# HG changeset patch
# User devteam
# Date 1447087059 18000
# Node ID 9f3d6c3098acb1262119b5bd525d2e78b70edc6e
# Parent  14f952d2a9db514a662e5a055f0a32cf813cb6f8
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/freebayes commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b

diff -r 14f952d2a9db -r 9f3d6c3098ac freebayes.xml
--- a/freebayes.xml	Thu Dec 11 18:38:34 2014 -0500
+++ b/freebayes.xml	Mon Nov 09 11:37:39 2015 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
-<tool id="freebayes" name="FreeBayes" version="0.3">
+<tool id="freebayes" name="FreeBayes" version="0.4.1">
   <requirements>
-    <requirement type="package" version="0.9.18_0059bdf">freebayes</requirement>
+    <requirement type="package" version="0_9_20_b040236">freebayes</requirement>
     <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <description> - bayesian genetic variant detector</description>
@@ -76,21 +76,55 @@
       --min-coverage "${options_type.min_coverage}"
 
 ##    Command line direct text entry is not allowed at this time for security reasons
-
-##    #elif str( $options_type.options_type_selector ) == "cline":
-    
-##      ${options_type.cline}
-  
-##      @optional_inputs_outputs@
     
     #elif str( $options_type.options_type_selector ) == "full":
-    
-##optional inputs and outputs
+ 
+        #if $options_type.optional_inputs.optional_inputs_selector:
+       
+	  ${options_type.optional_inputs.report_monomorphic}
  
-        @optional_inputs_outputs@
+          #if $options_type.optional_inputs.output_trace_option:
+            --trace "${output_trace}"
+          #end if
+          
+          #if $options_type.optional_inputs.output_failed_alleles_option:
+            --failed-alleles "${output_failed_alleles_bed}"
+          #end if
+       
+          #if $options_type.optional_inputs.samples:
+              --samples "${options_type.optional_inputs.samples}"
+          #end if
+          
+          #if $options_type.optional_inputs.populations:
+            --populations "${options_type.optional_inputs.populations}"
+          #end if
+          
+          #if $options_type.optional_inputs.A:
+            --cnv-map "${options_type.optional_inputs.A}"
+          #end if
+          
+          #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
+            --variant-input "input_variant_vcf.vcf.gz"  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
+            ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
+          #end if
+          
+          #if $options_type.optional_inputs.haplotype_basis_alleles:
+            --haplotype-basis-alleles "${options_type.optional_inputs.haplotype_basis_alleles}"
+          #end if
+          
+          #if $options_type.optional_inputs.observation_bias:
+            --observation-bias "${options_type.optional_inputs.observation_bias}"
+          #end if
+          
+          #if $options_type.optional_inputs.contamination_estimates:
+            --contamination-estimates "${options_type.optional_inputs.contamination_estimates}"
+          #end if
+          
+        #end if
         
 ## REPORTING
-        
+
+
         #if str( $options_type.reporting.reporting_selector ) == "True":
             --pvar ${options_type.reporting.pvar}
         #end if
@@ -193,87 +227,6 @@
     
   </command>
   
-  <macros>
-      <token name="@optional_inputs_outputs@">     
-      ## This token gets injected in commane in two instances: when options_type.options_type_selector == "full" and "cline" ( cline is not supported at this time )
-      
-      #if $options_type.optional_inputs.optional_inputs_selector:
-        
-          #if $options_type.optional_inputs.output_trace_option:
-            --trace "${output_trace}"
-          #end if
-          
-          #if $options_type.optional_inputs.output_failed_alleles_option:
-            --failed-alleles "${output_failed_alleles_bed}"
-          #end if
-       
-          #if $options_type.optional_inputs.samples:
-              --samples "${options_type.optional_inputs.samples}"
-          #end if
-          
-          #if $options_type.optional_inputs.populations:
-            --populations "${options_type.optional_inputs.populations}"
-          #end if
-          
-          #if $options_type.optional_inputs.A:
-            --cnv-map "${options_type.optional_inputs.A}"
-          #end if
-          
-          #if str( $options_type.optional_inputs.input_variant_type.input_variant_type_selector ) == "provide_vcf":
-            --variant-input "input_variant_vcf.vcf.gz"  ## input_variant_vcf.vcf.gz is symlinked to a galaxy-generated dataset in "Tabixize optional input_varinat_vcf file" section of the command line above
-            ${options_type.optional_inputs.input_variant_type.only_use_input_alleles}
-          #end if
-          
-          #if $options_type.optional_inputs.haplotype_basis_alleles:
-            --haplotype-basis-alleles "${options_type.optional_inputs.haplotype_basis_alleles}"
-          #end if
-          
-          #if $options_type.optional_inputs.observation_bias:
-            --observation-bias "${options_type.optional_inputs.observation_bias}"
-          #end if
-          
-          #if $options_type.optional_inputs.contamination_estimates:
-            --contamination-estimates "${options_type.optional_inputs.contamination_estimates}"
-          #end if
-          
-        #end if
-    </token>
-    <xml name="optional_file_inputs">
-      <conditional name="optional_inputs">
-          <param name="optional_inputs_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to provide additional inputs?" help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates" />
-          <when value="set">
-            <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" help="--failed-alleles" />
-            <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" help="--trace"/>
-            <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/>
-            <param name="populations" type="data" format="txt" label="Populations File" optional="True" help="--populations; default=False. Each line of FILE should list a sample and a population which it is part of.  The population-based bayesian inference model will then be partitioned on the basis of the populations" />
-            <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" help="-A --cnv-map; default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format: reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."/>
-            <conditional name="input_variant_type">
-              <param name="input_variant_type_selector" type="select" label="Provide variants file">
-                <option value="do_not_provide" selected="True">Do not provide</option>
-                <option value="provide_vcf">Provide VCF file</option>
-              </param>
-              <when value="do_not_provide">
-                <!-- Do nothing here -->
-              </when>
-              <when value="provide_vcf">
-                <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm">
-                  <conversion name="Tabixized_input" type="tabix" />
-                </param>
-                <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />
-              </when>
-            </conditional>
-            <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" help="--haplotype-basis-alleles" />
-            <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False" label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes." help="--report-monomorphic  " />
-            <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from" help="--observation-bias; The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />           
-            <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." />
-          </when>
-          <when value="do_not_set">
-            <!-- do nothing -->
-          </when>
-      </conditional>
-    </xml>
-  </macros>
-  
   <inputs>
     <conditional name="reference_source">
       <param name="reference_source_selector" type="select" label="Load reference genome from">
@@ -332,8 +285,39 @@
         -->
       </param>
       <when value="full">
-   
-        <expand macro="optional_file_inputs" /> <!-- see macros section -->
+        
+        <conditional name="optional_inputs">
+          <param name="optional_inputs_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to provide additional inputs?" help="Sets --samples, --populations, --cnv-map, --trace, --failed-alleles, --varinat-input, --only-use-input-alleles, --haplotype-basis-alleles, --report-all-haplotype-alleles, --report-monomorphic options, --observation-bias, and --contamination-estimates" />
+          <when value="set">
+            <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" help="--failed-alleles" />
+            <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" help="--trace"/>
+            <param name="samples" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" help="-s --samples; default=By default FreeBayes will analyze all samples in its input BAM files"/>
+            <param name="populations" type="data" format="txt" label="Populations File" optional="True" help="--populations; default=False. Each line of FILE should list a sample and a population which it is part of.  The population-based bayesian inference model will then be partitioned on the basis of the populations" />
+            <param name="A" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" help="-A --cnv-map; default=copy number is set to as specified by --ploidy. Read a copy number map from the BED file FILE, which has the format: reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy."/>
+            <conditional name="input_variant_type">
+              <param name="input_variant_type_selector" type="select" label="Provide variants file">
+                <option value="do_not_provide" selected="True">Do not provide</option>
+                <option value="provide_vcf">Provide VCF file</option>
+              </param>
+              <when value="do_not_provide">
+                <!-- Do nothing here -->
+              </when>
+              <when value="provide_vcf">
+                <param name="input_variant_vcf" type="data" format="vcf_bgzip" label="Use variants reported in VCF file as input to the algorithm">
+                  <conversion name="Tabixized_input" type="tabix" />
+                </param>
+                <param name="only_use_input_alleles" type="boolean" truevalue="--only-use-input-alleles" falsevalue="" checked="False" label="Only provide variant calls and genotype likelihoods for sites in VCF" />
+              </when>
+            </conditional>
+            <param name="haplotype_basis_alleles" type="data" format="vcf" label="Only use variant alleles provided in this input VCF for the construction of complex or haplotype alleles" optional="True" help="--haplotype-basis-alleles" />
+            <param name="report_monomorphic" type="boolean" truevalue="--report-monomorphic" falsevalue="" checked="False" label="Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes." help="--report-monomorphic  " />
+            <param name="observation_bias" optional="True" type="data" format="tabular" label="Load read length-dependent allele observation biases from" help="--observation-bias; The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias" />           
+            <param name="contamination_estimates" optional="True" type="data" format="tabular" label="Upload per-sample estimates of contamination from" help="--contamination-estimates; The format should be: sample p(read=R|genotype=AR) p(read=A|genotype=AA) Sample '*' can be used to set default contamination estimates." />
+          </when>
+          <when value="do_not_set">
+            <!-- do nothing -->
+          </when>
+        </conditional>
         
         <!-- reporting -->
         
@@ -368,7 +352,7 @@
         <param name="reference_allele_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Use reference allele?" help="Sets --use-reference-allele and --reference-quality options  " />
         <when value="set">
           <param name="Z" type="boolean" truevalue="-Z" falsevalue="" checked="False" label="Include the reference allele in the analysis as if it is another sample from the same population" help="-Z --use-reference-allele; default=False" />
-          <param name="reference_quality" type="text" size="8" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60  " />
+          <param name="reference_quality" type="text" value="100,60" label="Assign mapping quality of MQ (100) to the reference allele at each site and base quality of BQ (60)" help="--reference-quality; default=100,60  " />
         </when>
         <when value="do_not_set">
            <!-- do nothing -->
@@ -471,7 +455,7 @@
         <param name="report_genotype_likelihood_max" type="boolean" truevalue="--report-genotype-likelihood-max" falsevalue="" checked="False" label="Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods." help="--report-genotype-likelihood-max; default=False" />
         <param name="B" type="integer" value="1000" label="Iterate no more than N times during genotyping step" help="-B --genotyping-max-iterations; default=1000." />
         <param name="genotyping_max_banddepth" type="integer" value="6" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" help="--genotyping-max-banddepth; default=6" />
-        <param name="W" type="text" size="8" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" />
+        <param name="W" type="text" value="1,3" label="Integrate all genotype combinations in our posterior space which include no more than N (1) samples with their Mth (3) best data likelihood" help="-W --posterior-integration-limits; default=1,3" />
         <param name="N" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" help="-N --exclude-unobserved-genotypes; default=False" />
         <conditional name="genotype_variant_threshold">
           <param name="genotype_variant_threshold_selector" type="boolean" truevalue="set" falsevalue="do_not_set" label="Do you want to to limit posterior integration" help="-S --genotype-variant-threshold" />
@@ -506,28 +490,10 @@
     <!-- do nothing build command line using haplotype-length 0 min-alternate-count 1 min-alternate-fraction 0 pooled-continuous report-monomorphic standard-filters-->
     <param name="min_coverage" type="integer" value="0" label="Require at least this coverage to process a site" help="-! --min-coverage; default=0  " />
   </when>
-  
-  <!-- We will not allow command line textboxes at this time
-  <when value="cline">
-    
-    <expand macro="optional_file_inputs" /> 
-    
-    <param name="cline" size="60" type="text" value="-m 20 -q 30" label="Type command line tags here" help="All paremeters that DO NOT involve filenames can be typed here. Use &quot;Do you want to provide additional inputs?&quot; section above to control input and output files. For full syntax check help section below">
-      <sanitizer>
-        <valid initial="string.printable">
-         <remove value="&apos;"/>
-        </valid>
-        <mapping initial="none">
-          <add source="&apos;" target="__sq__"/>
-        </mapping>
-      </sanitizer>
-    </param>
-  </when>
-  -->
-
 </conditional>
 
   </inputs>
+  
   <outputs>
     <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string} (variants)" />
     <data format="bed" name="output_failed_alleles_bed" label="${tool.name} on ${on_string} (failed alleles)">
@@ -545,6 +511,14 @@
       <param name="options_type_selector" value="simple"/>
       <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
     </test>
+    <test>
+     <param name="reference_source_selector" value="history" />
+      <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
+      <param name="input_bam" ftype="bam" value="freebayes-phix174.bam"/>
+      <param name="options_type_selector" value="naive_w_filters"/>
+      <param name="min_coverage" value="14"/>
+      <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
+    </test>
   </tests>
   <stdio>
     <exit_code range="1:" />
@@ -556,7 +530,7 @@
 
 See https://github.com/ekg/freebayes for details on FreeBayes.
 
-This Galaxy instance of FreeBayes corresponds to release 0.9.18
+This Galaxy instance of FreeBayes corresponds to release 0.9.20
 
 ------
 
diff -r 14f952d2a9db -r 9f3d6c3098ac leftalign.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/leftalign.xml	Mon Nov 09 11:37:39 2015 -0500
@@ -0,0 +1,85 @@
+<?xml version="1.0"?>
+<tool id="bamleftalign" name="BamLeftAlign" version="0.4">
+  <requirements>
+    <requirement type="package" version="0_9_20_b040236">freebayes</requirement>
+    <requirement type="package" version="0.1.18">samtools</requirement>
+  </requirements>
+  <description> indels in BAM datasets</description>
+  <command>
+    ##set up input files
+    #set $reference_fasta_filename = "localref.fa"
+    #if str( $reference_source.reference_source_selector ) == "history":
+        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
+        samtools faidx "${reference_fasta_filename}" 2&gt;&amp;1 || echo "Error running samtools faidx for leftalign" &gt;&amp;2 &amp;&amp;
+    #else:
+        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
+    #end if
+
+    ##finished setting up inputs
+    
+    ##start leftalign commandline
+    samtools view -bh "${input_bam}" | bamleftalign
+    --fasta-reference "${reference_fasta_filename}"
+    -c
+    --max-iterations "${iterations}"
+    ##outputs
+    > "${output_bam}"
+  </command>
+  <inputs>
+    <conditional name="reference_source">
+      <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
+        <option value="cached">Locally cached</option>
+        <option value="history">History</option>
+      </param>
+      <when value="cached">
+            <param name="input_bam" type="data" format="bam" label="Select BAM dataset to leftalign">
+              <validator type="unspecified_build" />
+              <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+            </param>
+        <param name="ref_file" type="select" label="Using reference genome">
+          <options from_data_table="fasta_indexes"></options>
+          <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+      </when>
+      <when value="history"> 
+            <param name="input_bam" type="data" format="bam" label="BAM dataset to re-align" />
+        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+      </when>
+    </conditional>
+    <param name="iterations" type="integer" value="5" label="Maximum number of iterations" help="Iterate the left-realignment no more than this many times" />
+  </inputs>
+  <outputs>
+    <data format="bam" name="output_bam" label="${tool.name} on ${on_string} (alignments)" />
+  </outputs>
+  <tests>
+    <test>
+     <param name="reference_source_selector" value="history" />
+      <param name="ref_file" ftype="fasta" value="leftalign.fa"/>
+      <param name="input_bam" ftype="bam" value="left-align-input.bam"/>
+      <param name="iterations" value="5"/>
+      <output name="output_bam" file="left-align-output.bam" />
+    </test>
+  </tests>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <help>
+
+When calling indels, it is important to homogenize the positional distribution of insertions and deletions in the input by using left realignment. Left realignment will place all indels in homopolymer and microsatellite repeats at the same position, provided that doing so does not introduce mismatches between the read and reference other than the indel. This method is computationally inexpensive and handles the most common classes of alignment inconsistency.
+
+This is leftalign utility from FreeBayes package developed and maintained by Erik Garrison (https://github.com/ekg/freebayes).
+  </help>
+
+  <citations>
+    <citation type="bibtex">
+      @misc{1207.3907,
+      Author = {Erik Garrison},
+      Title = {Haplotype-based variant detection from short-read sequencing},
+      Year = {2012},
+      Eprint = {arXiv:1207.3907},
+      url = {http://arxiv.org/abs/1207.3907}
+      }
+    </citation>
+  </citations>
+
+</tool>
diff -r 14f952d2a9db -r 9f3d6c3098ac test-data/freebayes-phix174-test1.vcf
--- a/test-data/freebayes-phix174-test1.vcf	Thu Dec 11 18:38:34 2014 -0500
+++ b/test-data/freebayes-phix174-test1.vcf	Mon Nov 09 11:37:39 2015 -0500
@@ -1,27 +1,26 @@
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	unknown
-phiX174	311	.	A	G	6.48411	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPP=7.35324;RPPR=3.32051;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:478:2:70:-5.49703,0,-10
-phiX174	374	.	T	G	30.6931	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=7.0665;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPP=3.0103;RPPR=7.35324;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:4:2:141:2:75:-6.69903,0,-10
-phiX174	913	.	A	C	13.1703	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=29;NS=1;NUMALT=1;ODDS=2.98318;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=171;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:171:2:58:-5.00485,0,-10
-phiX174	1205	.	A	C	2.30262	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=0.357718;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPP=7.35324;RPPR=7.35324;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:10:8:456:2:67:-5.00791,0,-10
-phiX174	1245	.	G	T	6.48411	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPP=7.35324;RPPR=3.32051;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:389:2:70:-5.49703,0,-10
-phiX174	1249	.	T	G	15.3287	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=3.4998;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPP=3.0103;RPPR=5.80219;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:464:2:74:-5.87703,0,-10
-phiX174	1445	.	C	A	24.4745	.	AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=5.63189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPP=3.0103;RPPR=6.91895;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:7:5:273:2:76:-6.43501,0,-10
-phiX174	1577	.	A	C	4.06305	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=0.437365;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPP=3.0103;RPPR=10.7656;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:460:2:60:-4.54703,0,-10
-phiX174	1631	.	T	G	2.719	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=0.138972;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:10:8:500:2:68:-5.10291,0,-10
-phiX174	1772	.	T	G	2.16317	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=0.437618;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPP=3.0103;RPPR=3.32051;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:10:7:425:2:59:-4.16703,0,-10
-phiX174	1945	.	T	G	11.7103	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.62656;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:263:2:59:-4.97491,0,-10
-phiX174	2230	.	T	G	1.61813	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=0.795209;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=491;RO=8;RPP=7.35324;RPPR=4.09604;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:10:8:491:2:65:-4.81791,0,-10
-phiX174	2699	.	C	A	31.6424	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=7.28525;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPP=3.0103;RPPR=3.0103;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:4:2:109:2:76:-6.79403,0,-9.92903
-phiX174	2722	.	T	G	21.5364	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=7.35324;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=4.95189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=150;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:150:2:67:-5.85985,0,-10
-phiX174	2814	.	T	G	8.81714	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.88946;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=135;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=9.52472;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:135:2:53:-4.52985,0,-10
-phiX174	2828	.	T	G	37.7173	.	AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31;NS=1;NUMALT=1;ODDS=8.68456;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=348;RO=6;RPP=7.35324;RPPR=4.45795;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:8:6:348:2:100:-8.53892,0,-10
-phiX174	2983	.	T	G	12.2712	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=2.76444;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPP=3.0103;RPPR=3.73412;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:150:2:57:-4.90985,0,-10
-phiX174	3110	.	T	C	34.4848	.	AB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=7.94006;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPP=9.52472;RPPR=3.0103;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:6:361:3:94:-7.98834,0,-10
-phiX174	3155	.	T	G	23.5283	.	AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=5.41314;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPP=3.0103;RPPR=3.44459;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:7:5:299:2:75:-6.34001,0,-10
-phiX174	3325	.	A	C	5.77196	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=1.02152;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:284:2:58:-4.87991,0,-10
-phiX174	3418	.	A	C	0.61163	.	AB=0.2;ABP=10.8276;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=1.88894;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPP=7.35324;RPPR=4.09604;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:10:8:526:2:60:-4.34291,0,-10
-phiX174	3729	.	C	T	8.03017	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.67776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=232;RO=4;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:232:2:61:-5.16491,0,-10
-phiX174	4031	.	T	G	23.4861	.	AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=5.40338;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPP=7.35324;RPPR=8.80089;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:8:6:322:2:85:-7.11392,0,-10
-phiX174	4502	.	A	C	8.30185	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=1.75158;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPP=3.0103;RPPR=11.6962;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:284:2:55:-4.59491,0,-10
-phiX174	4558	.	C	G	6.48999	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=1.24027;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPP=7.35324;RPPR=11.6962;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:204:2:59:-4.97491,0,-10
-phiX174	4655	.	T	G	21.8853	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=5.03277;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPP=3.0103;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:193:2:70:-6.01991,0,-10
+phiX174	311	.	A	G	6.48411	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=5.80219;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33.5714;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=478;RO=7;RPL=0;RPP=7.35324;RPPR=3.32051;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=5.80219;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:478:2:70:-5.49703,0,-42.5499
+phiX174	374	.	T	G	30.6931	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=25;NS=1;NUMALT=1;ODDS=7.0665;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=141;RO=2;RPL=1;RPP=3.0103;RPPR=7.35324;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:4:2:141:2:75:-6.69903,0,-12.969
+phiX174	913	.	A	C	13.1703	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=29;NS=1;NUMALT=1;ODDS=2.98318;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=171;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=9.52472;SRR=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:171:2:58:-5.00485,0,-15.4549
+phiX174	1205	.	A	C	2.30262	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=34;NS=1;NUMALT=1;ODDS=0.357718;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=456;RO=8;RPL=2;RPP=7.35324;RPPR=7.35324;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=7.35324;SRR=6;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:10:8:456:2:67:-5.00791,0,-40.2529
+phiX174	1245	.	G	T	6.48411	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=28.4286;NS=1;NUMALT=1;ODDS=1.23853;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=389;RO=7;RPL=2;RPP=7.35324;RPPR=3.32051;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=18.2106;SRR=7;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:389:2:70:-5.49703,0,-34.4127
+phiX174	1249	.	T	G	15.3287	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=30.1429;NS=1;NUMALT=1;ODDS=3.4998;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=464;RO=7;RPL=1;RPP=3.0103;RPPR=5.80219;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=5.80219;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:464:2:74:-5.87703,0,-41.2699
+phiX174	1445	.	C	A	24.4745	.	AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=7.35324;EPPR=6.91895;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=32.2;NS=1;NUMALT=1;ODDS=5.63189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=273;RO=5;RPL=1;RPP=3.0103;RPPR=6.91895;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=2;SRP=3.44459;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:7:5:273:2:76:-6.43501,0,-24.331
+phiX174	1577	.	A	C	4.06305	.	AB=0.222222;ABP=9.04217;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=7.35324;EPPR=3.32051;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35.2857;NS=1;NUMALT=1;ODDS=0.437365;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=460;RO=7;RPL=1;RPP=3.0103;RPPR=10.7656;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=4;SRP=3.32051;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:7:460:2:60:-4.54703,0,-40.9042
+phiX174	1631	.	T	G	2.719	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=4.09604;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=0.138972;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=500;RO=8;RPL=0;RPP=7.35324;RPPR=3.0103;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:10:8:500:2:68:-5.10291,0,-44.2679
+phiX174	1772	.	T	G	2.16317	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=3.32051;GTI=0;LEN=1;MEANALT=2;MQM=31;MQMR=31.8571;NS=1;NUMALT=1;ODDS=0.437618;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=425;RO=7;RPL=1;RPP=3.0103;RPPR=3.32051;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=10.7656;SRR=6;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:10:7:425:2:59:-4.16703,0,-37.3833
+phiX174	1945	.	T	G	11.7103	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=2.62656;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=263;RO=4;RPL=1;RPP=3.0103;RPPR=5.18177;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.0103;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:263:2:59:-4.97491,0,-23.6974
+phiX174	2230	.	T	G	1.61813	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=35.5;NS=1;NUMALT=1;ODDS=0.795209;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=65;QR=491;RO=8;RPL=0;RPP=7.35324;RPPR=4.09604;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=4.09604;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:10:8:491:2:65:-4.81791,0,-43.4467
+phiX174	2699	.	C	A	31.6424	.	AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=7.28525;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=109;RO=2;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=7.35324;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:4:2:109:2:76:-6.79403,0,-9.92903
+phiX174	2722	.	T	G	21.5364	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=7.35324;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=4.95189;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=9.52472;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:150:2:67:-5.85985,0,-13.4949
+phiX174	2814	.	T	G	8.81714	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=33;NS=1;NUMALT=1;ODDS=1.88946;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=53;QR=135;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=9.52472;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:135:2:53:-4.52985,0,-12.0949
+phiX174	2828	.	T	G	37.7173	.	AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=31;NS=1;NUMALT=1;ODDS=8.68456;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=348;RO=6;RPL=0;RPP=7.35324;RPPR=4.45795;RPR=2;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:8:6:348:2:100:-8.53892,0,-30.9389
+phiX174	2983	.	T	G	12.2712	.	AB=0.4;ABP=3.44459;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.0103;EPPR=3.73412;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=33;NS=1;NUMALT=1;ODDS=2.76444;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=57;QR=150;RO=3;RPL=1;RPP=3.0103;RPPR=3.73412;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=2;SRP=3.73412;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:5:3:150:2:57:-4.90985,0,-13.4949
+phiX174	3110	.	T	C	34.4848	.	AB=0.333333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=3;CIGAR=1X;DP=9;DPB=9;DPRA=0;EPP=3.73412;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=35;NS=1;NUMALT=1;ODDS=7.94006;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=94;QR=361;RO=6;RPL=0;RPP=9.52472;RPPR=3.0103;RPR=3;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=1;SRP=8.80089;SRR=5;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:9:6:361:3:94:-7.98834,0,-32.3067
+phiX174	3155	.	T	G	23.5283	.	AB=0.285714;ABP=5.80219;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=3.0103;EPPR=3.44459;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=29.8;NS=1;NUMALT=1;ODDS=5.41314;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=75;QR=299;RO=5;RPL=1;RPP=3.0103;RPPR=3.44459;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=4;SRP=6.91895;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:7:5:299:2:75:-6.34001,0,-26.723
+phiX174	3325	.	A	C	5.77196	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=31;NS=1;NUMALT=1;ODDS=1.02152;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=58;QR=284;RO=4;RPL=2;RPP=7.35324;RPPR=3.0103;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:284:2:58:-4.87991,0,-25.6399
+phiX174	3418	.	A	C	0.61163	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=2;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=34;NS=1;NUMALT=1;ODDS=1.88894;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=60;QR=526;RO=8;RPL=2;RPP=7.35324;RPPR=4.09604;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=5;SRP=4.09604;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:10:8:526:2:60:-4.34291,0,-46.6404
+phiX174	3729	.	C	T	8.03017	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=37;NS=1;NUMALT=1;ODDS=1.67776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=61;QR=232;RO=4;RPL=2;RPP=7.35324;RPPR=5.18177;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=11.6962;SRR=4;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:232:2:61:-5.16491,0,-20.8299
+phiX174	4031	.	T	G	23.4861	.	AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=4.45795;GTI=0;LEN=1;MEANALT=1;MQM=31;MQMR=27;NS=1;NUMALT=1;ODDS=5.40338;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=85;QR=322;RO=6;RPL=2;RPP=7.35324;RPPR=8.80089;RPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=3;SRP=3.0103;SRR=3;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:8:6:322:2:85:-7.11392,0,-28.5556
+phiX174	4502	.	A	C	8.30185	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=1.75158;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=55;QR=284;RO=4;RPL=1;RPP=3.0103;RPPR=11.6962;RPR=1;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=3;SRP=5.18177;SRR=1;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:284:2:55:-4.59491,0,-25.6399
+phiX174	4558	.	C	G	6.48999	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=28;NS=1;NUMALT=1;ODDS=1.24027;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=59;QR=204;RO=4;RPL=2;RPP=7.35324;RPPR=11.6962;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=2;SRP=3.0103;SRR=2;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:204:2:59:-4.97491,0,-18.2399
+phiX174	4655	.	T	G	21.8853	.	AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=3.0103;EPPR=3.0103;GTI=0;LEN=1;MEANALT=1;MQM=25;MQMR=37;NS=1;NUMALT=1;ODDS=5.03277;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=193;RO=4;RPL=1;RPP=3.0103;RPPR=3.0103;RPR=1;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=11.6962;SRR=4;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/1:6:4:193:2:70:-6.01991,0,-17.2224
diff -r 14f952d2a9db -r 9f3d6c3098ac test-data/freebayes-phix174-test2.vcf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174-test2.vcf	Mon Nov 09 11:37:39 2015 -0500
@@ -0,0 +1,19 @@
+phiX174	1134	.	A	.	1.75185e-15	.	DP=14;DPB=14;EPPR=3.0103;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=916;RO=14;RPPR=8.59409	GT:DP:RO:QR:AO:QA:GL	0/0:14:14:916:.:.:0
+phiX174	1135	.	C	.	1.75538e-15	.	DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=957;RO=14;RPPR=5.49198	GT:DP:RO:QR:AO:QA:GL	0/0:14:14:957:.:.:0
+phiX174	1136	.	G	.	1.75185e-15	.	DP=14;DPB=14;EPPR=8.59409;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=919;RO=14;RPPR=3.0103	GT:DP:RO:QR:AO:QA:GL	0/0:14:14:919:.:.:0
+phiX174	1137	.	C	.	1.75349e-15	.	DP=14;DPB=14;EPPR=5.49198;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=14;RPPR=3.63072	GT:DP:RO:QR:AO:QA:GL	0/0:14:14:927:.:.:0
+phiX174	1138	.	C	.	1.75538e-15	.	DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=876;RO=14;RPPR=5.49198	GT:DP:RO:QR:AO:QA:GL	0/0:14:14:876:.:.:0
+phiX174	1139	.	G	.	1.75538e-15	.	DP=14;DPB=14;EPPR=3.63072;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=946;RO=14;RPPR=5.49198	GT:DP:RO:QR:AO:QA:GL	0/0:14:14:946:.:.:0
+phiX174	1140	.	T	.	6.10945e-16	.	DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=927;RO=15;RPPR=4.31318	GT:DP:RO:QR:AO:QA:GL	0/0:15:15:927:.:.:0
+phiX174	1141	.	T	G	0.000113755	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=3.63072;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=10.55;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=50;QR=880;RO=14;RPL=0;RPP=5.18177;RPPR=5.49198;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=5.49198;SRR=9;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:15:14:880:1:50:-1.66064,0,-76.4892
+phiX174	1142	.	G	.	0	.	DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1082;RO=16;RPPR=3.55317	GT:DP:RO:QR:AO:QA:GL	0/0:16:16:1082:.:.:0
+phiX174	1143	.	G	.	0	.	DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1029;RO=16;RPPR=3.55317	GT:DP:RO:QR:AO:QA:GL	0/0:16:16:1029:.:.:0
+phiX174	1144	.	C	.	0	.	DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1114;RO=16;RPPR=3.55317	GT:DP:RO:QR:AO:QA:GL	0/0:16:16:1114:.:.:0
+phiX174	1145	.	G	.	6.0859e-16	.	DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1042;RO=15;RPPR=3.15506	GT:DP:RO:QR:AO:QA:GL	0/0:15:15:1042:.:.:0
+phiX174	1146	.	C	.	6.0859e-16	.	DP=15;DPB=15;EPPR=6.62942;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1058;RO=15;RPPR=3.15506	GT:DP:RO:QR:AO:QA:GL	0/0:15:15:1058:.:.:0
+phiX174	1147	.	T	.	6.10945e-16	.	DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=999;RO=15;RPPR=4.31318	GT:DP:RO:QR:AO:QA:GL	0/0:15:15:999:.:.:0
+phiX174	1148	.	C	.	6.10945e-16	.	DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=1003;RO=15;RPPR=4.31318	GT:DP:RO:QR:AO:QA:GL	0/0:15:15:1003:.:.:0
+phiX174	1149	.	T	C	7.90879e-06	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=5.18177;EPPR=3.17734;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=13.2161;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=33;QR=830;RO=13;RPL=0;RPP=5.18177;RPPR=7.18621;RPR=1;RUN=1;SAF=0;SAP=5.18177;SAR=1;SRF=5;SRP=4.51363;SRR=8;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:14:13:830:1:33:-0.231708,0,-72.2702
+phiX174	1151	.	C	T	5.70134e-07	.	AB=0;ABP=0;AC=0;AF=0;AN=2;AO=1;CIGAR=1X;DP=15;DPB=15;DPRA=0;EPP=5.18177;EPPR=8.59409;GTI=0;LEN=1;MEANALT=1;MQM=37;MQMR=37;NS=1;NUMALT=1;ODDS=15.8459;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=27;QR=946;RO=14;RPL=1;RPP=5.18177;RPPR=3.0103;RPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=0;SRF=3;SRP=12.937;SRR=11;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	0/0:15:14:946:1:27:0,-0.639359,-83.1157
+phiX174	1152	.	G	.	0	.	DP=16;DPB=16;EPPR=5.18177;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=993;RO=16;RPPR=5.18177	GT:DP:RO:QR:AO:QA:GL	0/0:16:16:993:.:.:0
+phiX174	1153	.	T	.	0	.	DP=15;DPB=15;EPPR=4.31318;GTI=0;MQMR=37;NS=1;NUMALT=0;ODDS=0;PAIREDR=0;PQR=0;PRO=0;QR=880;RO=15;RPPR=4.31318	GT:DP:RO:QR:AO:QA:GL	0/0:15:15:880:.:.:0
diff -r 14f952d2a9db -r 9f3d6c3098ac tool-data/tool_data_table_conf.xml.sample
--- a/tool-data/tool_data_table_conf.xml.sample	Thu Dec 11 18:38:34 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
-<tables>
-    <!-- Location of SAMTools indexes for FASTA files -->
-    <table name="fasta_indexes" comment_char="#">
-        <columns>value, dbkey, name, path</columns>
-        <file path="tool-data/fasta_indexes.loc" />
-    </table>
-</tables>
diff -r 14f952d2a9db -r 9f3d6c3098ac tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Mon Nov 09 11:37:39 2015 -0500
@@ -0,0 +1,8 @@
+<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc-->
+<tables>
+    <!-- Location of SAMTools indexes for FASTA files -->
+    <table name="fasta_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/fasta_indexes.loc" />
+    </table>
+</tables>
diff -r 14f952d2a9db -r 9f3d6c3098ac tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Dec 11 18:38:34 2014 -0500
+++ b/tool_dependencies.xml	Mon Nov 09 11:37:39 2015 -0500
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="freebayes" version="0.9.18_0059bdf">
-        <repository changeset_revision="0873b583229a" name="package_freebayes_0_9_18_0059bdf" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="freebayes" version="0_9_20_b040236">
+        <repository changeset_revision="4fe037b74be9" name="package_freebayes_0_9_20_b040236" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="samtools" version="0.1.18">
         <repository changeset_revision="c0f72bdba484" name="package_samtools_0_1_18" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />