changeset 12:aaf568580946 draft

Uploaded
author devteam
date Fri, 20 Jun 2014 17:16:05 -0400
parents e9ebed0c12f6
children 2dd40b601766
files freebayes.xml sam_fa_indices.loc.sample test-data/fake_phiX_reads_1.bam test-data/freebayes-phix174-test1.vcf test-data/freebayes-phix174.bam test-data/freebayes-phix174.fasta test-data/freebayes_out_1.output_trace test-data/freebayes_out_1.vcf.contains test-data/phiX.fasta tool-data/sam_fa_indices.loc.sample tool-data/tool_data_table_conf.xml.sample tool_data_table_conf.xml.sample tool_dependencies.xml
diffstat 13 files changed, 65 insertions(+), 814 deletions(-) [+]
line wrap: on
line diff
--- a/freebayes.xml	Mon Feb 17 10:53:56 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,680 +0,0 @@
-<?xml version="1.0"?>
-<tool id="freebayes" name="FreeBayes" version="0.0.3">
-  <requirements>
-    <requirement type="package" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">freebayes</requirement>
-    <requirement type="package" version="0.1.18">samtools</requirement>
-  </requirements>
-  <description> - Bayesian genetic variant detector</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 FreeBayes" &gt;&amp;2 &amp;&amp;
-    #else:
-        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
-    #end if
-    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
-        ln -s "${input_bam.input_bam}" "localbam_${bam_count}.bam" &amp;&amp;
-        ln -s "${input_bam.input_bam.metadata.bam_index}" "localbam_${bam_count}.bam.bai" &amp;&amp;
-    #end for
-    ##finished setting up inputs
-    
-    ##start FreeBayes commandline
-    freebayes
-    #for $bam_count, $input_bam in enumerate( $reference_source.input_bams ):
-        --bam "localbam_${bam_count}.bam"
-    #end for
-    --fasta-reference "${reference_fasta_filename}" 
-    
-    ##outputs
-    --vcf "${output_vcf}"
-    
-    ##advanced options
-    #if str( $options_type.options_type_selector ) == "advanced":
-        ##additional outputs
-        #if $options_type.output_trace_option:
-            --trace "${output_trace}"
-        #end if
-        #if $options_type.output_failed_alleles_option:
-            --failed-alleles "${output_failed_alleles_bed}"
-        #end if
-        
-        ##additional inputs
-        #if str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_target_file":
-            --targets "${options_type.target_limit_type.input_target_bed}"
-        #elif str( $options_type.target_limit_type.target_limit_type_selector ) == "limit_by_region":
-            --region "${options_type.target_limit_type.region_chromosome}:${options_type.target_limit_type.region_start}..${options_type.target_limit_type.region_end}"
-        #end if
-        #if $options_type.input_sample_file:
-            --samples "${options_type.input_sample_file}"
-        #end if
-        #if $options_type.input_populations_file:
-            --populations "${options_type.input_populations_file}"
-        #end if
-        #if $options_type.input_cnv_map_bed:
-            --cnv-map "${options_type.input_cnv_map_bed}"
-        #end if
-        #if str( $options_type.input_variant_type.input_variant_type_selector ) == "provide_vcf":
-            --variant-input "${options_type.input_variant_type.input_variant_vcf}"
-            ${options_type.input_variant_type.only_use_input_alleles}
-        #end if
-        #if $options_type.haplotype_basis_alleles:
-            --haplotype-basis-alleles "${options_type.haplotype_basis_alleles}"
-        #end if
-        
-        
-        ##reporting
-        #if str( $options_type.section_reporting_type.section_reporting_type_selector ) == "set":
-            --pvar "${options_type.section_reporting_type.pvar}"
-            ${options_type.section_reporting_type.show_reference_repeats}
-        #end if
-        
-        ##population model
-        #if str( $options_type.section_population_model_type.section_population_model_type_selector ) == "set":
-            --theta "${options_type.section_population_model_type.theta}"
-            --ploidy "${options_type.section_population_model_type.ploidy}"
-            ${options_type.section_population_model_type.pooled}
-        #end if
-        
-        ##reference allele
-        #if str( $options_type.use_reference_allele_type.use_reference_allele_type_selector ) == "include_reference_allele":
-            --use-reference-allele
-            ${options_type.use_reference_allele_type.diploid_reference}
-            --reference-quality "${options_type.use_reference_allele_type.reference_quality_mq},${options_type.use_reference_allele_type.reference_quality_bq}"
-        #end if
-        
-        ##allele scope
-        #if str( $options_type.section_allele_scope_type.section_allele_scope_type_selector ) == "set":
-            ${options_type.section_allele_scope_type.no_snps}
-            ${options_type.section_allele_scope_type.no_indels}
-            ${options_type.section_allele_scope_type.no_mnps}
-            ${options_type.section_allele_scope_type.no_complex}
-            --use-best-n-alleles "${options_type.section_allele_scope_type.use_best_n_alleles}"
-            #if $options_type.section_allele_scope_type.max_complex_gap:
-                --max-complex-gap "${options_type.section_allele_scope_type.max_complex_gap}"
-            #end if
-        #end if
-        
-        ##indel realignment
-        ${options_type.left_align_indels}
-        
-        ##input filters
-        #if str( $options_type.section_input_filters_type.section_input_filters_type_selector ) == "set":
-            ${options_type.section_input_filters_type.use_duplicate_reads}
-            #if str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "apply_filters":
