# HG changeset patch # User galaxyp # Date 1494609447 14400 # Node ID bc10f130dbecb5613ebbf7517b9fce4e3e94718d # Parent 37cd89a40cea29aadd40fc5e1bad5f6b9930ae6d planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit e025f5b4d590c44537cf0702e2fb040a28f98fec diff -r 37cd89a40cea -r bc10f130dbec README.md --- a/README.md Tue Mar 14 14:14:25 2017 -0400 +++ b/README.md Fri May 12 13:17:27 2017 -0400 @@ -48,7 +48,6 @@ Authors and contributors: * Matt Chambers - Vanderbilt University Medical Center -* Xiaojing Wang - Vanderbilt University Medical Center +* Xiaojing Wang + Baylor Medical College diff -r 37cd89a40cea -r bc10f130dbec customProDB.R --- a/customProDB.R Tue Mar 14 14:14:25 2017 -0400 +++ b/customProDB.R Fri May 12 13:17:27 2017 -0400 @@ -27,64 +27,146 @@ option_list$cosmic <- make_option('--cosmic', type='character') option_list$annotationFromHistory <- make_option('--annotationFromHistory', type='logical', action="store_true", default=FALSE) option_list$rpkmCutoff <- make_option('--rpkmCutoff', type='character') -#option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE) +option_list$outputIndels <- make_option('--outputIndels', type='logical', action="store_true", default=FALSE) #option_list$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE) -option_list$outputFile <- make_option('--outputFile', type='character') +#option_list$bedFile <- make_option('--bedFile', type='character') +#option_list$bsGenome <- make_option('--bsGenome', type='character') +option_list$outputRData <- make_option('--outputRData', type='logical', action="store_true", default=FALSE) +option_list$outputSQLite <- make_option('--outputSQLite', type='logical', action="store_true", default=FALSE) opt <- parse_args(OptionParser(option_list=option_list)) customProDB <- function( - bam_file = GalaxyInputFile(required=TRUE), - bai_file = GalaxyInputFile(required=TRUE), - vcf_file = GalaxyInputFile(required=TRUE), - exon_anno_file = GalaxyInputFile(required=TRUE), - proteinseq_file = GalaxyInputFile(required=TRUE), - procodingseq_file = GalaxyInputFile(required=TRUE), - ids_file = GalaxyInputFile(required=TRUE), - dbsnpinCoding_file = GalaxyInputFile(required=FALSE), - cosmic_file = GalaxyInputFile(required=FALSE), - annotationFromHistory = GalaxyLogicalParam(required=FALSE), - rpkmCutoff = GalaxyNumericParam(required=TRUE), - #outputIndels = GalaxyLogicalParam(required=FALSE), - #outputNovelJunctions = GalaxyLogicalParam(required=FALSE), - outputFile = GalaxyOutput("FASTA","fasta")) + bam_file = GalaxyInputFile(required=TRUE), + bai_file = GalaxyInputFile(required=TRUE), + vcf_file = GalaxyInputFile(required=TRUE), + exon_anno_file = GalaxyInputFile(required=TRUE), + proteinseq_file = GalaxyInputFile(required=TRUE), + procodingseq_file = GalaxyInputFile(required=TRUE), + ids_file = GalaxyInputFile(required=TRUE), + dbsnpinCoding_file = GalaxyInputFile(required=FALSE), + cosmic_file = GalaxyInputFile(required=FALSE), + annotationFromHistory = GalaxyLogicalParam(required=FALSE), + rpkmCutoff = GalaxyNumericParam(required=TRUE), + outputIndels = GalaxyLogicalParam(required=FALSE), + outputRData = GalaxyLogicalParam(required=FALSE), + outputSQLite = GalaxyLogicalParam(required=FALSE) + #,outputNovelJunctions = GalaxyLogicalParam(required=FALSE) + #,bedFile = GalaxyInputFile(required=FALSE) + #,bsGenome = GalaxyCharacterParam(required=FALSE) + ) { + old <- options(stringsAsFactors = FALSE, gsubfn.engine = "R") + on.exit(options(old), add = TRUE) + file.symlink(exon_anno_file, paste(getwd(), "exon_anno.RData", sep="/")) file.symlink(proteinseq_file, paste(getwd(), "proseq.RData", sep="/")) file.symlink(procodingseq_file, paste(getwd(), "procodingseq.RData", sep="/")) file.symlink(ids_file, paste(getwd(), "ids.RData", sep="/")) + load(exon_anno_file) + load(proteinseq_file) + load(procodingseq_file) + load(ids_file) + if (length(dbsnpinCoding_file) > 0) { file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/")) - labelrsid = T + labelrsid = TRUE + load(dbsnpinCoding_file) } else { - labelrsid = F + dbsnpinCoding = NULL + labelrsid = FALSE } if (length(cosmic_file) > 0) { file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/")) - cosmic = T + use_cosmic = TRUE + load(cosmic_file) } else { - cosmic = F + cosmic = NULL + use_cosmic = FALSE } bamLink = "input.bam" file.symlink(bam_file, bamLink) file.symlink(bai_file, paste(bamLink, ".bai", sep="")) - suppressPackageStartupMessages(library(customProDB)) + # load from GitHub until conda package is available + download.file("https://github.com/ggrothendieck/sqldf/archive/master.zip", "sqldf.zip", quiet=TRUE) + unzip("sqldf.zip") + devtools::load_all("sqldf-master") + + # load customProDB from GitHub (NOTE: downloading the zip is faster than cloning the repo with git2r or devtools::install_github) + download.file("https://github.com/chambm/customProDB/archive/master.zip", "customProDB.zip", quiet=TRUE) + unzip("customProDB.zip") + devtools::load_all("customProDB-master") easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=getwd(), rpkm_cutoff=rpkmCutoff, outfile_path=".", outfile_name="output", - nov_junction=F, INDEL=T, lablersid=labelrsid, COSMIC=cosmic) + nov_junction=FALSE, INDEL=outputIndels, + lablersid=labelrsid, COSMIC=use_cosmic) + + # save variant annotations to an RData file (needed by proBAMr) + if (outputRData || outputSQLite) + { + variantAnnotation = getVariantAnnotation(vcf_file, ids, exon, proteinseq, procodingseq, dbsnpinCoding, cosmic) + if (outputRData) save(variantAnnotation, file="output.rdata") + } + + if (outputSQLite) + { + # create protein-centric variant annotation table (needed by Galaxy-P viewer MVP) + varproseq = unique(rbind(variantAnnotation$snvproseq, variantAnnotation$indelproseq)) + ref_vs_var_seq = sqldf::sqldf("SELECT reference.pro_name, variant.pro_name AS var_pro_name, reference.peptide AS ref_seq, variant.peptide AS var_seq + FROM proteinseq reference, varproseq variant + WHERE reference.tx_name=variant.tx_name + GROUP BY variant.pro_name") + getCigarishString = function(ref, var) + { + a = Biostrings::pairwiseAlignment(ref, var) + d = gsub("[A-Z]", "=", Biostrings::compareStrings(a@pattern, a@subject)) + r = rle(strsplit(d, "")[[1]]) + gsub("-", "D", gsub("\\+", "I", gsub("\\?", "X", paste0(r$lengths, r$values, collapse="")))) + } + ref_vs_var_seq$cigar = mapply(FUN=getCigarishString, ref_vs_var_seq$ref_seq, ref_vs_var_seq$var_seq, USE.NAMES=FALSE) + ref_vs_var_seq$annotation = substring(ref_vs_var_seq$var_pro_name, stringr::str_length(ref_vs_var_seq$pro_name)+2) + + variant_annotation_sqlite = dbConnect(RSQLite::SQLite(), "output_variant_annotation.sqlite") + dbWriteTable(variant_annotation_sqlite, + "variant_annotation", + sqldf::sqldf("SELECT var_pro_name, pro_name, cigar, annotation FROM ref_vs_var_seq")) + DBI::dbExecute(variant_annotation_sqlite, "CREATE INDEX variant_annotation_var_pro_name ON variant_annotation (var_pro_name)") + + # save genomic mapping to a SQLite file (needed by Galaxy-P viewer MVP) + exon$cds_start = as.integer(exon$cds_start) + exon$cds_end = as.integer(exon$cds_end) + genomic_mapping_sqlite = dbConnect(RSQLite::SQLite(), "output_genomic_mapping.sqlite") + varprocoding = unique(rbind(variantAnnotation$snvprocoding, variantAnnotation$indelprocoding)) + dbWriteTable(genomic_mapping_sqlite, + "genomic_mapping", + sqldf::sqldf("SELECT exon.gene_name, exon.tx_name, varprocoding.pro_name, cds_start, cds_end, + chromosome_name AS chr_name, cds_chr_start, cds_chr_end, exon.strand + FROM exon, varprocoding + WHERE exon.tx_id=varprocoding.tx_id AND cds_chr_start > 0 + GROUP BY exon.tx_id, rank + UNION + SELECT gene_name, tx_name, pro_name, cds_start, cds_end, + chromosome_name AS chr_name, cds_chr_start, cds_chr_end, exon.strand + FROM exon + WHERE cds_chr_start > 0 + GROUP BY tx_id, rank")) + DBI::dbExecute(genomic_mapping_sqlite, "CREATE INDEX genomic_mapping_pro_name ON genomic_mapping (pro_name)") + } + + invisible(NULL) } diff -r 37cd89a40cea -r bc10f130dbec customProDB.xml --- a/customProDB.xml Tue Mar 14 14:14:25 2017 -0400 +++ b/customProDB.xml Fri May 12 13:17:27 2017 -0400 @@ -1,8 +1,24 @@ - + Generate protein FASTAs from exosome or transcriptome data - bioconductor-customprodb + r-base + bioconductor-rgalaxy + bioconductor-biocinstaller + bioconductor-variantannotation + r-devtools + r-xml + r-rmysql + r-testthat + r-getoptlong + r-stringi + r-stringr + r-data.table + + r-gsubfn + r-chron + r-proto + r-plyr @@ -13,7 +29,9 @@ --bai='${genome_annotation.bamInput.metadata.bam_index}' --vcf='$genome_annotation.vcfInput' --rpkmCutoff=$rpkmCutoff - --outputFile='${output_rpkm}' + $outputIndels + $outputSQLite + $outputRData #if str($genome_annotation.source) == 'history': --exon_anno='$genome_annotation.exonAnno' @@ -24,7 +42,7 @@ --dbsnpinCoding='$genome_annotation.dbsnpInCoding' #end if #if str($genome_annotation.cosmic) != 'None': - --cosmic='$genome_annotation.cosmic" + --cosmic='$genome_annotation.cosmic' #end if #else: #set index_path = $genome_annotation.builtin.fields.path @@ -87,24 +105,77 @@ + + + - + + outputIndels is True + + + outputRData is True + + + outputSQLite is True + + + outputSQLite is True + - - - + + + + + + + + + + + + + + + + + + + + + - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -113,8 +184,7 @@ Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). 10.1093/bioinformatics/btt543 - @misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub -repository}, + @misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub repository}, year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}} diff -r 37cd89a40cea -r bc10f130dbec test-data/exon_anno.RData Binary file test-data/exon_anno.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/cosmic.RData Binary file test-data/hg19/cosmic.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/dbsnpinCoding.RData Binary file test-data/hg19/dbsnpinCoding.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/exon_anno.RData Binary file test-data/hg19/exon_anno.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/ids.RData Binary file test-data/hg19/ids.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/junctions1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19/junctions1.bed Fri May 12 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/procodingseq.RData Binary file test-data/hg19/procodingseq.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/proseq.RData Binary file test-data/hg19/proseq.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/splicemax.RData Binary file test-data/hg19/splicemax.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/test1.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19/test1.vcf Fri May 12 13:17:27 2017 -0400 @@ -0,0 +1,87 @@ +##fileformat=VCFv4.1 +##samtoolsVersion=0.1.17 (r973:277) +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##INFO= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +##FORMAT= +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test +chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15 +chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36 +chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30 +chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99 +chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21 +chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16 +chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87 +chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33 +chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39 +chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21 +chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81 +chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99 +chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99 +chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81 +chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99 +chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27 +chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57 +chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54 +chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39 +chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99 +chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28 +chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34 +chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21 +chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99 +chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99 +chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99 +chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78 +chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99 +chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34 +chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51 +chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27 +chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55 +chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99 +chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21 +chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62 +chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16 +chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21 +chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61 +chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39 +chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45 +chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51 +chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70 +chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21 +chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99 +chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21 +chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21 +chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82 +chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99 +chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99 +chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26 +chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40 +chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33 +chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50 +chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8 +chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21 +chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99 +chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75 +chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96 +chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99 +chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99 +chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/test1_sort.bam Binary file test-data/hg19/test1_sort.bam has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/test1_sort.bam.bai Binary file test-data/hg19/test1_sort.bam.bai has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19/txdb.sqlite Binary file test-data/hg19/txdb.sqlite has changed diff -r 37cd89a40cea -r bc10f130dbec 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 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec 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 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_dbsnp_variant_annotation.sqlite Binary file test-data/hg19_dbsnp_variant_annotation.sqlite has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_genomic_mapping.sqlite Binary file test-data/hg19_genomic_mapping.sqlite has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_indel.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_indel.fasta Fri May 12 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_rpkm0.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_rpkm0.fasta Fri May 12 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_rpkm1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_rpkm1.fasta Fri May 12 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_rpkm1000.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_rpkm1000.fasta Fri May 12 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_snv.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19_snv.fasta Fri May 12 13:17:27 2017 -0400 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_variant_annotation.rdata Binary file test-data/hg19_variant_annotation.rdata has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/hg19_variant_annotation.sqlite Binary file test-data/hg19_variant_annotation.sqlite has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/ids.RData Binary file test-data/ids.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/procodingseq.RData Binary file test-data/procodingseq.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/proseq.RData Binary file test-data/proseq.RData has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/test1.vcf --- a/test-data/test1.vcf Tue Mar 14 14:14:25 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -##fileformat=VCFv4.1 -##samtoolsVersion=0.1.17 (r973:277) -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test -chr1 32386425 . T C 24 . DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36 GT:PL:GQ 1/1:56,9,0:15 -chr1 32507666 . G T 6.2 . DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36 GT:PL:GQ 0/1:35,0,78:36 -chr1 32524459 . A C 3.54 . DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1 GT:PL:GQ 0/1:31,0,98:30 -chr1 32622505 . G A 101 . DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075 GT:PL:GQ 0/1:131,0,162:99 -chr12 25357574 . CAA C 109 . INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5 GT:PL:GQ 1/1:149,12,0:21 -chr12 25357628 . TA T 53.4 . INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5 GT:PL:GQ 1/1:93,9,0:16 -chr12 25358650 . A T 73 . DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72 GT:PL:GQ 1/1:106,45,0:87 -chr12 25358662 . CTTTTTTTT CTTTTTT,CTTTTTTT 31.6 . INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5 GT:PL:GQ 1/1:96,42,24,91,0,64:33 -chr12 25358943 . T C 67.1 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:100,21,0:39 -chr12 25358969 . T G 36.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:69,12,0:21 -chr12 25359352 . G A 172 . DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:205,42,0:81 -chr12 25359464 . TAA TA 123 . INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113 GT:PL:GQ 1/1:164,78,0:99 -chr12 25360138 . T C 169 . DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84 GT:PL:GQ 1/1:202,57,0:99 -chr12 25361091 . T C 93 . DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69 GT:PL:GQ 1/1:126,42,0:81 -chr12 25362217 . A G 179 . DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87 GT:PL:GQ 1/1:212,60,0:99 -chr12 25362465 . G A 38.3 . DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42 GT:PL:GQ 1/1:71,15,0:27 -chr12 25362552 . A C 156 . DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57 GT:PL:GQ 1/1:189,30,0:57 -chr12 25364387 . T C 21 . DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1 GT:PL:GQ 0/1:51,0,112:54 -chr12 25368462 . C T 112 . DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48 GT:PL:GQ 1/1:145,21,0:39 -chr17 37866082 . G A 141 . DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1 GT:PL:GQ 0/1:171,0,180:99 -chr17 37870047 . A G 30 . DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1 GT:PL:GQ 0/1:60,0,25:28 -chr17 37879466 . G A 7.8 . DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1 GT:PL:GQ 0/1:37,0,31:34 -chr17 37885332 . G A 83.5 . DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39 GT:PL:GQ 1/1:116,12,0:21 -chr17 37898543 . T C 165 . DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90 GT:PL:GQ 1/1:198,63,0:99 -chr17 7530271 . C T 143 . DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1 GT:PL:GQ 0/1:173,0,238:99 -chr17 7572657 . G T 225 . DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27 GT:PL:GQ 0/1:255,0,190:99 -chr17 7591866 . G T 45 . DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01 GT:PL:GQ 0/1:75,0,162:78 -chr17 7606153 . C T 74 . DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1 GT:PL:GQ 0/1:104,0,165:99 -chr2 48010558 . C A 12.3 . DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1 GT:PL:GQ 0/1:42,0,31:34 -chr2 48016554 . T C 32 . DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21 GT:PL:GQ 0/1:62,0,48:51 -chr2 48018081 . A G 77 . DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34 GT:PL:GQ 0/1:107,0,24:27 -chr2 48018221 . C T 22 . DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1 GT:PL:GQ 0/1:52,0,116:55 -chr2 48027990 . G T 122 . DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039 GT:PL:GQ 0/1:152,0,131:99 -chr2 48030458 . G C 105 . DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39 GT:PL:GQ 1/1:137,12,0:21 -chr5 112154737 . CT C 29 . INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012 GT:PL:GQ 0/1:59,0,85:62 -chr5 112162854 . T C 60 . DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36 GT:PL:GQ 1/1:92,9,0:16 -chr5 112164561 . G A 87.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:120,12,0:21 -chr5 112175639 . C T 31 . DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1 GT:PL:GQ 0/1:61,0,62:61 -chr5 112175897 . GAA GA 7.8 . INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33 GT:PL:GQ 0/1:37,0,97:39 -chr5 112176559 . T G 72 . DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51 GT:PL:GQ 1/1:105,24,0:45 -chr5 112176756 . T A 143 . DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54 GT:PL:GQ 1/1:176,27,0:51 -chr5 112180015 . C A 123 . DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1 GT:PL:GQ 0/1:153,0,67:70 -chr5 112204170 . G A 112 . DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39 GT:PL:GQ 1/1:144,12,0:21 -chr7 140043303 . C T 88 . DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42 GT:PL:GQ 0/1:118,0,167:99 -chr7 140065806 . T C 38.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:71,12,0:21 -chr7 140065845 . C A 44.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:77,12,0:21 -chr7 140152904 . CAAAA CAAAAA 41.5 . INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1 GT:PL:GQ 0/1:79,0,91:82 -chr7 140153495 . G T 140 . DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038 GT:PL:GQ 0/1:170,0,184:99 -chr7 140158851 . C G 153 . DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1 GT:PL:GQ 1/1:186,75,0:99 -chr7 140244560 . C T 78 . DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1 GT:PL:GQ 0/1:108,0,23:26 -chr7 140406430 . T A 8.64 . DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021 GT:PL:GQ 0/1:38,0,167:40 -chr7 140406436 . A G 4.77 . DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08 GT:PL:GQ 0/1:33,0,170:33 -chr7 140424582 . G C 18.1 . DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1 GT:PL:GQ 0/1:48,0,56:50 -chr7 140426098 . G A 10.2 . DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33 GT:PL:GQ 1/1:41,6,0:8 -chr7 140702871 . G A 77.5 . DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39 GT:PL:GQ 1/1:110,12,0:21 -chr7 140706061 . G T 119 . DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1 GT:PL:GQ 0/1:149,0,178:99 -chr7 140706157 . G T 42 . DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013 GT:PL:GQ 0/1:72,0,170:75 -chr9 86583076 . C T 64 . DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1 GT:PL:GQ 0/1:94,0,100:96 -chr9 86593314 . G C 186 . DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072 GT:PL:GQ 0/1:216,0,216:99 -chr9 86595070 . C T 140 . DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1 GT:PL:GQ 0/1:170,0,188:99 -chr9 86595498 . G A 66 . DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1 GT:PL:GQ 0/1:96,0,225:99 diff -r 37cd89a40cea -r bc10f130dbec test-data/test1_sort.bam Binary file test-data/test1_sort.bam has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/test1_sort.bam.bai Binary file test-data/test1_sort.bam.bai has changed diff -r 37cd89a40cea -r bc10f130dbec test-data/test_indel.fasta --- a/test-data/test_indel.fasta Tue Mar 14 14:14:25 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/test_rpkm.fasta --- a/test-data/test_rpkm.fasta Tue Mar 14 14:14:25 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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 diff -r 37cd89a40cea -r bc10f130dbec test-data/test_snv.fasta --- a/test-data/test_snv.fasta Tue Mar 14 14:14:25 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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