changeset 7:3c05abb4452e default tip

add missing files
author devteam@galaxyproject.org
date Wed, 22 Apr 2015 12:22:50 -0400
parents dccd7a3ee717
children
files Galaxy-Workflow-Estimate_minimum_informative_read_depth.ga Galaxy-Workflow-TR_genome_profiling.ga Galaxy-Workflow-microsatellite_profiling.ga README.md commandline_sample_STR-FM_estimate_mininum_informative_Read_Depth commandline_sample_STR-FM_reference_profiling commandline_sample_STR-FM_shortread_profiling test-data/C_sample_fastq test-data/C_sample_snoope test-data/PCRinclude.allrate.bymajorallele test-data/combineprob_out.txt test-data/microsatcompat_in.txt test-data/microsatcompat_out.txt test-data/microsatellite_flanking_L.fastq test-data/microsatellite_flanking_R.fastq test-data/microsatpurity_in.txt test-data/microsatpurity_out.txt test-data/nice1tab.py test-data/probvalueforhetero_in.txt test-data/probvalueforhetero_out.txt test-data/profilegenerator_in.txt test-data/profilegenerator_out.txt test-data/readdepth2seqdepth.out test-data/samplePESAM_2_profile_C.txt test-data/sampleTRgenotypingcorrection test-data/sampleTRprofile_C.txt test-data/samplefq.snoope test-data/samplefq.snoope.new test-data/sampleprofilegenerator_in test-data/sampleprofilegenerator_out test-data/samplesortedPESAM_C.sam test-data/shifted.2bit
diffstat 32 files changed, 2736 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-Estimate_minimum_informative_read_depth.ga	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,342 @@
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+            "input_connections": {}, 
+            "inputs": [
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+                    "name": "TR error rate"
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+            "annotation": "replace 'A' with motif of interest", 
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+            "input_connections": {
+                "input": {
+                    "id": 0, 
+                    "output_name": "output"
+                }
+            }, 
+            "inputs": [], 
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+                    "output_name": "out_file1"
+                }
+            }, 
+            "inputs": [], 
+            "name": "Evaluate the probability of the allele combination to generate read profile", 
+            "outputs": [
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+                    "name": "microsat_corrected", 
+                    "type": "tabular"
+                }
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+                "top": 913
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+            "inputs": [], 
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+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-TR_genome_profiling.ga	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,191 @@
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\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Galaxy-Workflow-microsatellite_profiling.ga	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,764 @@
+{
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+            "name": "Correct genotype for microsatellite errors", 
+            "outputs": [
+                {
+                    "name": "microsat_corrected", 
+                    "type": "tabular"
+                }
+            ], 
+            "position": {
+                "left": 1591.328125, 
+                "top": 456.8125
+            }, 
+            "post_job_actions": {
+                "RenameDatasetActionmicrosat_corrected": {
+                    "action_arguments": {
+                        "newname": "Genotype file"
+                    }, 
+                    "action_type": "RenameDatasetAction", 
+                    "output_name": "microsat_corrected"
+                }
+            }, 
+            "tool_errors": null, 
+            "tool_id": "toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/GenotypeSTR/2.0.0", 
+            "tool_state": "{\"microsat_raw\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"microsat_error_profile\": \"null\", \"expectedminorallele\": \"\\\"0.5\\\"\"}", 
+            "tool_version": "2.0.0", 
+            "type": "tool", 
+            "user_outputs": []
+        }
+    }
+}
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,103 @@
+# *STR-FM*, a short tandem repeat profiling using a flank-based mapping approach
+
+## User manual and guide
+We designed the STR profiling pipeline as a collection of tools which can be executed in both commandline or via a GUI on Galaxy. The easiest way to use STR-FM pipeline is to via Galaxy platform. Current, we have all tools in Galaxy main toolshed (See installation of STR-FM tools from toolshed below) and in Galaxy test website (STR-FM: microsatellite analysis).
+
+## Overview
+
+Our tools in ‘str_fm’ can be used to: 
+
+**(1) profile STRs from short read data with STR-FM pipeline** (tools: ‘STR detection’, ‘Read name modifier’, ‘Fetch bases flanking’, ‘Combine mapped faux paired-end reads’, ‘Check STR motif compatibility between reference and read STRs’, ‘Select uninterrupted STRs’)
+
+This pipeline needs several tools on Galaxy to complete the process. It can be customized with different mapper or STRs detection algorithm. Either single-end or paired-end sequencing data can be utilized; for paired-end read data, each read is treated separately. The core of the pipeline consists of the following three procedures 
+
+First, STR-FM runs a short-read STR detection tool using a string comparison algorithm (see publication details). The algorithm can detect exact (pure, or uninterrupted) STRs (mono- through hexanucleotide STRs greater than or equal to two repeats), incomplete motifs (e.g., ATATATA), interrupted STRs (e.g., AAAATAAAAA), or multiple STRs in a read. Reads that do not have sufficient upstream or downstream sequences flanking the STRs are discarded (we used a threshold of 20 bp on each side of an STR). Each read is split into two “pseudoreads,” containing the upstream and downstream flanks surrounding the STR. 
+
+Second, these are mapped to the reference genome using a standard paired-end read-mapping algorithm, e.g., BWA, Bowtie, or Bowtie2, treating each pair of flanking sequences as a faux paired-end read. 
+
+Finally, STR-FM runs a profiler tool, which groups all reads with STRs that are mapped to the same location in the reference genome. As a result, an array of all STR lengths from the reads mapping to a particular STR-containing locus is generated.
+
+**(2) genotype STRs with error correction** (tool ‘Correct genotype for STR errors’)
+
+This pipeline needs only one of our tools to complete process. It will take STR-profile file and sequencine error rates file as inputs. The program will calculate the maximum likelihood of genotype for each STR locus in STR-profile file. Then it will report the mostly likely genotype and the log odds ratio between their probabilities, which can be interpreted as a confidence of genotyping (the more this value deviates from 0, the more confidence we have in this genotype).
+
+**(3) estimate the minimum informative read depth from error rates** (tools: ‘Generate all possible combination of STR length profile’, ‘Evaluate the probability of the allele combination to generate read profile’, ‘Combine read profile probabilities’)
+
+This pipeline needs other tools on Galaxy to complete the process. This pipeline will generate all possible read profiles from sequencing error spectrum, select the profiles that can distinguish heterozygote from homozygote, calculate the probability to produce such profiles from sequencing error spectrum, and report the probability that a certain sequence depth can distinguish heterozygote from homozygote under a given sequencing error rates (see publication details). We recommend that you should try to run with less than 10x depth for initial trial.
+
+**(4) convert informative read depth to locus-specific and genome-wide sequencing depth** (tool ‘Convert informative read depth to sequencing depth’).  
+
+This pipeline needs only one of our tools to complete process. It will convert *informative read depth* to *locus-specific sequencing depth* (given read length) and *genome-wide sequencing depth* (given confidence intervals).
+
+
+## Description of tools
+
+The short description for each tool is provided below.
+
+1. “STR detection” = Detect STRs from short reads (FASTQ), reference genome (FASTA), or alignments (SAM)
+2. “Read name modifier” = Change space in read name to ‘_’ to prevent read name truncation by mapping tools
+3. “Fetch bases flanking” = Generate two FASTQ files containing flanking bases around STRs for mapping as faux paired-end reads
+4. “Combine mapped faux paired-end reads” = For each mapped faux paired-end reads, infer STR sequence in reference genome between the two mapped ends of the pair
+5. “Check STR motif compatibility between reference and read STRs” = Check if two STRs have the same motif
+6. “Select uninterrupted STRs” = Select STRs that do not contain an interruption
+7. “Correct genotype for STR errors” = Build error correction model from pre-defined error rates and identify most likely genotype of the input data
+8. “Generate all possible combination of STR length profile” = Use STR error spectrum to generate all possible combinations of read profile at each read depth
+9. “Evaluate the probability of the allele combination to generate read profile” = Calculate the probability of a given genotype to generate read profiles (instead of finding most likely genotype like tool number 7)
+10. “Combine read profile probabilities” = Sum the probability of the given allele combinations to generate read profile at certain read depth
+11. “Convert informative read depth to sequencing depth” = Calculate ‘locus-specific’ and ‘genome-wide’ sequencing depth from the given informative read depth
+The detailed description for each tool is embedded within the tool.