-                --min-mapping-quality "${options_type.section_input_filters_type.quality_filter_type.min_mapping_quality}"
-                --min-base-quality "${options_type.section_input_filters_type.quality_filter_type.min_base_quality}"
-                --min-supporting-quality "${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_mq},${options_type.section_input_filters_type.quality_filter_type.min_supporting_quality_bq}"
-            #elif str( $options_type.section_input_filters_type.quality_filter_type.quality_filter_type_selector ) == "standard_filters":
-                --standard-filters
-            #end if
-            --mismatch-base-quality-threshold "${options_type.section_input_filters_type.mismatch_base_quality_threshold}"
-            #if $options_type.section_input_filters_type.read_mismatch_limit:
-                --read-mismatch-limit "${options_type.section_input_filters_type.read_mismatch_limit}"
-            #end if
-            --read-max-mismatch-fraction "${options_type.section_input_filters_type.read_max_mismatch_fraction}"
-            #if $options_type.section_input_filters_type.read_snp_limit:
-                --read-snp-limit "${options_type.section_input_filters_type.read_snp_limit}"
-            #end if
-            #if $options_type.section_input_filters_type.read_indel_limit:
-                --read-indel-limit "${options_type.section_input_filters_type.read_indel_limit}"
-            #end if
-            --indel-exclusion-window "${options_type.section_input_filters_type.indel_exclusion_window}"
-            --min-alternate-fraction "${options_type.section_input_filters_type.min_alternate_fraction}"
-            --min-alternate-count "${options_type.section_input_filters_type.min_alternate_count}"
-            --min-alternate-qsum "${options_type.section_input_filters_type.min_alternate_qsum}"
-            --min-alternate-total "${options_type.section_input_filters_type.min_alternate_total}"
-            --min-coverage "${options_type.section_input_filters_type.min_coverage}"
-        #end if
-        
-        ##bayesian priors
-        #if str( $options_type.section_bayesian_priors_type.section_bayesian_priors_type_selector ) == "set":
-            ${options_type.section_bayesian_priors_type.no_ewens_priors}
-            ${options_type.section_bayesian_priors_type.no_population_priors}
-            ${options_type.section_bayesian_priors_type.hwe_priors}
-        #end if
-        
-        ##observation prior expectations
-        #if str( $options_type.section_observation_prior_expectations_type.section_observation_prior_expectations_type_selector ) == "set":
-            ${options_type.section_observation_prior_expectations_type.binomial_obs_priors}
-            ${options_type.section_observation_prior_expectations_type.allele_balance_priors}
-        #end if
-        
-        ##algorithmic features
-        #if str( $options_type.section_algorithmic_features_type.section_algorithmic_features_type_selector ) == "set":
-            --site-selection-max-iterations "${options_type.section_algorithmic_features_type.site_selection_max_iterations}"
-            --genotyping-max-iterations "${options_type.section_algorithmic_features_type.genotyping_max_iterations}"
-            --genotyping-max-banddepth "${options_type.section_algorithmic_features_type.genotyping_max_banddepth}"
-            --posterior-integration-limits "${options_type.section_algorithmic_features_type.posterior_integration_limits_n},${options_type.section_algorithmic_features_type.posterior_integration_limits_m}"
-            ${options_type.section_algorithmic_features_type.no_permute}
-            ${options_type.section_algorithmic_features_type.exclude_unobserved_genotypes}
-            #if $options_type.section_algorithmic_features_type.genotype_variant_threshold:
-                --genotype-variant-threshold "${options_type.section_algorithmic_features_type.genotype_variant_threshold}"
-            #end if
-            ${options_type.section_algorithmic_features_type.use_mapping_quality}
-            --read-dependence-factor "${options_type.section_algorithmic_features_type.read_dependence_factor}"
-            ${options_type.section_algorithmic_features_type.no_marginals}
-        #end if
-    #end if
-  </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">
-        <repeat name="input_bams" title="Sample BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file">
-              <validator type="unspecified_build" />
-              <validator type="dataset_metadata_in_data_table" table_name="sam_fa_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
-            </param>
-        </repeat>
-        <param name="ref_file" type="select" label="Using reference genome">
-          <options from_data_table="sam_fa_indexes">
-            <!-- <filter type="sam_fa_indexes" key="dbkey" ref="input_bam" column="value"/> does not yet work in a repeat...--> 
-          </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"> <!-- FIX ME!!!! -->
-        <repeat name="input_bams" title="Sample BAM file" min="1">
-            <param name="input_bam" type="data" format="bam" label="BAM file" />
-        </repeat>
-        <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-      </when>
-    </conditional>
-    
-    <conditional name="options_type">
-      <param name="options_type_selector" type="select" label="Basic or Advanced options">
-        <option value="basic" selected="True">Basic</option>
-        <option value="advanced">Advanced</option>
-      </param>
-      <when value="basic">
-        <!-- Do nothing here -->
-      </when>
-      <when value="advanced">
-        
