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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/customProDB commit 98f3323d4b92a4a3668788b3e1bad1a6529fd6df-dirty
author galaxyp
date Wed, 03 Feb 2016 12:37:47 -0500
parents 6db27bef602f
children b83a4002aab1
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
diffstat 14 files changed, 336 insertions(+), 46 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/COPYING	Wed Feb 03 12:37:47 2016 -0500
@@ -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	Wed Feb 03 12:37:47 2016 -0500
@@ -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
--- a/customProDB.R	Fri Jan 29 16:03:10 2016 -0500
+++ b/customProDB.R	Wed Feb 03 12:37:47 2016 -0500
@@ -17,10 +17,12 @@
 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$ids <- make_option('--ids', type='character')
 option_list$outputFile <- make_option('--outputFile', type='character')
 
 
@@ -29,36 +31,28 @@
 
 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),
 	outputFile = GalaxyOutput("FASTA","fasta"))
 {
-    if (dirname(exon_anno_file) != dirname(proteinseq_file) ||
-        dirname(exon_anno_file) != dirname(procodingseq_file))
-    {
-        gstop("parent directory of annotation files must all be the same")
-    }
-
-    if (file.exists(outputFile))
-    {
-        if (file.info(outputFile)$size > 0) { gstop("output file already exists") }
-        else
-        {
-            tryCatch(
-            {
-                file.remove(outputFile)
-            }, error=function(err)
-            {
-                gstop("failed to remove empty existing file")
-            })
-        }
-    }
+    file.symlink(exon_anno_file, paste(dirname(exon_anno_file), "exon_anno.RData", sep="/"))
+    file.symlink(proteinseq_file, paste(dirname(exon_anno_file), "proseq.RData", sep="/"))
+    file.symlink(procodingseq_file, paste(dirname(exon_anno_file), "procodingseq.RData", sep="/"))
+    file.symlink(ids_file, paste(dirname(exon_anno_file), "ids.RData", sep="/"))
+    
+    bamLink = paste(dirname(bam_file), "input.bam", sep="/")
+    file.symlink(bam_file, bamLink)
+    file.symlink(bai_file, paste(bamLink, ".bai", sep=""))
 
     suppressPackageStartupMessages(library(customProDB))
 
-    easyRun(bamFile=bamFile, vcfFile=vcfFile, annotation_path=dirname(exon_anno_file), outfile_path=dirname(outputFile), outfile_name=basename(outputFile))
+    easyRun(bamFile=bamLink, vcfFile=vcf_file, annotation_path=dirname(exon_anno_file),
+            outfile_path=".", outfile_name="output",
+            nov_junction=F, INDEL=T, lablersid=F, COSMIC=F)
 }
 
 
--- a/customProDB.xml	Fri Jan 29 16:03:10 2016 -0500
+++ b/customProDB.xml	Wed Feb 03 12:37:47 2016 -0500
@@ -5,34 +5,30 @@
   </stdio>
   <command interpreter="Rscript --vanilla">customProDB.R
 
-       --bam="$bamInput"
-       --vcf="$vcfInput"
-       --outputFile="$output"
+       --bam="$genome_annotation.bamInput"
+       --bai="${genome_annotation.bamInput.metadata.bam_index}"
+       --vcf="$genome_annotation.vcfInput"
+       --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"
        #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"
        #end if
 
 2&gt;&amp;1</command>
   <inputs>
-    <param name="bamInput" type="data" format="bam" help="A BAM file to translate to FASTA." label="Input BAM">
-      <validator type="empty_field" message="This field is required."/>
-    </param>
-    <param name="vcfInput" type="data" format="vcf" help="A VCF file to create variant proteins based on individual variation." label="Input Variant Calls">
-      <validator type="empty_field" message="This field is required."/>
-    </param>
-
     <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 a genome from the history and build index</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">
@@ -41,29 +37,53 @@
             <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>
       </when>
       <when value="history">
-        <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" optional="true" />
-        <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" optional="true" />
-        <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" optional="true" />
+        <param name="exonAnno" type="data" format="RData" metadata_name="dbkey" help="A dataframe of exon annotations in an RData file" label="Exon Annotations" />
+        <param name="proteinSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe containing protein ids and protein sequences in an RData file" label="Protein Sequences" />
+        <param name="proCodingSeq" type="data" format="RData" metadata_name="dbkey" help="A dataframe cotaining coding sequences for each protein in an RData file" label="Protein Coding Sequences" />
+        <param name="ids" type="data" format="RData" metadata_name="dbkey" 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" />
       </when>
     </conditional>
   </inputs>
   <outputs>
-    <data format="fasta" name="output" label="${input.name.rsplit('.',1)[0]}.fasta"/>
+    <data format="fasta" name="output_rpkm" from_work_dir="output_rpkm.fasta" label="${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>
+  <tests>
     <test>
-      <param name="input" value="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.idpDB.gz" />
-      <param name="scoreColumn" value="Myrimatch:MVH" />
-      <output name="output" file="dbo_z_20101126_JK_Res_Sens_Set2_H1819_A_07-subset.sam" />
+      <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>
-    <test>
-      <param name="input" value="Ellis_033_2700_261_07-unrefined-subset.idpDB.gz" />
-      <param name="scoreColumn" value="Myrimatch:MVH" />
-      <output name="output" file="Ellis_033_2700_261_07-unrefined-subset.sam" />
-    </test>
-  </tests>-->
+  </tests>
   <help>
 **Description**
 
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	Wed Feb 03 12:37:47 2016 -0500
@@ -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	Wed Feb 03 12:37:47 2016 -0500
@@ -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	Wed Feb 03 12:37:47 2016 -0500
@@ -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	Wed Feb 03 12:37:47 2016 -0500
@@ -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