+
+## Citing *STR-FM*
+Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research
+
+## Installation of STR-FM tools from toolshed
+
+
+The installation can be done as follows
+
+
+1 Install and set configuration of local Galaxy 
+
+1.1 Download and install Galaxy (https://wiki.galaxyproject.org/Admin/GetGalaxy). Galaxy works on both Unix and Mac OS.
+
+1.2 From your Galaxy directory, add your E-mail as admin E-mail to the Galaxy configuration file. Depending on the Galaxy version, this file can be either universe_wsgi.ini or config/galaxy.ini (https://wiki.galaxyproject.org/Admin/Interface)
+
+1.3 Set directory for tool dependencies (step 2 in https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial). 
+
+1.4 Run local Galaxy from the command line by running ‘sh run.sh’ from your Galaxy directory. 
+
+1.5 Open your Galaxy from your browser at address http://localhost:8080 (https://wiki.galaxyproject.org/Admin/GetGalaxy)
+
+1.6 Register using your admin E-mail in the ‘User’ tab on the top.
+
+1.7 Refresh your browser
+
+
+2 Install tools and dependencies
+
+2.1 From your local galaxy, click ‘Admin’ tab on the top.
+
+2.2 On the left panel, click ‘Search and browse tool sheds’ under ‘Tool sheds’. ‘Accessible Galaxy tool sheds’ will appear on main panel.
+
+2.3 Click on ‘Galaxy main tool shed’ and select ‘Browse valid repositories’. (https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial)
+
+2.4 Type ‘str_fm in search box and click enter.
+
+2.5 The ‘suite_str_fm_0_1’ repository that has ‘arkarachai-fungtammasan’ as the owner will appear. The user may click on this repository name and click ‘Preview and install’. The ‘Install to Galaxy’ button will appear on upper right corner. This button allows the user to install all our tools and workflows -- pipelines containing tools for specific purpose such as STR profiling from short read sequencing data, microsatellite detection of the reference genome, and estimating minimum informative read depth. None of our tools have any dependencies. However, some of the other tools that used in our workflows (e.g. SAM flag filter, unique element selection, etc.) are not included in the standard Galaxy installation. For the user’s convenience, we included all dependency tools for the workflows in this repository. Therefore, installing ‘suite_str_fm_0_1’ will be sufficient to operate all workflows we provided. 
+
+2.6 After clicking on ‘Install to Galaxy’ and ‘Install’ button in confirmation page, all our tools, workflows, and test datasets will be downloaded to your local Galaxy. After the download is completed, all our tools will be available on your local Galaxy. If the user wants to use the workflows that we suggested (i.e. STR profiling from short read sequencing data, microsatellite detection of the reference genome, and estimating minimum informative read depth), please proceed to step 3.
+
+2.7 Refresh your browser
+
+
+3 Install workflows
+
+3.1 Click on the ‘Admin’ tab at the top again.
+
+3.2 On the right panel, click ‘Manage installed tool shed repositories’ under ‘Server’. ‘Installed tool shed repositories’ will appear on main panel.
+
+3.3 Click to open ‘str_fm’ repository. 
+
+3.4 Scroll down to ‘Workflows’ section and select the workflow that you want to install. The SGV graphic of the workflow will appear.
+
+3.5 Click on the ‘Repository Actions’ on the upper right corner and select ‘Import workflow to Galaxy’. If success, the ‘Workflow <workflow name> imported successfully’ will appear. Once the workflow is imported to your Galaxy, you can view and modify it from ‘Workflow’ tab on the top. 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commandline_sample_STR-FM_estimate_mininum_informative_Read_Depth	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,35 @@
+## This is a sample PBS script for profiling STR from reference genome using STR-FM
+##   
+##requirement
+##1 STR error rates (can be downloaded from https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files) --> errorrate.bymajorallele
+##
+echo " "
+echo " "
+echo "Job started on `hostname` at `date`"
+cd /working/directory/
+echo ${MOTIF}
+echo ${OUTPUT}
+echo " "
+echo "Generate all possible combination of STR length profile" ## See detail in profilegenerator.xml on https://github.com/Arkarachai/STR-FM
+python  profilegenerator.py errorrate.bymajorallele ${MOTIF} 30 > ${OUTPUT}.30
+
+echo "remove duplicated profiles"
+cat ${OUTPUT}.30 | sort | uniq > ${OUTPUT}.30.sort
+
+echo "genotyping using error correction model" ## See detail in GenotypingSTR.xml on https://github.com/Arkarachai/STR-FM
+python  GenotypeTRcorrection.py  ${OUTPUT}.30.sort errorrate.bymajorallele ${OUTPUT}.30.prob 0.5
+
+echo "select only full motif different --> need to replace 4 with motif size (1-6)"
+cat ${OUTPUT}.30.prob | grep  hetero | awk '(($7-$8)==4) || (($8-$7)==4) {print $0}' > ${OUTPUT}.30.prob.screen
+
+echo "Evaluate the probability of the allele combination to generate read profile" ## See detail in  probvalueforhetero.xml on https://github.com/Arkarachai/STR-FM
+python heteroprob.py  ${OUTPUT}.30.prob.screen  ${INPUT} >  ${OUTPUT}.30.bino
+
+echo "formatting"
+cat  ${OUTPUT}.30.bino | sort  -k 12n,12 -k 6n,6 > ${OUTPUT}.30.bino.sort
+
+echo "Combine read profile probabilities" ## See detail in  combineprobforallelecombination.xml on https://github.com/Arkarachai/STR-FM
+python combinedprobforallelecombination.py ${OUTPUT}.30.bino.sort > ${OUTPUT}.30.bino.sort.plot
+
+
+echo "Job end on `hostname` at `date`"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commandline_sample_STR-FM_reference_profiling	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,25 @@
+## This is a sample PBS script for profiling STR from reference genome using STR-FM version 1.0.0 (April 20, 2014)
+##   
+##requirement
+##1 reference genome in FASTA format --> ${INPUT}.fa
+##
+echo " "
+echo " "
+echo "Job started on `hostname` at `date`"
+cd /working/directory/
+echo " "
+echo " detect STR in reference genome" ## See detail in microsatellite.xml on https://github.com/Arkarachai/STR-FM
+python microsatellite.py ${INPUT}.fa --fasta --period=1 --partialmotifs --minlength=4 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0  --splitbyvalidity  >${INPUT}.mono.out
+python microsatellite.py ${INPUT}.fa --fasta --period=2 --partialmotifs --minlength=6 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0  --splitbyvalidity  >${INPUT}.di.out
+python microsatellite.py ${INPUT}.fa --fasta --period=3 --partialmotifs --minlength=6 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0  --splitbyvalidity  >${INPUT}.tri.out
+python microsatellite.py ${INPUT}.fa --fasta --period=4 --partialmotifs --minlength=8 --prefix=0 --suffix=0 --hamming=0 --multipleruns --flankdisplay=0  --splitbyvalidity  >${INPUT}.tetra.out
+
+echo "formatting"
+cat ${INPUT}.mono.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.mono.TR
+cat ${INPUT}.di.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.di.TR
+cat ${INPUT}.tri.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.tri.TR
+cat ${INPUT}.tetra.out | awk 'BEGIN{FS="\t";OFS="\t"};{print $6,$2,$2+$1,$4,$1,length($4) }' > ${INPUT}.tetra.TR
+
+
+
+echo "Job end on `hostname` at `date`"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commandline_sample_STR-FM_shortread_profiling	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,124 @@
+## This is a sample PBS script for profiling STR from short read using STR-FM version 2.0.0 (April 20, 2015)
+##   
+##requirement
+##1 fastq input in sangerfq Phred scale --> ${INPUT}.fastq
+##2 index of mapping program (bwa, bowtie, etc) 
+##3 location of all STR in reference genome (use PBS script name "sampleSTR_reference_profiling.txt) --> /path/to/STR/in/reference/genome.TR (you can make 4 separated TR files for 4 types of STRs)
+##4 reference genome in FASTA and in 2bit file --> /path/to/2bit/ref.2bit (use utility from UCSC genome browser to create 2bit file version of reference genome)
+##5 local Galaxy (available from Galaxy website for Mac and Unix computer)
+##6 STR error rates (can be downloaded from https://usegalaxy.org/u/guru%40psu.edu/h/error-rates-files) --> errorrate.bymajorallele
+##
+echo " "
+echo " "
+echo "Job started on `hostname` at `date`"
+ref=/path/to/reference/sequence/and/bwa/index/ref.fa
+export PYTHONPATH=/path/to/galaxy-dist/lib/
+galaxydir=/path/to/galaxy-dist/tools
+cd /working/directory/
+echo " "
+echo " detect STR in short read" ## See detail in microsatellite.xml on https://github.com/Arkarachai/STR-FM
+python microsatellite.py ${INPUT}.fastq  --fastq --period=1 --partialmotifs --minlength=5 --prefix=20 --suffix=20 --hamming=0 --multipleruns  >${INPUT}.mono.out
+python microsatellite.py ${INPUT}.fastq  --fastq --period=2 --partialmotifs --minlength=6 --prefix=20 --suffix=20 --hamming=0 --multipleruns  >${INPUT}.di.out
+python microsatellite.py ${INPUT}.fastq  --fastq --period=3 --partialmotifs --minlength=9 --prefix=20 --suffix=20 --hamming=0 --multipleruns  >${INPUT}.tri.out
+python microsatellite.py ${INPUT}.fastq  --fastq --period=4 --partialmotifs --minlength=12 --prefix=20 --suffix=20 --hamming=0 --multipleruns  >${INPUT}.tetra.out
+
+echo "change read name at " ## See detail in space2underscore_readname.xml on https://github.com/Arkarachai/STR-FM
+python changespacetounderscore_readname.py ${INPUT}.mono.out  ${INPUT}.mono.new 6
+python changespacetounderscore_readname.py ${INPUT}.di.out  ${INPUT}.di.new 6
+python changespacetounderscore_readname.py ${INPUT}.tri.out  ${INPUT}.tri.new 6
+python changespacetounderscore_readname.py ${INPUT}.tetra.out  ${INPUT}.tetra.new 6
+
+echo "start fetch flanking at `date`" ## See detail in fetchflank.xml on https://github.com/Arkarachai/STR-FM
+python pair_fetch_DNA_ff.py ${INPUT}.mono.new ${INPUT}.mono_ff_L.txt ${INPUT}.mono_ff_R.txt 20 20
+python pair_fetch_DNA_ff.py ${INPUT}.di.new ${INPUT}.di_ff_L.txt ${INPUT}.di_ff_R.txt 20 20
+python pair_fetch_DNA_ff.py ${INPUT}.tri.new ${INPUT}.tri_ff_L.txt ${INPUT}.tri_ff_R.txt 20 20
+python pair_fetch_DNA_ff.py ${INPUT}.tetra.new ${INPUT}.tetra_ff_L.txt ${INPUT}.tetra_ff_R.txt 20 20
+
+echo "BWA uniquely mapped no indel no deletion "
+bwa aln -n 0 -o 0 ${ref} ${INPUT}.mono_ff_L.txt > ${INPUT}.mono_ff_L.sai 
+bwa aln	-n 0 -o 0 ${ref} ${INPUT}.mono_ff_R.txt > ${INPUT}.mono_ff_R.sai
+bwa sampe ${ref} ${INPUT}.mono_ff_L.sai ${INPUT}.mono_ff_R.sai ${INPUT}.mono_ff_L.txt ${INPUT}.mono_ff_R.txt  > ${INPUT}.mono.sam
+samtools view -Sb -F 12 -q 1 ${INPUT}.mono.sam > ${INPUT}.mono.n.all.bam
+bwa aln -n 0 -o 0 ${ref} ${INPUT}.di_ff_L.txt > ${INPUT}.di_ff_L.sai 
+bwa aln	-n 0 -o 0 ${ref} ${INPUT}.di_ff_R.txt > ${INPUT}.di_ff_R.sai
+bwa sampe ${ref} ${INPUT}.di_ff_L.sai ${INPUT}.di_ff_R.sai ${INPUT}.di_ff_L.txt ${INPUT}.di_ff_R.txt  > ${INPUT}.di.sam
+samtools view -Sb -F 12 -q 1 ${INPUT}.di.sam > ${INPUT}.di.n.all.bam
+bwa aln -n 0 -o 0 ${ref} ${INPUT}.tri_ff_L.txt > ${INPUT}.tri_ff_L.sai 
+bwa aln	-n 0 -o 0 ${ref} ${INPUT}.tri_ff_R.txt > ${INPUT}.tri_ff_R.sai
+bwa sampe ${ref} ${INPUT}.tri_ff_L.sai ${INPUT}.tri_ff_R.sai ${INPUT}.tri_ff_L.txt ${INPUT}.tri_ff_R.txt  > ${INPUT}.tri.sam
+samtools view -Sb -F 12 -q 1 ${INPUT}.tri.sam > ${INPUT}.tri.n.all.bam
+bwa aln -n 0 -o 0 ${ref} ${INPUT}.tetra_ff_L.txt > ${INPUT}.tetra_ff_L.sai 
+bwa aln	-n 0 -o 0 ${ref} ${INPUT}.tetra_ff_R.txt > ${INPUT}.tetra_ff_R.sai
+bwa sampe ${ref} ${INPUT}.tetra_ff_L.sai ${INPUT}.tetra_ff_R.sai ${INPUT}.tetra_ff_L.txt ${INPUT}.tetra_ff_R.txt  > ${INPUT}.tetra.sam
+samtools view -Sb -F 12 -q 1 ${INPUT}.tetra.sam > ${INPUT}.tetra.n.all.bam
+
+echo "sort result by read name"
+samtools sort -n ${INPUT}.mono.n.all.bam ${INPUT}.mono.n.sorted.all
+samtools sort -n ${INPUT}.di.n.all.bam ${INPUT}.di.n.sorted.all
+samtools sort -n ${INPUT}.tri.n.all.bam ${INPUT}.tri.n.sorted.all
+samtools sort -n ${INPUT}.tetra.n.all.bam ${INPUT}.tetra.n.sorted.all
+samtools view -h -o ${INPUT}.mono.n.sorted.all.sam ${INPUT}.mono.n.sorted.all.bam
+samtools view -h -o ${INPUT}.di.n.sorted.all.sam ${INPUT}.di.n.sorted.all.bam
+samtools view -h -o ${INPUT}.tri.n.sorted.all.sam ${INPUT}.tri.n.sorted.all.bam
+samtools view -h -o ${INPUT}.tetra.n.sorted.all.sam ${INPUT}.tetra.n.sorted.all.bam
+
+echo "merge faux paired end reads" ## See detail in PEsortedSAM2readprofile.xml on https://github.com/Arkarachai/STR-FM
+python PEsortedSAM2readprofile.py ${INPUT}.mono.n.sorted.all.sam /path/to/2bit/ref.2bit 100 250  ${INPUT}.mono.RF 
+python PEsortedSAM2readprofile.py ${INPUT}.di.n.sorted.all.sam /path/to/2bit/ref.2bit 100 250  ${INPUT}.mono.RF 
+python PEsortedSAM2readprofile.py ${INPUT}.tri.n.sorted.all.sam /path/to/2bit/ref.2bit 100 250  ${INPUT}.mono.RF 
+python PEsortedSAM2readprofile.py ${INPUT}.tetra.n.sorted.all.sam /path/to/2bit/ref.2bit 100 250  ${INPUT}.mono.RF 
+
+echo "join mapped coordinate with STR length using read name" 
+python ${galaxydir}/filters/join.py ${INPUT}.mono.new ${INPUT}.mono.RF 6 1 ${INPUT}.mono.RF.j "" "" --index_depth=3 --buffer=50000000 --fill_options_file='None'
+python ${galaxydir}/filters/join.py ${INPUT}.di.new ${INPUT}.di.RF 6 1 ${INPUT}.mono.RF.j "" "" --index_depth=3 --buffer=50000000 --fill_options_file='None'
+python ${galaxydir}/filters/join.py ${INPUT}.tri.new ${INPUT}.tri.RF 6 1 ${INPUT}.mono.RF.j "" "" --index_depth=3 --buffer=50000000 --fill_options_file='None'
+python ${galaxydir}/filters/join.py ${INPUT}.tetra.new ${INPUT}.tetra.RF 6 1 ${INPUT}.mono.RF.j "" "" --index_depth=3 --buffer=50000000 --fill_options_file='None'
+
+echo "join mapped coordinate and STR length with STR location in genome"
+python ${galaxydir}/new_operations/gops_join.py /path/to/STR/in/reference/genome.TR ${INPUT}.mono.RF.j ${INPUT}.mono.gop -1 1,2,3,0 -2 10,13,14,0 -m 1 -f
+python ${galaxydir}/new_operations/gops_join.py /path/to/STR/in/reference/genome.TR ${INPUT}.di.RF.j ${INPUT}.di.gop -1 1,2,3,0 -2 10,13,14,0 -m 1 -f
+python ${galaxydir}/new_operations/gops_join.py /path/to/STR/in/reference/genome.TR ${INPUT}.tri.RF.j ${INPUT}.tri.gop -1 1,2,3,0 -2 10,13,14,0 -m 1 -f
+python ${galaxydir}/new_operations/gops_join.py /path/to/STR/in/reference/genome.TR ${INPUT}.tetra.RF.j ${INPUT}.tetra.gop -1 1,2,3,0 -2 10,13,14,0 -m 1 -f
+
+echo "remove incompatible motif (remove incorrect mapped reads given that there is no STR motif difference from reference genome)" ## See detail in microsatcompat.xml on https://github.com/Arkarachai/STR-FM
+python microsatcompat.py ${INPUT}.mono.gop 4 10 > ${INPUT}.mono.fulltable1 
+python microsatcompat.py ${INPUT}.di.gop 4 10 > ${INPUT}.di.fulltable1 
+python microsatcompat.py ${INPUT}.tri.gop 4 10 > ${INPUT}.tri.fulltable1 
+python microsatcompat.py ${INPUT}.tetra.gop 4 10 > ${INPUT}.tetra.fulltable1 
+
+echo "remove shifting flanking location (remove cases that come from STR interruption or flanking bases are misread as STRs)"
+cat ${INPUT}.mono.fulltable1 | awk '($19==$2) && ($20==$3) {print $0}' > ${INPUT}.mono.fulltable2
+cat ${INPUT}.di.fulltable1 | awk '($19==$2) && ($20==$3) {print $0}' > ${INPUT}.di.fulltable2
+cat ${INPUT}.tri.fulltable1 | awk '($19==$2) && ($20==$3) {print $0}' > ${INPUT}.tri.fulltable2
+cat ${INPUT}.tetra.fulltable1 | awk '($19==$2) && ($20==$3) {print $0}' > ${INPUT}.tetra.fulltable2
+
+echo "keep only column that are necessary for profiling" 
+cat ${INPUT}.mono.fulltable2| cut -f 1,2,3,4,5,7 | sort -k 1n,1 -k 2n,2 -k 3n,3 > ${INPUT}.mono.cuttmp0
+cat ${INPUT}.di.fulltable2| cut -f 1,2,3,4,5,7 | sort -k 1n,1 -k 2n,2 -k 3n,3 > ${INPUT}.di.cuttmp0
+cat ${INPUT}.tri.fulltable2| cut -f 1,2,3,4,5,7 | sort -k 1n,1 -k 2n,2 -k 3n,3 > ${INPUT}.tri.cuttmp0
+cat ${INPUT}.tetra.fulltable2| cut -f 1,2,3,4,5,7 | sort -k 1n,1 -k 2n,2 -k 3n,3 > ${INPUT}.tetra.cuttmp0
+
+echo "If you multiple analysis by splitting initial fastq, you should merge (cat) all results from the same sample after this step"
+
+echo "create genomic coordinate column and group by that column"
+perl ${galaxydir}/filters/fixedValueColumn.pl ${INPUT}.mono.cuttmp0 ${INPUT}.mono.cuttmp1 "_" "no"
+python ${galaxydir}/filters/mergeCols.py ${INPUT}.mono.cuttmp1 ${INPUT}.mono.cuttmp2 1 7 2 7 3
+python ${galaxydir}/stats/grouping.py ${INPUT}.mono.cuttmp3 ${INPUT}.mono.cuttmp2 8 0 'cat 6 0' 'cat_uniq 4 0'
+perl ${galaxydir}/filters/fixedValueColumn.pl ${INPUT}.di.cuttmp0 ${INPUT}.di.cuttmp1 "_" "no"
+python ${galaxydir}/filters/mergeCols.py ${INPUT}.di.cuttmp1 ${INPUT}.di.cuttmp2 1 7 2 7 3
+python ${galaxydir}/stats/grouping.py ${INPUT}.di.cuttmp3 ${INPUT}.di.cuttmp2 8 0 'cat 6 0' 'cat_uniq 4 0'
+perl ${galaxydir}/filters/fixedValueColumn.pl ${INPUT}.tri.cuttmp0 ${INPUT}.tri.cuttmp1 "_" "no"
+python ${galaxydir}/filters/mergeCols.py ${INPUT}.tri.cuttmp1 ${INPUT}.tri.cuttmp2 1 7 2 7 3
+python ${galaxydir}/stats/grouping.py ${INPUT}.tri.cuttmp3 ${INPUT}.tri.cuttmp2 8 0 'cat 6 0' 'cat_uniq 4 0'
+perl ${galaxydir}/filters/fixedValueColumn.pl ${INPUT}.tetra.cuttmp0 ${INPUT}.tetra.cuttmp1 "_" "no"
+python ${galaxydir}/filters/mergeCols.py ${INPUT}.tetra.cuttmp1 ${INPUT}.tetra.cuttmp2 1 7 2 7 3
+python ${galaxydir}/stats/grouping.py ${INPUT}.tetra.cuttmp3 ${INPUT}.tetra.cuttmp2 8 0 'cat 6 0' 'cat_uniq 4 0'
+
+echo "you may filter for minimum sequencing depth here"
+
+echo "genotyping using error correction model" ## See detail in GenotypingSTR.xml on https://github.com/Arkarachai/STR-FM
+cat ${INPUT}.mono.cuttmp2 ${INPUT}.di.cuttmp2 ${INPUT}.tri.cuttmp2 ${INPUT}.tetra.cuttmp2 > ${INPUT}.step5
+python GenotypeTRcorrection.py ${INPUT}.step5 errorrate.bymajorallele ${INPUT}.step5.result 0.5
+## final output is ${INPUT}.step5.result
+
+echo "Job end on `hostname` at `date`"
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/C_sample_fastq	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,8 @@
+@IL2_40_2_1_735_755
+ATTTTCCAGCACCGTCATGTGGTTCCAGAGGTTAAAGTGCTGAAATAACAT
++
+IIIIIIIIIIIIIIIIIIIIIIII4IIIIIIIII5IIDI)'7%*8%%%%5*
+@IL2_40_2_1_919_700
+ATAAGGAAAAAAAAAAAAAAAACCAGGTCTTTTTTTTTTTTTTTTTGTTAT
++
+IIIIIIIIIIIIIIIIIIIIII@IIII2III4-II47I?CII>-%:C-;$&
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/C_sample_snoope	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,4 @@
+3	33	15	A	0	IL2_40_2_1_735_755_1_per1_2	ATTTTCCAGCACCGTCATGTGGTTCCAGAGGTTaaaGTGCTGAAATAACAT	IIIIIIIIIIIIIIIIIIIIIIII4IIIIIIIII5IIDI)'7%*8%%%%5*
+3	42	6	A	0	IL2_40_2_1_735_755_1_per1_3	ATTTTCCAGCACCGTCATGTGGTTCCAGAGGTTAAAGTGCTGaaaTAACAT		IIIIIIIIIIIIIIIIIIIIIIII4IIIIIIIII5IIDI)'7%*8%%%%5*
+16	6	29	A	0	IL2_40_2_1_919_700_1_per1_1	ATAAGGaaaaaaaaaaaaaaaaCCAGGTCTTTTTTTTTTTTTTTTTGTTAT	IIIIIIIIIIIIIIIIIIIIII@IIII2III4-II47I?CII>-%:C-;$&
+17	29	5	T	0	IL2_40_2_1_919_700_1_per1_2	ATAAGGAAAAAAAAAAAAAAAACCAGGTCtttttttttttttttttGTTAT		IIIIIIIIIIIIIIIIIIIIII@IIII2III4-II47I?CII>-%:C-;$&
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/PCRinclude.allrate.bymajorallele	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,997 @@
+10	10	91456	A
+10	9	1259	A
+10	11	605	A
+10	8	16	A
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+17	17	51	AACT
+18	18	7	AACT
+20	20	21	AACT
+21	21	27	AACT
+23	23	7	AACT
+24	24	11	AACT
+30	30	5	AACT
+12	12	346	AAGC
+13	13	83	AAGC
+14	14	60	AAGC
+15	15	40	AAGC
+16	16	21	AAGC
+18	18	9	AAGC
+19	19	7	AAGC
+12	12	4943	AAGG
+13	13	2714	AAGG
+14	14	1385	AAGG
+14	15	3	AAGG
+15	15	949	AAGG
+16	16	612	AAGG
+16	14	4	AAGG
+17	17	331	AAGG
+18	18	362	AAGG
+19	19	204	AAGG
+20	20	138	AAGG
+21	21	149	AAGG
+22	22	68	AAGG
+23	23	49	AAGG
+24	24	27	AAGG
+25	25	44	AAGG
+26	26	8	AAGG
+27	27	14	AAGG
+28	28	14	AAGG
+29	29	14	AAGG
+30	30	12	AAGG
+31	31	23	AAGG
+34	34	11	AAGG
+43	43	6	AAGG
+12	12	2676	AAGT
+13	13	1438	AAGT
+14	14	940	AAGT
+15	15	649	AAGT
+16	16	305	AAGT
+17	17	291	AAGT
+18	18	181	AAGT
+19	19	55	AAGT
+20	20	73	AAGT
+21	21	8	AAGT
+22	22	43	AAGT
+22	26	1	AAGT
+23	23	32	AAGT
+23	19	1	AAGT
+24	24	18	AAGT
+25	25	19	AAGT
+26	26	8	AAGT
+27	27	12	AAGT
+29	29	18	AAGT
+30	30	12	AAGT
+31	31	12	AAGT
+32	32	11	AAGT
+33	33	35	AAGT
+34	34	9	AAGT
+35	35	6	AAGT
+12	12	594	AATC
+13	13	205	AATC
+14	14	88	AATC
+15	15	112	AATC
+16	16	20	AATC
+17	17	81	AATC
+18	18	23	AATC
+21	21	13	AATC
+22	22	8	AATC
+24	24	19	AATC
+26	26	7	AATC
+28	28	9	AATC
+33	33	6	AATC
+12	12	2293	AATG
+13	13	1226	AATG
+14	14	678	AATG
+15	15	455	AATG
+16	16	222	AATG
+17	17	211	AATG
+18	18	104	AATG
+19	19	79	AATG
+20	20	40	AATG
+21	21	33	AATG
+22	22	73	AATG
+23	23	24	AATG
+24	24	16	AATG
+25	25	18	AATG
+26	26	15	AATG
+27	27	22	AATG
+27	23	1	AATG
+28	28	5	AATG
+32	32	17	AATG
+33	33	16	AATG
+12	12	2633	AATT
+13	13	1086	AATT
+14	14	1052	AATT
+15	15	386	AATT
+16	16	393	AATT
+17	17	98	AATT
+18	18	104	AATT
+19	19	105	AATT
+20	20	34	AATT
+21	21	12	AATT
+22	22	20	AATT
+25	25	18	AATT
+26	26	25	AATT
+27	27	7	AATT
+29	29	7	AATT
+35	35	12	AATT
+12	12	1406	ACAG
+13	13	964	ACAG
+14	14	300	ACAG
+15	15	130	ACAG
+16	16	102	ACAG
+17	17	49	ACAG
+18	18	30	ACAG
+19	19	88	ACAG
+20	20	5	ACAG
+23	23	5	ACAG
+12	12	4868	ACAT
+12	15	4	ACAT
+13	13	3216	ACAT
+14	14	957	ACAT
+15	15	1052	ACAT
+16	16	588	ACAT
+17	17	422	ACAT
+18	18	239	ACAT
+19	19	238	ACAT
+19	15	1	ACAT
+20	20	25	ACAT
+21	21	79	ACAT
+22	22	20	ACAT
+23	23	38	ACAT
+27	27	42	ACAT
+29	29	18	ACAT
+31	31	5	ACAT
+32	32	5	ACAT
+35	35	6	ACAT
+36	36	9	ACAT
+41	41	14	ACAT
+44	44	8	ACAT
+44	40	1	ACAT
+50	50	12	ACAT
+12	12	833	ACCC
+13	13	345	ACCC
+14	14	190	ACCC
+15	15	60	ACCC
+16	16	12	ACCC
+17	17	15	ACCC
+19	19	8	ACCG
+12	12	416	ACCT
+13	13	123	ACCT
+14	14	140	ACCT
+15	15	69	ACCT
+16	16	41	ACCT
+17	17	45	ACCT
+19	19	18	ACCT
+20	20	27	ACCT
+21	21	19	ACCT
+22	22	6	ACCT
+27	27	13	ACCT
+28	28	7	ACCT
+29	29	9	ACCT
+30	30	7	ACCT
+34	34	6	ACCT
+45	45	5	ACCT
+12	12	84	ACGC
+13	13	52	ACGC
+15	15	63	ACGC
+12	12	433	ACGG
+13	13	163	ACGG
+14	14	38	ACGG
+15	15	44	ACGG
+16	16	7	ACGG
+17	17	11	ACGG
+19	19	6	ACGG
+25	25	10	ACGG
+12	12	1119	ACGT
+13	13	509	ACGT
+14	14	338	ACGT
+15	15	16	ACGT
+16	16	66	ACGT
+17	17	7	ACGT
+19	19	27	ACGT
+12	12	2211	ACTC
+13	13	685	ACTC
+14	14	188	ACTC
+15	15	151	ACTC
+16	16	91	ACTC
+18	18	17	ACTC
+19	19	24	ACTC
+20	20	23	ACTC
+21	21	13	ACTC
+23	23	19	ACTC
+45	45	8	ACTC
+12	12	161	ACTG
+13	13	69	ACTG
+14	14	7	ACTG
+15	15	14	ACTG
+16	16	15	ACTG
+12	12	3118	AGAT
+13	13	1216	AGAT
+14	14	1084	AGAT
+15	15	869	AGAT
+16	16	508	AGAT
+17	17	322	AGAT
+18	18	159	AGAT
+19	19	258	AGAT
+20	20	63	AGAT
+21	21	84	AGAT
+22	22	69	AGAT
+22	14	6	AGAT
+23	23	112	AGAT
+24	24	107	AGAT
+25	25	36	AGAT
+26	26	113	AGAT
+27	27	42	AGAT
+28	28	58	AGAT
+29	29	37	AGAT
+30	30	16	AGAT
+31	31	32	AGAT
+32	32	24	AGAT
+33	33	10	AGAT
+34	34	43	AGAT
+35	35	6	AGAT
+36	36	13	AGAT
+36	32	1	AGAT
+37	37	35	AGAT
+38	38	34	AGAT
+39	39	20	AGAT
+39	35	2	AGAT
+40	40	27	AGAT
+41	41	29	AGAT
+42	42	30	AGAT
+43	43	87	AGAT
+44	44	67	AGAT
+45	45	20	AGAT
+46	46	15	AGAT
+47	47	28	AGAT
+48	48	26	AGAT
+49	49	13	AGAT
+50	50	11	AGAT
+52	52	5	AGAT
+54	54	6	AGAT
+12	12	236	AGCC
+13	13	109	AGCC
+14	14	17	AGCC
+15	15	14	AGCC
+16	16	8	AGCC
+18	18	12	AGCC
+21	21	18	AGCC
+23	23	13	AGCC
+12	12	23	AGCG
+13	13	19	AGCG
+18	18	9	AGCG
+12	12	272	AGCT
+13	13	89	AGCT
+14	14	108	AGCT
+15	15	49	AGCT
+16	16	19	AGCT
+17	17	19	AGCT
+18	18	19	AGCT
+19	19	44	AGCT
+22	22	12	AGCT
+27	27	16	AGCT
+12	12	87	AGGC
+13	13	19	AGGC
+14	14	16	AGGC
+18	18	7	AGGC
+12	12	3610	AGGG
+13	13	1980	AGGG
+14	14	1095	AGGG
+15	15	624	AGGG
+16	16	159	AGGG
+17	17	59	AGGG
+18	18	43	AGGG
+19	19	60	AGGG
+20	20	49	AGGG
+21	21	12	AGGG
+23	23	10	AGGG
+12	12	531	ATCC
+13	13	323	ATCC
+14	14	221	ATCC
+15	15	58	ATCC
+16	16	78	ATCC
+17	17	38	ATCC
+18	18	12	ATCC
+19	19	19	ATCC
+20	20	17	ATCC
+21	21	44	ATCC
+22	22	12	ATCC
+23	23	39	ATCC
+24	24	11	ATCC
+25	25	12	ATCC
+27	27	10	ATCC
+32	32	6	ATCC
+39	39	8	ATCC
+40	40	6	ATCC
+48	48	7	ATCC
+12	12	272	ATCG
+13	13	89	ATCG
+14	14	108	ATCG
+15	15	49	ATCG
+16	16	19	ATCG
+17	17	19	ATCG
+18	18	19	ATCG
+19	19	44	ATCG
+22	22	12	ATCG
+27	27	16	ATCG
+12	12	1119	ATGC
+13	13	509	ATGC
+14	14	338	ATGC
+15	15	16	ATGC
+16	16	66	ATGC
+17	17	7	ATGC
+19	19	27	ATGC
+12	12	13	CCCG
+12	12	178	AGTC
+13	13	77	AGTC
+14	14	13	AGTC
+15	15	12	AGTC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/combineprob_out.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,7 @@
+read_depth	allele	heterozygous_prob	motif
+2	10_11	0.485943568663	A
+2	11_12	0.472130683091	A
+2	9_10	0.494635026326	A
+3	10_11	0.71878954705	A
+3	11_12	0.688571908761	A
+3	9_10	0.73801798345	A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/microsatcompat_in.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,3 @@
+15	64416346	64416378	AT	32	16	18	22	61	TA	0	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	TTCCTTTATAAGAAATCTTTACatatatatatatatatatGACTGTTTTGCTTTGTTTTGAGTTTCATAAAAATAGTATCATGGGGGCCGGTCACGGTGGC	CCCFFFFFGHHFFIJIHGHIGIGGEGGIGHEGBHIIIJIFGCHGGIIJJEEIEIADHGICBFIGIGCGIJIIIGIIHIGDHGIIJHF>C888=@DB92<@?	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	15	64416324	64416346	64416346	64416378	64416378	64416439	32	ATATATATATATATATATATATATATATATAT
+17	52191125	52191133	GA	8	4	8	26	67	AC	0	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	CTTCCAGGGCCCTTCCAATGCCAAAAacacacacCTTTTTCCCCTGACCCTCTGTCAGTCTTCTGAATTTAAAGCTGGGCTCTGGGACTTACCAGTGTGAG	CCCFFFFFHHHHHJJJJJJJJJJJJJJIHIIJIJJJJJJJJJJJIGIJJJJJJJHIJJIIJJJHHHHHHHFFFFFCEEDDDDDDDDBDDDDDDDDDCCCDC	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	17	52191099	52191125	52191125	52191133	52191133	52191200	8	ACACACAC
+17	52191125	52191133	AC	8	4	8	26	67	AG	0	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	CTTCCAGGGCCCTTCCAATGCCAAAAacacacacCTTTTTCCCCTGACCCTCTGTCAGTCTTCTGAATTTAAAGCTGGGCTCTGGGACTTACCAGTGTGAG	CCCFFFFFHHHHHJJJJJJJJJJJJJJIHIIJIJJJJJJJJJJJIGIJJJJJJJHIJJIIJJJHHHHHHHFFFFFCEEDDDDDDDDBDDDDDDDDDCCCDC	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	17	52191099	52191125	52191125	52191133	52191133	52191200	8	AGAGAGAG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/microsatcompat_out.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,1 @@
+15	64416346	64416378	AT	32	16	18	22	61	TA	0	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	TTCCTTTATAAGAAATCTTTACatatatatatatatatatGACTGTTTTGCTTTGTTTTGAGTTTCATAAAAATAGTATCATGGGGGCCGGTCACGGTGGC	CCCFFFFFGHHFFIJIHGHIGIGGEGGIGHEGBHIIIJIFGCHGGIIJJEEIEIADHGICBFIGIGCGIJIIIGIIHIGDHGIIJHF>C888=@DB92<@?	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	15	64416324	64416346	64416346	64416378	64416378	64416439	32	ATATATATATATATATATATATATATATATAT
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/microsatellite_flanking_L.fastq	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,4 @@
+@SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
+TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCT
++SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
+GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/microsatellite_flanking_R.fastq	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,4 @@
+@SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
+TTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG
++SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1
+GGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=9;(/=5'6=4:?>C*A<
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/microsatpurity_in.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,3 @@
+15	64416346	64416378	AT	32	16	18	22	61	AT	0	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	TTCCTTTATAAGAAATCTTTACatatatatatatatatatGACTGTTTTGCTTTGTTTTGAGTTTCATAAAAATAGTATCATGGGGGCCGGTCACGGTGGC	CCCFFFFFGHHFFIJIHGHIGIGGEGGIGHEGBHIIIJIFGCHGGIIJJEEIEIADHGICBFIGIGCGIJIIIGIIHIGDHGIIJHF>C888=@DB92<@?	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	15	64416324	64416346	64416346	64416378	64416378	64416439	32	ATATATATATATATATATATATATATATATAT
+15	64416346	64416378	AT	32	16	18	22	61	AT	0	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	TTCCTTTATAAGAAATCTTTACatatatatatatatatatGACTGTTTTGCTTTGTTTTGAGTTTCATAAAAATAGTATCATGGGGGCCGGTCACGGTGGC	CCCFFFFFGHHFFIJIHGHIGIGGEGGIGHEGBHIIIJIFGCHGGIIJJEEIEIADHGICBFIGIGCGIJIIIGIIHIGDHGIIJHF>C888=@DB92<@?	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	15	64416324	64416346	64416346	64416378	64416378	64416439	32	ATATATATATATATATATTATATATATATAT
+17	52191125	52191133	AC	8	4	8	26	67	AC	0	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	CTTCCAGGGCCCTTCCAATGCCAAAAacacacacCTTTTTCCCCTGACCCTCTGTCAGTCTTCTGAATTTAAAGCTGGGCTCTGGGACTTACCAGTGTGAG	CCCFFFFFHHHHHJJJJJJJJJJJJJJIHIIJIJJJJJJJJJJJIGIJJJJJJJHIJJIIJJJHHHHHHHFFFFFCEEDDDDDDDDBDDDDDDDDDCCCDC	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	17	52191099	52191125	52191125	52191133	52191133	52191200	8	ACACACAC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/microsatpurity_out.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,2 @@
+15	64416346	64416378	AT	32	16	18	22	61	AT	0	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	TTCCTTTATAAGAAATCTTTACatatatatatatatatatGACTGTTTTGCTTTGTTTTGAGTTTCATAAAAATAGTATCATGGGGGCCGGTCACGGTGGC	CCCFFFFFGHHFFIJIHGHIGIGGEGGIGHEGBHIIIJIFGCHGGIIJJEEIEIADHGICBFIGIGCGIJIIIGIIHIGDHGIIJHF>C888=@DB92<@?	ERR194158.789781069_HSQ1008:176:D0UYCACXX:2:1201:4831:11242/1_1_per2_1	15	64416324	64416346	64416346	64416378	64416378	64416439	32	ATATATATATATATATATATATATATATATAT
+17	52191125	52191133	AC	8	4	8	26	67	AC	0	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	CTTCCAGGGCCCTTCCAATGCCAAAAacacacacCTTTTTCCCCTGACCCTCTGTCAGTCTTCTGAATTTAAAGCTGGGCTCTGGGACTTACCAGTGTGAG	CCCFFFFFHHHHHJJJJJJJJJJJJJJIHIIJIJJJJJJJJJJJIGIJJJJJJJHIJJIIJJJHHHHHHHFFFFFCEEDDDDDDDDBDDDDDDDDDCCCDC	ERR194158.781426177_HSQ1008:176:D0UYCACXX:2:1109:7175:90983/1_1_per2_1	17	52191099	52191125	52191125	52191133	52191133	52191200	8	ACACACAC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nice1tab.py	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,6 @@
+import sys
+fd=open(sys.argv[1])
+lines=fd.readlines()
+for line in lines:
+    temp=line.strip().split()
+    print '\t'.join(temp)
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/probvalueforhetero_in.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,9 @@
+chr	9,10	A	hetero	-1.27220836321	10	10	9
+chr	10,11	A	hetero	-0.939119957032	11	11	10
+chr	11,12	A	hetero	-0.720375026792	12	12	11
+chr	9,9,10	A	hetero	-1.6841441619	9	9	10
+chr	9,10,10	A	hetero	-0.97233405327	10	10	9
+chr	10,10,11	A	hetero	-1.29451118958	10	10	11
+chr	10,11,11	A	hetero	-0.641022011041	11	11	10
+chr	11,11,12	A	hetero	-1.01921634129	11	11	12
+chr	11,12,12	A	hetero	-0.425116661902	12	12	11
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/probvalueforhetero_out.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,9 @@
+chr	9,10	A	hetero	-1.27220836321	10	10	9	0.247317513163	2	0.494635026326	2
+chr	10,11	A	hetero	-0.939119957032	11	11	10	0.242971784331	2	0.485943568663	2
+chr	11,12	A	hetero	-0.720375026792	12	12	11	0.236065341545	2	0.472130683091	2
+chr	9,9,10	A	hetero	-1.6841441619	9	9	10	0.124528157268	3	0.373584471803	3
+chr	9,10,10	A	hetero	-0.97233405327	10	10	9	0.121477837216	3	0.364433511647	3
+chr	10,10,11	A	hetero	-1.29451118958	10	10	11	0.122575544751	3	0.367726634253	3
+chr	10,11,11	A	hetero	-0.641022011041	11	11	10	0.117020970932	3	0.351062912797	3
+chr	11,11,12	A	hetero	-1.01921634129	11	11	12	0.11865253007	3	0.35595759021	3
+chr	11,12,12	A	hetero	-0.425116661902	12	12	11	0.110871439517	3	0.332614318551	3
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profilegenerator_in.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,6 @@
+9	9	100000
+10	10	91456
+10	9	1259
+11	11	39657
+11	10	1211
+11	12	514
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/profilegenerator_out.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,30 @@
+chr	9,9	A
+chr	9,10	A
+chr	9,11	A
+chr	9,12	A
+chr	10,10	A
+chr	10,11	A
+chr	10,12	A
+chr	11,11	A
+chr	11,12	A
+chr	12,12	A
+chr	9,9,9	A
+chr	9,9,10	A
+chr	9,9,11	A
+chr	9,9,12	A
+chr	9,10,10	A
+chr	9,10,11	A
+chr	9,10,12	A
+chr	9,11,11	A
+chr	9,11,12	A
+chr	9,12,12	A
+chr	10,10,10	A
+chr	10,10,11	A
+chr	10,10,12	A
+chr	10,11,11	A
+chr	10,11,12	A
+chr	10,12,12	A
+chr	11,11,11	A
+chr	11,11,12	A
+chr	11,12,12	A
+chr	12,12,12	A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/readdepth2seqdepth.out	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,2 @@
+repeat_length	read_length	informative_read_depth	=locus_specific_sequencing_depth	=genome_wide_sequencing_depth
+10	100	5	10	15
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplePESAM_2_profile_C.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,5 @@
+M01368:22:000000000-A4T24:1:1101:10010:3775_1:N:0:2_1_per1_1	shifted	540	713	713	719	719	759	6	GGGGGG
+M01368:22:000000000-A4T24:1:1101:10015:2849_1:N:0:2_1_per1_2	shifted	4007	4082	4082	4088	4088	4258	6	TTTTTT
+M01368:22:000000000-A4T24:1:1101:10070:4955_1:N:0:2_1_per1_1	shifted	1849	1930	1930	1936	1936	2100	6	CCCCCC
+M01368:22:000000000-A4T24:1:1101:10070:4955_1:N:0:2_1_per1_2	shifted	1849	2025	2025	2030	2030	2100	5	GGGGG
+M01368:22:000000000-A4T24:1:1101:10126:5433_1:N:0:2_1_per1_1	shifted	1428	1517	1517	1522	1522	1543	5	AAAAA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleTRgenotypingcorrection	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,2 @@
+chr1	14,13,13,13	A	hetero	-0.429451855856	13	13	14
+chr1	5,6,6,6,6,7,7,8,8	A	hetero	-14.8744881854	7	6	8
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleTRprofile_C.txt	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,2 @@
+chr1	14,13,13,13	A
+chr1	5,6,6,6,6,7,7,8,8	A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplefq.snoope	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,1 @@
+6	40	54	G	0	SRR345592.75000006 HS2000-192_107:1:63:5822:176818_1_per1_1	TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCTggggggTTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG	GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG?FFDFGGGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=9;(/=5'6=4:?>C*A<
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplefq.snoope.new	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,1 @@
+6	40	54	G	0	SRR345592.75000006_HS2000-192_107:1:63:5822:176818_1_per1_1	TACCCTCCTGTCTTCCCAGACTGATTTCTGTTCCTGCCCTggggggTTCTTGACTCCTCTGAATGGGTACGGGAGTGTGGACCTCAGGGAGGCCCCCTTG	GGGGGGGGGGGGGGGGGFGGGGGGGGGFEGGGGGGGGGGG?FFDFGGGGGG?FFFGGGGGDEGGEFFBEFCEEBD@BACB*?=9;(/=5'6=4:?>C*A<
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleprofilegenerator_in	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,6 @@
+9	9	100000
+10	10	91456
+10	9	1259
+11	11	39657
+11	10	1211
+11	12	514
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sampleprofilegenerator_out	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,30 @@
+chr	9,9	A
+chr	9,10	A
+chr	9,11	A
+chr	9,12	A
+chr	10,10	A
+chr	10,11	A
+chr	10,12	A
+chr	11,11	A
+chr	11,12	A
+chr	12,12	A
+chr	9,9,9	A
+chr	9,9,10	A
+chr	9,9,11	A
+chr	9,9,12	A
+chr	9,10,10	A
+chr	9,10,11	A
+chr	9,10,12	A
+chr	9,11,11	A
+chr	9,11,12	A
+chr	9,12,12	A
+chr	10,10,10	A
+chr	10,10,11	A
+chr	10,10,12	A
+chr	10,11,11	A
+chr	10,11,12	A
+chr	10,12,12	A
+chr	11,11,11	A
+chr	11,11,12	A
+chr	11,12,12	A
+chr	12,12,12	A
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samplesortedPESAM_C.sam	Wed Apr 22 12:22:50 2015 -0400
@@ -0,0 +1,10 @@
+M01368:22:000000000-A4T24:1:1101:10010:3775_1:N:0:2_1_per1_1	113	shifted	720	37	40M	=	541	-46	TTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACACC	HHFG@IIHHHHHIHHFHHGFGGGGDBDDEDDDBBB?????	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:40
+M01368:22:000000000-A4T24:1:1101:10010:3775_1:N:0:2_1_per1_1	177	shifted	541	37	173M	=	720	46	CTTCTAGTGTAGCCGTAGTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTCTGCTAATCCTGTTACCAGTGGCTGCTGCCAGTGGCGATAAGTCGTGTCTTACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGGCTGAAC	::GECC:*:)D<GEGGGECCCEC?00E?::CCCCEEECC:C*GEC4'.>ACGGEC:CC?>><DCE?C:EC?GECE?:CCECGEEC*GEECEC:GEEGE?GGECC:ECA2CC*CCC8DEGGEGC=CGECEAEGEEDGGEDEGD=EBGGGFDHHHHHHHHEEHHHHHIIHFIIHH	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:173
+M01368:22:000000000-A4T24:1:1101:10015:2849_1:N:0:2_1_per1_2	113	shifted	4089	37	170M	=	4008	-176	GCACAACATGGGGGATCATGTAACTCGCCTTGATCGTTGGGAACCGGAGCTGAATGAAGCCATACCAAACGACGAGCGTGACACCACGATGCCTGTAGCAATGGCAACAACGTTGCGCAAACTATTAACTGGCGAACTACTTACTCTAGCTTCCCGGCAACAATTAATAG	GECGGGGGGGGGGGGEGEGGGGD>2GEGGGGGEEGGGGGGGGGGGGGEEECEGEAGGEEGEB>=GGFGEAGHHHEHHHFHFF?ED;HFIHHIIIIHIIHHHHIHHHHIHHHHHHHHIIIIHIHHHHIHHHHHIIHHIIHHIIHIIIIIGGGGGGDDDDDDDDBBB????<	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:170
+M01368:22:000000000-A4T24:1:1101:10015:2849_1:N:0:2_1_per1_2	177	shifted	4008	37	75M	=	4089	176	TGCCATAACCATGAGTGATAACACTGCGGCCAACTTACTTCTGACAACGATCGGAGGACCGAAGGAGCTAACCGC	CEGGEEEECC?:EEGECGGGGECGGGGEEGGEEGCCGEGGGGGGGGGGDGGGGGE>EEGGGGGGGGGGGAGGGGE	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:75
+M01368:22:000000000-A4T24:1:1101:10070:4955_1:N:0:2_1_per1_1	129	shifted	1937	37	164M	=	1850	-87	TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGT	HHHHIHHHHHHHHHHHHHHHHHHHHHGGFGGGGGGGHGGGGGGGGGGGGEGGGGGGAEEGGGEGGGGGGEGEEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGECGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGCEGEGG	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:138T25
+M01368:22:000000000-A4T24:1:1101:10070:4955_1:N:0:2_1_per1_1	65	shifted	1850	37	81M	=	1937	87	CCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGA	?????BBBEEDBBDDDGGGGGGIIIIIIIIIIIIIHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHIHHHIIIIIIHGH	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:81
+M01368:22:000000000-A4T24:1:1101:10070:4955_1:N:0:2_1_per1_2	129	shifted	2031	37	70M	=	1850	-181	TAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGT	GGGGGGGGECGGGGGGGGGGGGGGAGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGCEGEGG	XT:A:U	NM:i:1	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:1	XO:i:0	XG:i:0	MD:Z:44T25
+M01368:22:000000000-A4T24:1:1101:10070:4955_1:N:0:2_1_per1_2	65	shifted	1850	37	176M	=	2031	181	CCCTTAACAGTACATAGTACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCGCTCCGGGCCCATAACACTT	?????BBBEEDBBDDDGGGGGGIIIIIIIIIIIIIHHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIHIHHHIIIIIIHGHIIIHHHHHHHIHHHHHHHHHHHHHHHHHHHHHGGFGGGGGGGHGGGGGGGGGGGGEGGGGGGAEEGGGEGGGGGGEGEEGGGGGGGGGGGGGGGG	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:176
+M01368:22:000000000-A4T24:1:1101:10126:5433_1:N:0:2_1_per1_1	129	shifted	1523	37	21M	=	1429	-94	GTCTTTAACTCCACCATTAGC	GGGEGGEGGGGGCGGGGGEGG	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:21
+M01368:22:000000000-A4T24:1:1101:10126:5433_1:N:0:2_1_per1_1	65	shifted	1429	37	89M	=	1523	94	CTATGCATCCAACGCGTTGGGAGCTCTCCCATATGGTCGACCTGCAGGCGGCCGCGAATTCACTAGTGATTTCCAAGGACAAATCAGAG	?????BBBDDDDDDDDGGGFGGFEHIIIIIIIHIIIHIHHHHHIIHFHHHHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGGGGEGEE	XT:A:U	NM:i:0	SM:i:37	AM:i:37	X0:i:1	X1:i:0	XM:i:0	XO:i:0	XG:i:0	MD:Z:89
Binary file test-data/shifted.2bit has changed