-        <!-- output -->
-        <param name="output_failed_alleles_option" type="boolean" truevalue="--failed-alleles" falsevalue="" checked="False" label="Write out failed alleles file" />
-        <param name="output_trace_option" type="boolean" truevalue="--trace" falsevalue="" checked="False" label="Write out algorithm trace file" />
-        
-        
-        <!-- input -->
-        <conditional name="target_limit_type">
-          <param name="target_limit_type_selector" type="select" label="Limit analysis to listed targets">
-            <option value="do_not_limit" selected="True">Do not limit</option>
-            <option value="limit_by_target_file">Limit by target file</option>
-            <option value="limit_by_region">Limit to region</option>
-          </param>
-          <when value="do_not_limit">
-            <!-- Do nothing here -->
-          </when>
-          <when value="limit_by_target_file">
-            <param name="input_target_bed" type="data" format="bed" label="Limit analysis to targets listed in the BED-format FILE." />
-          </when>
-          <when value="limit_by_region">
-            <param name="region_chromosome" type="text" label="Region Chromosome" value="" /> <!--only once? -->
-            <param name="region_start" type="integer" label="Region Start" value="" />
-            <param name="region_end" type="integer" label="Region End" value="" />
-          </when>
-        </conditional>
-        <param name="input_sample_file" type="data" format="txt" label="Limit analysis to samples listed (one per line) in the FILE" optional="True" />
-        <param name="input_populations_file" type="data" format="txt" label="Populations File" optional="True" />
-        <param name="input_cnv_map_bed" type="data" format="bed" label="Read a copy number map from the BED file FILE" optional="True" />
-        <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" label="Use variants reported in VCF file as input to the algorithm" />
-            <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" />
-        
-        <!-- reporting -->
-        <conditional name="section_reporting_type">
-          <param name="section_reporting_type_selector" type="select" label="Set Reporting options">
-            <option value="do_not_set" selected="True">Do not set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="do_not_set">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="pvar" type="float" label="Report sites if the probability that there is a polymorphism at the site is greater" value="0.0001" />
-            <param name="show_reference_repeats" type="boolean" truevalue="--show-reference-repeats" falsevalue="" checked="False" label="Calculate and show information about reference repeats" />
-          </when>
-        </conditional>
-        
-        
-        <!-- population model -->
-        <conditional name="section_population_model_type">
-          <param name="section_population_model_type_selector" type="select" label="Set population model options">
-            <option value="do_not_set" selected="True">Do not set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="do_not_set">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="theta" type="float" label="expected mutation rate or pairwise nucleotide diversity among the population" value="0.001" help="This serves as the single parameter to the Ewens Sampling Formula prior model"/>
-            <param name="ploidy" type="integer" label="default ploidy for the analysis" value="2" />
-            <param name="pooled" type="boolean" truevalue="--pooled" falsevalue="" checked="False" label="Assume that samples result from pooled sequencing" help="When using this flag, set --ploidy to the number of alleles in each sample." />
-          </when>
-        </conditional>
-        
-        <!-- reference allele -->
-            <conditional name="use_reference_allele_type">
-              <param name="use_reference_allele_type_selector" type="select" label="Include the reference allele in the analysis">
-                <option value="do_not_include_reference_allele" selected="True">Do not include</option>
-                <option value="include_reference_allele">Include</option>
-              </param>
-              <when value="do_not_include_reference_allele">
-                <!-- Do nothing here -->
-              </when>
-              <when value="include_reference_allele">
-                <param name="diploid_reference" type="boolean" truevalue="--diploid-reference" falsevalue="" checked="False" label="Treat reference as diploid" />
-                <param name="reference_quality_mq" type="integer" label="Assign mapping quality" value="100" />
-                <param name="reference_quality_bq" type="integer" label="Assign base quality" value="60" />
-              </when>
-            </conditional>     
-        
-        <!-- allele scope -->
-        <conditional name="section_allele_scope_type">
-          <param name="section_allele_scope_type_selector" type="select" label="Set allele scope options">
-            <option value="do_not_set" selected="True">Do not set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="do_not_set">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="no_snps" type="boolean" truevalue="--no-snps" falsevalue="" checked="False" label="Ignore SNP alleles" />
-            <param name="no_indels" type="boolean" truevalue="--no-indels" falsevalue="" checked="False" label="Ignore insertion and deletion alleles" />
-            <param name="no_mnps" type="boolean" truevalue="--no-mnps" falsevalue="" checked="False" label="Ignore multi-nuceotide polymorphisms, MNPs" />
-            <param name="no_complex" type="boolean" truevalue="--no-complex" falsevalue="" checked="False" label="Ignore complex events (composites of other classes)" />
-            <param name="use_best_n_alleles" type="integer" label="Evaluate only the best N SNP alleles" value="0" min="0" help="Ranked by sum of supporting quality scores; Set to 0 to use all" />
-            <param name="max_complex_gap" type="integer" label="Allow complex alleles with contiguous embedded matches of up to this length" value="" optional="True"/>
-          </when>
-        </conditional>
-        
-        <!-- indel realignment -->
-        <!-- in FreeBayes < 0.9.9 the default is to not left-align indels and the available option is - -left-align-indels,
-             in FreeBayes >= 0.9.9 the default is to left-align indels and the available option is - -dont-left-align-indels -->
-        <param name="left_align_indels" type="boolean" truevalue="--left-align-indels" falsevalue="" checked="False" label="Left align indels" />
-        
-        <!-- input filters -->
-        <conditional name="section_input_filters_type">
-          <param name="section_input_filters_type_selector" type="select" label="Set input filters options">
-            <option value="do_not_set" selected="True">Do not set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="do_not_set">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="use_duplicate_reads" type="boolean" truevalue="--use-duplicate-reads" falsevalue="" checked="False" label="Include duplicate-marked alignments in the analysis" />
-            <conditional name="quality_filter_type">
-              <param name="quality_filter_type_selector" type="select" label="Apply Quality filters">
-                <option value="standard_filters" selected="True">Apply standard</option>
-                <option value="apply_filters">Apply specified</option>
-              </param>
-              <when value="standard_filters">
-                <!-- Do nothing here --> <!-- standard-filters -->
-              </when>
-              <when value="apply_filters">
-                <param name="min_mapping_quality" type="integer" label="Exclude alignments from analysis if they have a mapping quality less than" value="0" />
-                <param name="min_base_quality" type="integer" label="Exclude alleles from analysis if their supporting base quality less than" value="0" />
-                <param name="min_supporting_quality_mq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have mapping quality" value="0" />
-                <param name="min_supporting_quality_bq" type="integer" label="In order to consider an alternate allele, at least one supporting alignment must have base quality" value="0" />
-              </when>
-            </conditional>
-            <param name="mismatch_base_quality_threshold" type="integer" label="Count mismatches toward read-mismatch-limit if the base quality of the mismatch is &gt;=" value="10" />
-            <param name="read_mismatch_limit" type="integer" label="Exclude reads with more than N mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold" value="" optional="True" />
-            <param name="read_max_mismatch_fraction" type="float" label="Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality &gt;= mismatch-base-quality-threshold" value="1.0" />
-            <param name="read_snp_limit" type="integer" label="Exclude reads with more than N base mismatches, ignoring gaps with quality &gt;= mismatch-base-quality-threshold" value="" optional="True" />
-            <param name="read_indel_limit" type="integer" label="Exclude reads with more than N separate gaps" value="" optional="True" />
-            <param name="indel_exclusion_window" type="integer" label="Ignore portions of alignments this many bases from a putative insertion or deletion allele" value="0" />
-            <param name="min_alternate_fraction" type="float" label="Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position" value="0" />
-            <param name="min_alternate_count" type="integer" label="Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position" value="1" />
-            <param name="min_alternate_qsum" type="integer" label="Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position" value="0" />
-            <param name="min_alternate_total" type="integer" label="Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis" value="1" />
-            <param name="min_coverage" type="integer" label="Require at least this coverage to process a site" value="0" />
-          </when>
-        </conditional>
-        
-        
-        <!-- bayesian priors -->
-        <conditional name="section_bayesian_priors_type">
-          <param name="section_bayesian_priors_type_selector" type="select" label="Set bayesian priors options">
-            <option value="do_not_set" selected="True">Do not set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="do_not_set">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="no_ewens_priors" type="boolean" truevalue="--no-ewens-priors" falsevalue="" checked="False" label="Turns off the Ewens' Sampling Formula component of the priors" />
-            <param name="no_population_priors" type="boolean" truevalue="--no-population-priors" falsevalue="" checked="False" label="No population priors" help="Equivalent to --pooled --no-ewens-priors" />
-            <param name="hwe_priors" type="boolean" truevalue="--hwe-priors" falsevalue="" checked="False" label="Use the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency" />
-          </when>
-        </conditional>
-        
-        <!-- observation prior expectations -->
-        <conditional name="section_observation_prior_expectations_type">
-          <param name="section_observation_prior_expectations_type_selector" type="select" label="Set observation prior expectations options">
-            <option value="do_not_set" selected="True">Do not set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="do_not_set">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="binomial_obs_priors" type="boolean" truevalue="--binomial-obs-priors" falsevalue="" checked="False" label="Incorporate expectations about osbervations into the priors, Uses read placement probability, strand balance probability, and read position (5'-3') probability" />
-            <param name="allele_balance_priors" type="boolean" truevalue="--allele-balance-priors" falsevalue="" checked="False" label="Use aggregate probability of observation balance between alleles as a component of the priors.  Best for observations with minimal inherent reference bias" />
-          </when>
-        </conditional>
-        
-        
-        <!-- algorithmic features -->
-        <conditional name="section_algorithmic_features_type">
-          <param name="section_algorithmic_features_type_selector" type="select" label="Set algorithmic features options">
-            <option value="do_not_set" selected="True">Do not set</option>
-            <option value="set">Set</option>
-          </param>
-          <when value="do_not_set">
-            <!-- do nothing here -->
-          </when>
-          <when value="set">
-            <param name="site_selection_max_iterations" type="integer" label="Uses hill-climbing algorithm to search posterior space for N iterations to determine if the site should be evaluated." value="5" help="Set to 0 to prevent use of this algorithm for site selection, and to a low integer for improvide site selection at a slight performance penalty" />
-            <param name="genotyping_max_iterations" type="integer" label="Iterate no more than N times during genotyping step" value="25" />
-            <param name="genotyping_max_banddepth" type="integer" label="Integrate no deeper than the Nth best genotype by likelihood when genotyping" value="6" />
-            <param name="posterior_integration_limits_n" type="integer" label="Posteriror integration limit N" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="1" />
-            <param name="posterior_integration_limits_m" type="integer" label="Posteriror integration limit M" help="Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood." value="3" />
-            <param name="no_permute" type="boolean" truevalue="--no-permute" falsevalue="" checked="False" label="Do not scale prior probability of genotype combination given allele frequency by the number of permutations of included genotypes" />
-            <param name="exclude_unobserved_genotypes" type="boolean" truevalue="--exclude-unobserved-genotypes" falsevalue="" checked="False" label="Skip sample genotypings for which the sample has no supporting reads" />
-            <param name="genotype_variant_threshold" type="integer" label="Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample" value="" optional="True" />
-            <param name="use_mapping_quality" type="boolean" truevalue="--use-mapping-quality" falsevalue="" checked="False" label="Use mapping quality of alleles when calculating data likelihoods" />
-            <param name="read_dependence_factor" type="float" label="Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations" value="0.9" />
-            <param name="no_marginals" type="boolean" truevalue="--no-marginals" falsevalue="" checked="False" label="Do not calculate the marginal probability of genotypes.  Saves time and improves scaling performance in large populations" />
-          </when>
-        </conditional>
-        
-        
-      </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 ${on_string} (failed alleles)">
-        <filter>options_type['options_type_selector'] == "advanced" and options_type['output_failed_alleles_option'] is True</filter>
-    </data>
-    <data format="txt" name="output_trace" label="${tool.name} on ${on_string} (trace)">
-        <filter>options_type['options_type_selector'] == "advanced" and options_type['output_trace_option'] is True</filter>
-    </data>
-  </outputs>
-  <tests>
-    <test>
-     <param name="reference_source_selector" value="history" />
-      <param name="ref_file" ftype="fasta" value="phiX.fasta"/>
-      <param name="input_bam" ftype="bam" value="fake_phiX_reads_1.bam"/>
-      <param name="options_type_selector" value="basic"/>
-      <output name="output_vcf" file="freebayes_out_1.vcf.contains" compare="contains"/>
-    </test>
-  </tests>
-  <stdio>
-    <exit_code range="1:" />
-  </stdio>
-  <help>
-**What it does**
-
-This tool uses FreeBayes to call SNPS given a reference sequence and a BAM alignment file.
-
-FreeBayes is a high-performance, flexible, and open-source Bayesian genetic variant detector. It operates on BAM alignment files, which are produced by most contemporary short-read aligners.
-
-In addition to substantial performance improvements over its predecessors (PolyBayes, GigaBayes, and BamBayes), it expands the scope of SNP and small-indel variant calling to populations of individuals with heterogeneous copy number. FreeBayes is currently under active development. 
-
-Go `here &lt;http://bioinformatics.bc.edu/marthlab/FreeBayes&gt;`_ for details on FreeBayes.
-
-------
-
-**Inputs**
-
-FreeBayes accepts an input aligned BAM file.
-
-
-**Outputs**
-
-The output is in the VCF format.
-
--------
-
-**Settings**::
-
-  input and output:
-
-   -b --bam FILE   Add FILE to the set of BAM files to be analyzed.
-   -c --stdin      Read BAM input on stdin.
-   -v --vcf FILE   Output VCF-format results to FILE.
-   -f --fasta-reference FILE
-                   Use FILE as the reference sequence for analysis.
-                   An index file (FILE.fai) will be created if none exists.
-                   If neither --targets nor --region are specified, FreeBayes
-                   will analyze every position in this reference.
-   -t --targets FILE
-                   Limit analysis to targets listed in the BED-format FILE.
-   -r --region &lt;chrom&gt;:&lt;start_position&gt;..&lt;end_position&gt;
-                   Limit analysis to the specified region, 0-base coordinates,
-                   end_position not included (same as BED format).
-   -s --samples FILE
-                   Limit analysis to samples listed (one per line) in the FILE.
-                   By default FreeBayes will analyze all samples in its input
-                   BAM files.
-   --populations FILE
-                   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.
-   -A --cnv-map FILE
-                   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.
-   -L --trace FILE  Output an algorithmic trace to FILE.
-   --failed-alleles FILE
-                   Write a BED file of the analyzed positions which do not
-                   pass --pvar to FILE.
-   -@ --variant-input VCF
-                   Use variants reported in VCF file as input to the algorithm.
-                   A report will be generated for every record in the VCF file.
-   -l --only-use-input-alleles
-                   Only provide variant calls and genotype likelihoods for sites
-                   and alleles which are provided in the VCF input, and provide
-                   output in the VCF for all input alleles, not just those which
-                   have support in the data.
-   --haplotype-basis-alleles VCF
-                   When specified, only variant alleles provided in this input
-                   VCF will be used for the construction of complex or haplotype
-                   alleles.
-
-  reporting:
-
-   -P --pvar N     Report sites if the probability that there is a polymorphism
-                   at the site is greater than N.  default: 0.0001
-   -_ --show-reference-repeats
-                   Calculate and show information about reference repeats in
-                   the VCF output.
-
-  population model:
-
-   -T --theta N    The expected mutation rate or pairwise nucleotide diversity
-                   among the population under analysis.  This serves as the
-                   single parameter to the Ewens Sampling Formula prior model
-                   default: 0.001
-   -p --ploidy N   Sets the default ploidy for the analysis to N.  default: 2
-   -J --pooled     Assume that samples result from pooled sequencing.
-                   When using this flag, set --ploidy to the number of
-                   alleles in each sample.
-
-  reference allele:
-
-   -Z --use-reference-allele
-                   This flag includes the reference allele in the analysis as
-                   if it is another sample from the same population.
-   -H --diploid-reference
-                   If using the reference sequence as a sample (-Z),
-                   treat it as diploid.  default: false (reference is haploid)
-   --reference-quality MQ,BQ
-                   Assign mapping quality of MQ to the reference allele at each
-                   site and base quality of BQ.  default: 100,60
-
-  allele scope:
-
-   -I --no-snps    Ignore SNP alleles.
-   -i --no-indels  Ignore insertion and deletion alleles.
-   -X --no-mnps    Ignore multi-nuceotide polymorphisms, MNPs.
-   -u --no-complex Ignore complex events (composites of other classes).
-   -n --use-best-n-alleles N
-                   Evaluate only the best N SNP alleles, ranked by sum of
-                   supporting quality scores.  (Set to 0 to use all; default: all)
-   -E --max-complex-gap N
-                   Allow complex alleles with contiguous embedded matches of up
-                   to this length.
-
-  indel realignment:
-
-   -O --left-align-indels
-                   Left-realign and merge gaps embedded in reads. default: false
-
-  input filters:
-
-   -4 --use-duplicate-reads
-                   Include duplicate-marked alignments in the analysis.
-                   default: exclude duplicates
-   -m --min-mapping-quality Q
-                   Exclude alignments from analysis if they have a mapping
-                   quality less than Q.  default: 30
-   -q --min-base-quality Q
-                   Exclude alleles from analysis if their supporting base
-                   quality is less than Q.  default: 20
-   -R --min-supporting-quality MQ,BQ
-                   In order to consider an alternate allele, at least one supporting
-                   alignment must have mapping quality MQ, and one supporting 
-                   allele must have base quality BQ. default: 0,0, unset
-   -Q --mismatch-base-quality-threshold Q
-                   Count mismatches toward --read-mismatch-limit if the base
-                   quality of the mismatch is &gt;= Q.  default: 10
-   -U --read-mismatch-limit N
-                   Exclude reads with more than N mismatches where each mismatch
-                   has base quality &gt;= mismatch-base-quality-threshold.
-                   default: ~unbounded
-   -z --read-max-mismatch-fraction N
-                   Exclude reads with more than N [0,1] fraction of mismatches where
-                   each mismatch has base quality &gt;= mismatch-base-quality-threshold
-                   default: 1.0
-   -$ --read-snp-limit N
-                   Exclude reads with more than N base mismatches, ignoring gaps
-                   with quality &gt;= mismatch-base-quality-threshold.
-                   default: ~unbounded
-   -e --read-indel-limit N
-                   Exclude reads with more than N separate gaps.
-                   default: ~unbounded
-   -0 --standard-filters  Use stringent input base and mapping quality filters
-                   Equivalent to -m 30 -q 20 -R 0 -S 0
-   -x --indel-exclusion-window
-                   Ignore portions of alignments this many bases from a
-                   putative insertion or deletion allele.  default: 0
-   -F --min-alternate-fraction N
-                   Require at least this fraction of observations supporting
-                   an alternate allele within a single individual in the
-                   in order to evaluate the position.  default: 0.0
-   -C --min-alternate-count N
-                   Require at least this count of observations supporting
-                   an alternate allele within a single individual in order
-                   to evaluate the position.  default: 1
-   -3 --min-alternate-qsum N
-                   Require at least this sum of quality of observations supporting
-                   an alternate allele within a single individual in order
-                   to evaluate the position.  default: 0
-   -G --min-alternate-total N
-                   Require at least this count of observations supporting
-                   an alternate allele within the total population in order
-                   to use the allele in analysis.  default: 1
-   -! --min-coverage N
-                   Require at least this coverage to process a site.  default: 0
-
-  bayesian priors:
-
-   -Y --no-ewens-priors
-                   Turns off the Ewens' Sampling Formula component of the priors.
-   -k --no-population-priors
-                   Equivalent to --pooled --no-ewens-priors
-   -w --hwe-priors Use the probability of the combination arising under HWE given
-                   the allele frequency as estimated by observation frequency.
-
-  observation prior expectations:
-
-   -V --binomial-obs-priors
-                   Incorporate expectations about osbervations into the priors,
-                   Uses read placement probability, strand balance probability,
-                   and read position (5'-3') probability.
-   -a --allele-balance-priors
-                   Use aggregate probability of observation balance between alleles
-                   as a component of the priors.  Best for observations with minimal
-                   inherent reference bias.
-
-  algorithmic features:
-
-   -M --site-selection-max-iterations N
-                   Uses hill-climbing algorithm to search posterior space for N
-                   iterations to determine if the site should be evaluated.  Set to 0
-                   to prevent use of this algorithm for site selection, and
-                   to a low integer for improvide site selection at a slight
-                   performance penalty. default: 5.
-   -B --genotyping-max-iterations N
-                   Iterate no more than N times during genotyping step. default: 25.
-   --genotyping-max-banddepth N
-                   Integrate no deeper than the Nth best genotype by likelihood when
-                   genotyping. default: 6.
-   -W --posterior-integration-limits N,M
-                   Integrate all genotype combinations in our posterior space
-                   which include no more than N samples with their Mth best
-                   data likelihood. default: 1,3.
-   -K --no-permute
-                   Do not scale prior probability of genotype combination given allele
-                   frequency by the number of permutations of included genotypes.
-   -N --exclude-unobserved-genotypes
-                   Skip sample genotypings for which the sample has no supporting reads.
-   -S --genotype-variant-threshold N
-                   Limit posterior integration to samples where the second-best
-                   genotype likelihood is no more than log(N) from the highest
-                   genotype likelihood for the sample.  default: ~unbounded
-   -j --use-mapping-quality
-                   Use mapping quality of alleles when calculating data likelihoods.
-   -D --read-dependence-factor N
-                   Incorporate non-independence of reads by scaling successive
-                   observations by this factor during data likelihood
-                   calculations.  default: 0.9
-   -= --no-marginals
-                   Do not calculate the marginal probability of genotypes.  Saves
-                   time and improves scaling performance in large populations.
-
-
-------
-
-**Citation**
-
-For the underlying tool, please cite `Erik Garrison and Gabor Marth. Haplotype-based variant detection from short-read sequencing &lt;http://arxiv.org/abs/1207.3907&gt;`_.
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-  </help>
-</tool>
--- a/sam_fa_indices.loc.sample	Mon Feb 17 10:53:56 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of Samtools indexed sequences data files.  You will need
-#to create these data files and then create a sam_fa_indices.loc file 
-#similar to this one (store it in this directory) that points to 
-#the directories in which those files are stored. The sam_fa_indices.loc 
-#file has this format (white space characters are TAB characters):
-#
-#index	<seq>	<location>
-#
-#So, for example, if you had hg18 indexed stored in 
-#/depot/data2/galaxy/sam/, 
-#then the sam_fa_indices.loc entry would look like this:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#
-#and your /depot/data2/galaxy/sam/ directory
-#would contain hg18.fa and hg18.fa.fai files:
-#
-#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
-#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
-#
-#Your sam_fa_indices.loc file should include an entry per line for 
-#each index set you have stored.  The file in the path does actually
-#exist, but it should never be directly used. Instead, the name serves
-#as a prefix for the index file.  For example:
-#
-#index	hg18	/depot/data2/galaxy/sam/hg18.fa
-#index	hg19	/depot/data2/galaxy/sam/hg19.fa
Binary file test-data/fake_phiX_reads_1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174-test1.vcf	Fri Jun 20 17:16:05 2014 -0400
@@ -0,0 +1,27 @@
+#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
Binary file test-data/freebayes-phix174.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freebayes-phix174.fasta	Fri Jun 20 17:16:05 2014 -0400
@@ -0,0 +1,2 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTTCGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCGTCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTACGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCaGAAGGAGTGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTTGGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCgTGATGTTATTTCTTCATTTGGAGGTAAAACCTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGCTTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGCCTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGCCGGGCAATAAtGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGTTTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCTGGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGAGATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACCAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTATGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCAAACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTTCTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTTCTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGCATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATGTTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGAATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGGGACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTaCTATTCAGCGTTTGATGAATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCGCAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCAtTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAGCCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATATGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTGTCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGCAGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACCTGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
--- a/test-data/freebayes_out_1.output_trace	Mon Feb 17 10:53:56 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-phiX174,1411,allele,phiX174,phiX174,A,60,100
-phiX174,1412,allele,phiX174,phiX174,G,60,100
-phiX174,1413,allele,phiX174,phiX174,C,60,100
-phiX174,1414,allele,phiX174,phiX174,G,60,100
-phiX174,1415,allele,phiX174,phiX174,C,60,100
-phiX174,1416,allele,phiX174,phiX174,C,60,100
-phiX174,1417,allele,phiX174,phiX174,G,60,100
-phiX174,1418,allele,phiX174,phiX174,T,60,100
--- a/test-data/freebayes_out_1.vcf.contains	Mon Feb 17 10:53:56 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A
-
--- a/test-data/phiX.fasta	Mon Feb 17 10:53:56 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,79 +0,0 @@
->phiX174
-GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
-GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
-ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
-TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
-GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
-TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
-TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
-CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
-TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
-TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
-GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
-CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
-TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
-AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
-CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
-TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
-TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
-CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
-GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
-GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
-ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
-TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
-TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
-ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
-CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
-GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
-CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
-TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
-TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
-TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
-AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
-TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
-ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
-GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
-TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
-TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
-TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
-TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
-CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
-AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
-CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
-TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
-CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
-AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
-GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
-GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
-TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
-CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
-TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
-GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
-CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
-TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
-AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
-TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
-CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
-TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
-TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
-CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
-TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
-ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
-TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
-ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
-GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
-CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
-GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
-GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
-ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
-CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
-CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
-GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
-CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
-CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
-TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
-TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
-TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
-AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
-TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
-
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sam_fa_indices.loc.sample	Fri Jun 20 17:16:05 2014 -0400
@@ -0,0 +1,28 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Samtools indexed sequences data files.  You will need
+#to create these data files and then create a sam_fa_indices.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The sam_fa_indices.loc 
+#file has this format (white space characters are TAB characters):
+#
+#index	<seq>	<location>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/sam/, 
+#then the sam_fa_indices.loc entry would look like this:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#
+#and your /depot/data2/galaxy/sam/ directory
+#would contain hg18.fa and hg18.fa.fai files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.fa
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.fa.fai
+#
+#Your sam_fa_indices.loc file should include an entry per line for 
+#each index set you have stored.  The file in the path does actually
+#exist, but it should never be directly used. Instead, the name serves
+#as a prefix for the index file.  For example:
+#
+#index	hg18	/depot/data2/galaxy/sam/hg18.fa
+#index	hg19	/depot/data2/galaxy/sam/hg19.fa
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tool_data_table_conf.xml.sample	Fri Jun 20 17:16:05 2014 -0400
@@ -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 and other files -->
+    <table name="sam_fa_indexes" comment_char="#">
+        <columns>line_type, value, path</columns>
+        <file path="tool-data/sam_fa_indices.loc" />
+    </table>
+</tables>
--- a/tool_data_table_conf.xml.sample	Mon Feb 17 10:53:56 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 and other files -->
-    <table name="sam_fa_indexes" comment_char="#">
-        <columns>line_type, value, path</columns>
-        <file path="tool-data/sam_fa_indices.loc" />
-    </table>
-</tables>
--- a/tool_dependencies.xml	Mon Feb 17 10:53:56 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="freebayes" version="0.9.6_9608597d12e127c847ae03aa03440ab63992fedf">
-        <repository changeset_revision="7615ee9e216d" name="package_freebayes_0_9_6_9608597d" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="samtools" version="0.1.18">
-        <repository changeset_revision="171cd8bc208d" name="package_samtools_0_1_18" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>