changeset 2:2c7824a8d764 draft

Uploaded
author scisjnu123
date Thu, 12 Sep 2019 06:50:21 -0400
parents 0052747b878f
children 0d10255b5434
files GATK/gatk/analyze_covariates.xml GATK/gatk/base_recalibrator.xml GATK/gatk/combine_gvcfs.xml GATK/gatk/combine_variants.xml GATK/gatk/gatk.xml GATK/gatk/gatk_macros.xml GATK/gatk/generation/gatk.xsl GATK/gatk/generation/gatk.xsldb.xml GATK/gatk/genotype_gvcfs.xml GATK/gatk/haplotype_caller.xml GATK/gatk/indel_realigner.xml GATK/gatk/print_reads.xml GATK/gatk/realigner_target_creator.xml GATK/gatk/tool-data/destinations.py GATK/gatk/tool-data/picard_index.loc.sample GATK/gatk/tool_data_table_conf.xml.sample GATK/gatk/tool_dependencies.xml GATK/package_picard_1_135/tool_dependencies.xml GATK/package_r_for_gatk_3_4_0/tool_dependencies.xml ebola.len ebolamutant.fasta
diffstat 21 files changed, 1289 insertions(+), 276 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/analyze_covariates.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,37 @@
+<macros>
+    <xml name="AnalyzeCovariatesParameters" tokens="tag">
+
+        <!-- BQSR in main config -->
+
+        <param name="afterReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR second-pass report file" help="-after,&#8209;&#8209;afterReportFile &amp;lt;afterReportFile&amp;gt;" />
+
+        <param name="beforeReportFile" type="data" format="tabular" optional="true" label="file containing the BQSR first-pass report file" help="-before,&#8209;&#8209;beforeReportFile &amp;lt;beforeReportFile&amp;gt;" />
+
+    </xml>
+
+    <xml name="AnalyzeCovariatesOutput">
+        <data format="pdf" name="ac_plotsReportFile" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (PDF Recalibration Report)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="AnalyzeCovariatesPreprocessing">
+<![CDATA[
+]]>
+    </template>
+
+    <template name="AnalyzeCovariatesOptions">
+<![CDATA[
+        --plotsReportFile                   ${ac_plotsReportFile}
+
+        #if str($analysis_type.afterReportFile)
+            --afterReportFile $analysis_type.afterReportFile
+        #end if
+        #if str($analysis_type.beforeReportFile)
+            --beforeReportFile $analysis_type.beforeReportFile
+        #end if
+]]>
+    </template>
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/base_recalibrator.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,38 @@
+<macros>
+    <xml name="BaseRecalibratorParameters" tokens="tag">
+        
+        <expand macro="macro_bam_input" tag="@TAG@" />
+
+        <param name="knownSites" type="data" format="vcf,bcf,bed,pileup,tabular,table" label="Database of known Sites (ROD files; e.g. VCF format)" multiple="true" title="A database of known polymorphic sites to skip over in the recalibration algorithm" help="-knownSites,&#8209;&#8209;knownSites &amp;lt;knownSites&amp;gt;" />
+
+    </xml>
+
+    <xml name="BaseRecalibratorOutput">
+        <data format="tabular" name="br_table" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (Table)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="BaseRecalibratorPreprocessing">
+<![CDATA[
+        @token_bam_input_pre@
+        #for $i, $variant in enumerate($analysis_type.knownSites):
+            ln -s -f ${variant} variant_${i}.vcf &&
+        #end for
+]]>
+    </template>
+
+    <template name="BaseRecalibratorOptions">
+<![CDATA[
+        --out                   ${br_table}
+
+        @token_bam_input@
+
+        #for $i, $variant in enumerate($analysis_type.knownSites):
+            --knownSites variant_${i}.vcf
+        #end for
+]]>
+    </template>
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/combine_gvcfs.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,44 @@
+<macros>
+    <xml name="CombineGVCFsParameters" tokens="tag">
+        
+        <expand macro="macro_gvcf_input" tag="@TAG@" />
+
+        <expand macro="macro_optional_parameters">
+
+            <param name="breakBandsAtMultiplesOf" type="integer" value="0" label="If > 0, reference bands will be broken up at genomic positions that are multiples of this number" help="-breakBandsAtMultiplesOf,&#8209;&#8209;breakBandsAtMultiplesOf &amp;lt;breakBandsAtMultiplesOf&amp;gt;" />
