKDKIKRLELAVCDEPSEPEEEEEMEVGTTYVTDKSEEDNEIESEEEVQPKTQGSRRSSRQIKKRRVISDSESDIGGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMKGNWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQVLFEKGNLSKETKTILKSSLSCSLQEGLIPGSQFWDASKTLRTLLEEEYFREKLSDGIGVMLPQVLKGMTSESDSIGLTPGEKSELALSALGGCVFYLKKCLIDQELLSMANFEEYIPLDSDTVSTTRSGAIFTKAYQRMVLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLKKLPDLERLLSKIHNVGSPLKSQNHPDSRAIMYEETTYSKKKIIDFLSALEGFKVMCKIIGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKAGFDSDYDQALADIRENEQSLLEYLDKQRNRIGCRTIVYWGIGRNRYQLEIPENFTTRNLPEEYELKSTKKGCKRYWTKTIEKKLANLINAEERRDVSLKDCMRRLFYNFDKNYKDWQSAVECIAVLDVLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCVLVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDELGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLASERSTVDAEAVHKLLTLIKEL ->NP_001120983_R1432*,V1804D |665.1509|NM_001127511|APC|adenomatous polyposis coli protein isoform a -MYASLGSGPVAPLPASVPPSVLGSWSTGGSRSCVRQETKSPGGARTSGHWASVWQEVLKQLQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSREGSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDKEEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAMEEQLGTCQDMEKRAQRSSQNKHETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSAPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRYAGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYVFDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTSQEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMPYAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQYPADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVSPYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEEEQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKSSSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCKVSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSANTLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHKAVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRSIASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTK |