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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 4bb5b663989d5f04e8fb74b111456f16d6edaa66
author galaxyp
date Tue, 14 Mar 2017 14:14:38 -0400
parents
children ad130eaa3a05
files COPYING README.md customProDB.R customProDB.xml 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 tool-data/customProDB.loc.sample tool_data_table_conf.xml.sample
diffstat 16 files changed, 535 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Tue Mar 14 14:14:38 2017 -0400
@@ -0,0 +1,121 @@
+Creative Commons Legal Code
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Tue Mar 14 14:14:38 2017 -0400
@@ -0,0 +1,54 @@
+GalaxyP - CustomProDB
+===================
+
+* Home: <https://github.com/galaxyproteomics/tools-galaxyp/>
+* Galaxy Tool Shed: <http://toolshed.g2.bx.psu.edu/view/galaxyp/customProDB>
+* Tool ID: `customProDB`
+
+
+Description
+-----------
+
+Generate customized FASTA files based on the transcriptome or exome sequencing of an individual sample.
+
+See:
+
+* <https://www.bioconductor.org/packages/release/bioc/html/customProDB.html>
+
+
+GalaxyP Community
+-----------------
+
+Current governing community policies for [GalaxyP](https://github.com/galaxyproteomics/) and other information can be found at:
+
+<https://github.com/galaxyproteomics>
+
+
+License
+-------
+
+Copyright (c) 2016 Vanderbilt University and Authors listed below.
+
+To the extent possible under law, the author(s) have dedicated all copyright and related and neighboring rights to this software to the public domain worldwide. This software is distributed without any warranty.
+
+You should have received a copy of the CC0 Public Domain Dedication along with this software. If not, see <https://creativecommons.org/publicdomain/zero/1.0/>.
+
+You can copy, modify, distribute and perform the work, even for commercial purposes, all without asking permission.
+
+
+Contributing
+------------
+
+Contributions to this repository are reviewed through pull requests. If you would like your work acknowledged, please also add yourself to the Authors section. If your pull request is accepted, you will also be acknowledged in <https://github.com/galaxyproteomics/tools-galaxyp/>
+
+
+Authors
+-------
+
+Authors and contributors:
+
+* Matt Chambers <matt.chambers42@gmail.com>
+  Vanderbilt University Medical Center
+
+* Xiaojing Wang
+  Vanderbilt University Medical Center
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/customProDB.R	Tue Mar 14 14:14:38 2017 -0400
@@ -0,0 +1,113 @@
+#!/usr/bin/env Rscript
+
+initial.options <- commandArgs(trailingOnly = FALSE)
+script_parent_dir <- dirname(sub("--file=", "", initial.options[grep("--file=", initial.options)]))
+
+## begin warning handler
+withCallingHandlers({
+
+library(methods) # Because Rscript does not always do this
+
+options('useFancyQuotes' = FALSE)
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("RGalaxy"))
+
+
+option_list <- list()
+
+option_list$bam <- make_option('--bam', type='character')
+option_list$bai <- make_option('--bai', type='character')
+option_list$vcf <- make_option('--vcf', type='character')
+option_list$exon_anno <- make_option('--exon_anno', type='character')
+option_list$proteinseq <- make_option('--proteinseq', type='character')
+option_list$procodingseq <- make_option('--procodingseq', type='character')
+option_list$ids <- make_option('--ids', type='character')
+option_list$dbsnpinCoding <- make_option('--dbsnpinCoding', type='character')
+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$outputNovelJunctions <- make_option('--outputNovelJunctions', type='logical', action="store_true", default=FALSE)
+option_list$outputFile <- make_option('--outputFile', type='character')
+
+
+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"))
+{
+    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="/"))
+
+    if (length(dbsnpinCoding_file) > 0)
+    {
+        file.symlink(dbsnpinCoding_file, paste(getwd(), "dbsnpinCoding.RData", sep="/"))
+        labelrsid = T
+    }
+    else
+    {
+        labelrsid = F
+    }
+
+    if (length(cosmic_file) > 0)
+    {
+        file.symlink(cosmic_file, paste(getwd(), "cosmic.RData", sep="/"))
+        cosmic = T
+    }
+    else
+    {
+        cosmic = F
+    }
+
+    bamLink = "input.bam"
+    file.symlink(bam_file, bamLink)
+    file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
+
+    suppressPackageStartupMessages(library(customProDB))
+
+    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)
+}
+
+
+params <- list()
+for(param in names(opt))
+{
+    if (!param == "help")
+        params[param] <- opt[param]
+}
+
+setClass("GalaxyRemoteError", contains="character")
+wrappedFunction <- function(f)
+{
+    tryCatch(do.call(f, params),
+        error=function(e) new("GalaxyRemoteError", conditionMessage(e)))
+}
+
+
+suppressPackageStartupMessages(library(RGalaxy))
+do.call(customProDB, params)
+
+## end warning handler
+}, warning = function(w) {
+    cat(paste("Warning:", conditionMessage(w), "\n"))
+    invokeRestart("muffleWarning")
+})
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/customProDB.xml	Tue Mar 14 14:14:38 2017 -0400
@@ -0,0 +1,121 @@
+<tool id="custom_pro_db" name="CustomProDB" version="1.14.0">
+  <description>Generate protein FASTAs from exosome or transcriptome data</description>
+  <requirements>
+    <requirement type="package" version="1.14.0">bioconductor-customprodb</requirement>
+    <requirement type="package" version="1.18.0">bioconductor-rgalaxy</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Job Failed" />
+  </stdio>
+  <command><![CDATA[
+    Rscript --vanilla '$__tool_directory__/customProDB.R'
+       --bam='$genome_annotation.bamInput'
+       --bai='${genome_annotation.bamInput.metadata.bam_index}'
+       --vcf='$genome_annotation.vcfInput'
+       --rpkmCutoff=$rpkmCutoff
+       --outputFile='${output_rpkm}'
+
+       #if str($genome_annotation.source) == 'history':
+            --exon_anno='$genome_annotation.exonAnno'
+            --proteinseq='$genome_annotation.proteinSeq'
+            --procodingseq='$genome_annotation.proCodingSeq'
+            --ids='$genome_annotation.ids'
+            #if str($genome_annotation.dbsnpInCoding) != 'None':
+                --dbsnpinCoding='$genome_annotation.dbsnpInCoding'
+            #end if
+            #if str($genome_annotation.cosmic) != 'None':
+                --cosmic='$genome_annotation.cosmic"
+            #end if
+       #else:
+            #set index_path = $genome_annotation.builtin.fields.path
+            --exon_anno='$index_path/exon_anno.RData'
+            --proteinseq='$index_path/proseq.RData'
+            --procodingseq='$index_path/procodingseq.RData'
+            --ids='$index_path/ids.RData'
+            #if $genome_annotation.dbsnpInCoding:
+                --dbsnpinCoding='$index_path/dbsnpinCoding.RData'
+            #end if
+            #if $genome_annotation.cosmic:
+                --cosmic='$index_path/cosmic.RData'
+            #end if
+       #end if
+       2>1
+]]>
+  </command>
+  <inputs>
+    <conditional name="genome_annotation">
+      <param name="source" type="select" label="Will you select a genome annotation from your history or use a built-in annotation?" help="See `Annotations` section of help below">
+        <option value="builtin">Use a built-in genome annotation</option>
+        <option value="history">Use annotation from your history</option>
+      </param>
+      <when value="builtin">
+        <param name="builtin" type="select" label="Select genome annotation" help="If your genome of interest is not listed, contact the Galaxy team">
+          <options from_data_table="customProDB">
+            <filter type="sort_by" column="2"/>
+            <validator type="no_options" message="No annotations are available for the selected input dataset"/>
+          </options>
+        </param>
+        <param name="bamInput" type="data" format="bam" label="BAM file">
+            <validator type="unspecified_build" />
+            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
+        </param>
+        <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index (BAI) file">
+            <validator type="unspecified_build" />
+            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
+        </param>-->
+        <param name="vcfInput" type="data" format="vcf" label="VCF file">
+            <validator type="unspecified_build" />
+            <validator message="Sequences are not currently available for the specified build." metadata_column="1" metadata_name="dbkey" table_name="customProDB" type="dataset_metadata_in_data_table" />
+        </param>
+        <param name="dbsnpInCoding" type="boolean" value="" label="Annotate SNPs with rsid from dbSNP (select organisms only)" />
+        <param name="cosmic" type="boolean" value="" label="Annotate somatic SNPs from COSMIC (human only)" />
+      </when>
+      <when value="history">
+        <param name="exonAnno" type="data" format="RData" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
+        <param name="proteinSeq" type="data" format="RData" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
+        <param name="proCodingSeq" type="data" format="RData" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
+        <param name="ids" type="data" format="RData" help="A dataframe cotaining IDs for each protein in an RData file" label="Protein IDs" />
+        <param name="bamInput" type="data" format="bam" label="BAM file">
+            <validator check="bam_index" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
+        </param>
+        <!--<param name="baiInput" type="data" format="bam_index" label="BAM Index file">
+            <validator check="dbkey" message="Metadata missing, click the pencil icon in the history item and use the auto-detect feature to correct this issue." type="metadata" />
+        </param>-->
+        <param name="vcfInput" type="data" format="vcf" label="VCF file" />
+        <param name="dbsnpInCoding" type="data" format="RData" label="A dataframe containing dbSNP rsids" optional="true" />
+        <param name="cosmic" type="data" format="RData" label="A dataframe containing somatic SNPs from COSMIC (human only)" optional="true" />
+      </when>
+    </conditional>
+    <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." />
+  </inputs>
+  <outputs>
+    <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_rpkm.fasta"/>
+    <data format="fasta" name="output_snv" from_work_dir="output_snv.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_snv.fasta"/>
+    <data format="fasta" name="output_indel" from_work_dir="output_indel.fasta" label="${genome_annotation.bamInput.name.rsplit('.',1)[0]}_indel.fasta"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="bamInput" value="test1_sort.bam" dbkey="hg19" />
+      <param name="vcfInput" value="test1.vcf" dbkey="hg19" />
+      <param name="source" value="history" />
+      <param name="exonAnno" value="exon_anno.RData" />
+      <param name="proteinSeq" value="proseq.RData" />
+      <param name="proCodingSeq" value="procodingseq.RData" />
+      <param name="ids" value="ids.RData" />
+      <output name="output_rpkm" file="test_rpkm.fasta" />
+      <output name="output_snv" file="test_snv.fasta" />
+      <output name="output_indel" file="test_indel.fasta" />
+    </test>
+  </tests>
+  <help>
+**Description**
+
+Generate protein FASTAs from exosome or transcriptome data (in the form of BAM files). </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btt543</citation>
+    <citation type="bibtex">@misc{toolsGalaxyP, author = {Chambers MC, et al.}, title = {Galaxy Proteomics Tools}, publisher = {GitHub}, journal = {GitHub 
+repository},
+                                  year = {2017}, url = {https://github.com/galaxyproteomics/tools-galaxyp}}</citation> <!-- TODO: fix substitution of commit ", commit = 
+{$sha1$}" -->
+  </citations>
+</tool>
Binary file test-data/exon_anno.RData has changed
Binary file test-data/ids.RData has changed
Binary file test-data/procodingseq.RData has changed
Binary file test-data/proseq.RData has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test1.vcf	Tue Mar 14 14:14:38 2017 -0400
@@ -0,0 +1,87 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.17 (r973:277)
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
+#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
Binary file test-data/test1_sort.bam has changed
Binary file test-data/test1_sort.bam.bai has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_indel.fasta	Tue Mar 14 14:14:38 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_rpkm.fasta	Tue Mar 14 14:14:38 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_snv.fasta	Tue Mar 14 14:14:38 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/customProDB.loc.sample	Tue Mar 14 14:14:38 2017 -0400
@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>		<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3		/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19		Human (Homo sapiens): hg19 Canonical		/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19		Human (Homo sapiens): hg19 Full			/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Mar 14 14:14:38 2017 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all customProDB annotations under genome directory -->
+    <table name="customProDB" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/customProDB.loc" />
+    </table>
+</tables>