+
+        </expand>
+
+    </xml>
+
+    <xml name="CombineGVCFsOutput">
+        <data format="vcf" name="cg_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="CombineGVCFsPreprocessing">
+<![CDATA[
+        @token_gvcf_input_pre@
+]]>
+    </template>
+
+    <template name="CombineGVCFsOptions">
+<![CDATA[
+        --out ${cg_output_vcf}
+
+        @token_gvcf_input@
+
+        #set $optionals = $analysis_type.optional_parameters
+        #if $optionals.optional_parameters_enabled
+            #if $optionals.breakBandsAtMultiplesOf > 0
+                --breakBandsAtMultiplesOf $optionals.breakBandsAtMultiplesOf
+            #end if
+        #end if
+]]>
+    </template>
+
+
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/combine_variants.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,96 @@
+<macros>
+    <xml name="CombineVariantsParameters" tokens="tag">
+        
+        <expand macro="macro_vcf_input" tag="@TAG@" />
+
+        <expand macro="macro_optional_parameters">
+
+            <param name="filteredRecordsMergeType" type="select" label="Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields" help="-filteredRecordsMergeType,&#8209;&#8209;filteredrecordsmergetype &amp;lt;filteredrecordsmergetype&amp;gt;">
+                <option value="">No Selection</option>
+                <option value="KEEP_IF_ANY_UNFILTERED">KEEP_IF_ANY_UNFILTERED</option>
+                <option value="KEEP_IF_ALL_UNFILTERED">KEEP_IF_ALL_UNFILTERED</option>
+                <option value="KEEP_UNCONDITIONAL">KEEP_UNCONDITIONAL</option>
+            </param>
+
+            <param name="genotypeMergeOptions" type="select" label="Determines how we should merge genotype records for samples shared across the ROD files" help="-genotypeMergeOptions,&#8209;&#8209;genotypemergeoption &amp;lt;genotypemergeoption&amp;gt;">
+                <option value="">No Selection</option>
+                <option value="UNIQUIFY">UNIQUIFY</option>
+                <option value="PRIORITIZE">PRIORITIZE</option>
+                <option value="UNSORTED">UNSORTED</option>
+                <option value="REQUIRE_UNIQUE">REQUIRE_UNIQUE</option>
+            </param>
+
+            <param name="minimumN" type="integer" value="1" optional="true" label="Combine variants and output site only if the variant is present in at least N input files" help="-minN,&#8209;&#8209;minimumN &amp;lt;minimumN&amp;gt;" />
+
+            <param name="rod_priority_list" type="text" value="" optional="true" label="A comma-separated string describing the priority ordering for the genotypes as far as which record gets emitted" help="-priority,&#8209;&#8209;rod_priority_list &amp;lt;rod_priority_list&amp;gt;" />
+
+            <param name="setKey" type="text" value="" optional="true" label="Key used in the INFO key=value tag emitted describing which set the combined VCF record came from" help="-setKey,&#8209;&#8209;setKey &amp;lt;setKey&amp;gt;" />
+
+            <param name="assumeIdenticalSamples" type="boolean" truevalue="--assumeIdenticalSamples" falsevalue="" label="If true, assume input VCFs have identical sample sets and disjoint calls" help="-assumeIdenticalSamples,&#8209;&#8209;assumeIdenticalSamples" />
+
+            <param name="excludeNonVariants" type="boolean" truevalue="--excludeNonVariants" falsevalue="" label="Don't include loci found to be non-variant after the combining procedure" help="-env,&#8209;&#8209;excludeNonVariants" />
+
+            <param name="filteredAreUncalled" type="boolean" truevalue="--filteredAreUncalled" falsevalue="" label="If true, then filtered VCFs are treated as uncalled, so that filtered set annotations don't appear in the combined VCF" help="-filteredAreUncalled,&#8209;&#8209;filteredAreUncalled" />
+
+            <param name="mergeInfoWithMaxAC" type="boolean" truevalue="--mergeInfoWithMaxAC" falsevalue="" label="If true, when VCF records overlap the info field is taken from the one with the max AC instead of only taking the fields which are identical across the overlapping records." help="-mergeInfoWithMaxAC,&#8209;&#8209;mergeInfoWithMaxAC" />
+
+            <param name="minimalVCF" type="boolean" truevalue="--minimalVCF" falsevalue="" label="If true, then the output VCF will contain no INFO or genotype FORMAT fields" help="-minimalVCF,&#8209;&#8209;minimalVCF" />
+
+            <param name="printComplexMerges" type="boolean" truevalue="--printComplexMerges" falsevalue="" label="Print out interesting sites requiring complex compatibility merging" help="-printComplexMerges,&#8209;&#8209;printComplexMerges" />
+
+            <param name="suppressCommandLineHeader" type="boolean" truevalue="--suppressCommandLineHeader" falsevalue="" label="If true, do not output the header containing the command line used" help="-suppressCommandLineHeader,&#8209;&#8209;suppressCommandLineHeader" />
+
+        </expand>
+
+    </xml>
+
+    <xml name="CombineVariantsOutput">
+        <data format="vcf" name="cv_output_vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (VCF)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="CombineVariantsPreprocessing">
+<![CDATA[
+        @token_vcf_input_pre@
+]]>
+    </template>
+
+    <template name="CombineVariantsOptions">
+<![CDATA[
+        --out ${cv_output_vcf}
+
+        @token_vcf_input@
+
+        #set $optionals = $analysis_type.optional_parameters
+        #if $optionals.optional_parameters_enabled
+
+            #if $optionals.filteredRecordsMergeType
+                --filteredRecordsMergeType $optionals.filteredRecordsMergeType
+            #end if
+            #if $optionals.genotypeMergeOptions
+                --genotypeMergeOptions $optionals.genotypeMergeOptions
+            #end if
+            #if $optionals.minimumN != 1
+                --minimumN $optionals.minimumN
+            #end if
+            #if $optionals.rod_priority_list
+                --rod_priority_list $optionals.rod_priority_list
+            #end if
+
+            $optionals.assumeIdenticalSamples
+            $optionals.excludeNonVariants
+            $optionals.filteredAreUncalled
+            $optionals.mergeInfoWithMaxAC
+            $optionals.minimalVCF
+            $optionals.printComplexMerges
+            $optionals.suppressCommandLineHeader
+
+        #end if
+]]>
+    </template>
+
+
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/gatk.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,179 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="gatk" name="GATK" version="@VERSION@.d9">
+  <description>tool collection Version @VERSION@</description>
+  <macros>
+    <import>gatk_macros.xml</import>
+    <import>realigner_target_creator.xml</import>
+    <import>indel_realigner.xml</import>
+    <import>base_recalibrator.xml</import>
+    <import>analyze_covariates.xml</import>
+    <import>print_reads.xml</import>
+    <import>haplotype_caller.xml</import>
+    <import>genotype_gvcfs.xml</import>
+    <import>combine_gvcfs.xml</import>
+    <import>combine_variants.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <stdio>
+    <regex match="^INFO" level="log"/>
+    <regex match="^WARN" level="warning"/>
+    <regex match="Using .* implementation of PairHMM" level="warning"/>
+    <regex match="There is insufficient memory for the Java Runtime Environment to continue" level="fatal"/>
+    <regex match="^##### ERROR" level="fatal"/>
+    <exit_code range="1:" level="fatal"/>
+  </stdio>
+  <command><![CDATA[
+        ############################
+        ## import analysis specific preprocessings by using cheetahs internal searchList
+        ## if not defined, ignore
+        ############################
+        #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2]
+            #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"]
+            #include source=$analysisPreprocessing
+        #end if
+        
+        ############################
+        ## GATK tool unspecific options
+        ############################
+        @GATK_EXEC@
+        
+        --analysis_type ${analysis_type.analysis_type_selector}
+        --reference_sequence    ${ref_file.fields.path}
+
+        --log_to_file           ${output_log}
+
+        #if $cond_intervals.cond_intervals_enabled
+            #for $interval in $cond_intervals.intervals:
+                --intervals ${interval.L}
+            #end for
+        #end if
+
+        #if $cond_BQSR.cond_BQSR_enabled
+          --BQSR $cond_BQSR.BQSR
+        #end if
+
+        ############################
+        ## import analysis specific options by using cheetahs internal searchList
+        ## if not defined throw raw python error until better idea
+        ############################
+        #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2]
+            #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
+            #include source=$analysisOptions
+        #else
+            #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
+        #end if
+        
+        ############################
+        ## only put ERROR or FATAL log messages into stderr
+        ## but keep full log for printing into log file
+        ############################
+        2>&1 | awk '\$1 != "INFO" && \$1 != "WARN"' >&2
+]]></command>
+  <inputs>
+    <param name="ref_file" type="select" label="Using reference genome" help="-R,‑‑reference_sequence &amp;lt;reference_sequence&amp;gt;">
+      <options from_data_table="picard_indexes"/>
+      <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+    </param>
+    <conditional name="cond_intervals">
+      <param name="cond_intervals_enabled" type="boolean" label="Select interval subset to operate on?"/>
+      <when value="true">
+        <repeat name="intervals" title="genomic interval over which to operate" help="-L,‑‑intervals &amp;lt;intervals&amp;gt;">
+          <param name="L" type="text" value=""/>
+        </repeat>
+      </when>
+      <when value="false"/>
+    </conditional>
+    <conditional name="cond_BQSR">
+      <param name="cond_BQSR_enabled" type="boolean" label="Select covariates for on-the-fly recalibration?"/>
+      <when value="true">
+        <param name="BQSR" type="data" format="tabular" label="Input covariates table file for on-the-fly base quality score recalibration" help="-BQSR,‑‑BQSR &amp;lt;BQSR&amp;gt; intended primarily for use with BaseRecalibrator and PrintReads"/>
+      </when>
+      <when value="false"/>
+    </conditional>
+    <conditional name="cond_threads">
+      <param name="cond_threads_enabled" type="boolean" label="Set computational options (cpu, mem)?"/>
+      <when value="true">
+        <param name="nt" type="integer" value="1" label="Number of data threads to allocate to this analysis" help="make sure, the option is available for the chosen tool"/>
+        <param name="nct" type="integer" value="1" label="Number of CPU threads to allocate per data thread" help="make sure, the option is available for the chosen tool"/>
+        <param name="mem" type="integer" value="0" label="Overwrite Memory in MB (0 = don't overwrite)" help="Overwrites all other defaults and might lead to crash the run. States mem per data thread"/>
+      </when>
+      <when value="false"/>
+    </conditional>
+    <conditional name="analysis_type">
+      <param name="analysis_type_selector" type="select" label="Analysis Type">
+        <option value="RealignerTargetCreator">RealignerTargetCreator</option>
+        <option value="IndelRealigner">IndelRealigner</option>
+        <option value="BaseRecalibrator">BaseRecalibrator</option>
+        <option value="AnalyzeCovariates">AnalyzeCovariates</option>
+        <option value="PrintReads">PrintReads</option>
+        <option value="HaplotypeCaller">HaplotypeCaller</option>
+        <option value="GenotypeGVCFs">GenotypeGVCFs</option>
+        <option value="CombineGVCFs">CombineGVCFs</option>
+        <option value="CombineVariants">CombineVariants</option>
+      </param>
+      <when value="RealignerTargetCreator">
+        <expand macro="RealignerTargetCreatorParameters" tag="rtc"/>
+      </when>
+      <when value="IndelRealigner">
+        <expand macro="IndelRealignerParameters" tag="ir"/>
+      </when>
+      <when value="BaseRecalibrator">
+        <expand macro="BaseRecalibratorParameters" tag="br"/>
+      </when>
+      <when value="AnalyzeCovariates">
+        <expand macro="AnalyzeCovariatesParameters" tag="ac"/>
+      </when>
+      <when value="PrintReads">
+        <expand macro="PrintReadsParameters" tag="pr"/>
+      </when>
+      <when value="HaplotypeCaller">
+        <expand macro="HaplotypeCallerParameters" tag="hc"/>
+      </when>
+      <when value="GenotypeGVCFs">
+        <expand macro="GenotypeGVCFsParameters" tag="gg"/>
+      </when>
+      <when value="CombineGVCFs">
+        <expand macro="CombineGVCFsParameters" tag="cg"/>
+      </when>
+      <when value="CombineVariants">
+        <expand macro="CombineVariantsParameters" tag="cv"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <expand macro="RealignerTargetCreatorOutput" tag="rtc">
+      <filter>analysis_type['analysis_type_selector'] == 'RealignerTargetCreator'</filter>
+    </expand>
+    <expand macro="IndelRealignerOutput" tag="ir">
+      <filter>analysis_type['analysis_type_selector'] == 'IndelRealigner'</filter>
+    </expand>
+    <expand macro="BaseRecalibratorOutput" tag="br">
+      <filter>analysis_type['analysis_type_selector'] == 'BaseRecalibrator'</filter>
+    </expand>
+    <expand macro="AnalyzeCovariatesOutput" tag="ac">
+      <filter>analysis_type['analysis_type_selector'] == 'AnalyzeCovariates'</filter>
+    </expand>
+    <expand macro="PrintReadsOutput" tag="pr">
+      <filter>analysis_type['analysis_type_selector'] == 'PrintReads'</filter>
+    </expand>
+    <expand macro="HaplotypeCallerOutput" tag="hc">
+      <filter>analysis_type['analysis_type_selector'] == 'HaplotypeCaller'</filter>
+    </expand>
+    <expand macro="GenotypeGVCFsOutput" tag="gg">
+      <filter>analysis_type['analysis_type_selector'] == 'GenotypeGVCFs'</filter>
+    </expand>
+    <expand macro="CombineGVCFsOutput" tag="cg">
+      <filter>analysis_type['analysis_type_selector'] == 'CombineGVCFs'</filter>
+    </expand>
+    <expand macro="CombineVariantsOutput" tag="cv">
+      <filter>analysis_type['analysis_type_selector'] == 'CombineVariants'</filter>
+    </expand>
+    <data format="txt" name="output_log" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (log)"/>
+  </outputs>
+  <expand macro="macro_tests"/>
+  <citations>
+    <citation type="doi">10.1101/gr.107524.110</citation>
+    <citation type="doi">10.1038/ng.806</citation>
+    <citation type="doi">10.1002/0471250953.bi1110s43</citation>
+  </citations>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/gatk_macros.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,166 @@
+<macros>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package">gatk</requirement>
+            <requirement type="set_environment">GATK_PATH</requirement>
+            <requirement type="set_environment">GATK_SITE_OPTIONS</requirement>
+            <requirement type="package" version="3.1.2.1">package_r_for_gatk_3_4_0</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command><![CDATA[ @GATK_EXEC@ --help|grep '^The Genome' ]]></version_command>
+    </xml>
+
+    <token name="@VERSION@">3.4-0</token>
+    <token name="@OUTPUT_NAME_PREFIX@">${tool.name} - ${analysis_type.analysis_type_selector}</token>
+    <token name="@GATK_EXEC@">
+<![CDATA[
+        #if $cond_threads.cond_threads_enabled:
+            #if int($cond_threads.nct) > 1:
+                THREAD_STRING="-nct $cond_threads.nct" &&
+            #end if
+            #if int($cond_threads.nt) > 1:
+                THREAD_STRING=$THREAD_STRING" -nt $cond_threads.nt" &&
+            #end if
+            #if int($cond_threads.mem) > 0:
+                GATK_MEM=$cond_threads.mem &&
+            #end if
+        #end if
+        java -Xmx\${GATK_MEM:-\${SLURM_MEM_PER_NODE:-4096}}M -jar "\$GATK_PATH/GenomeAnalysisTK.jar" \${THREAD_STRING:-}
+]]>
+    </token>
+
+    <xml name="macro_vcf_input" tokens="tag">
+        <param name="input" type="data" format="vcf" multiple="true" label="Variant files (VCF format)" help="-V, &#8209;&#8209;variant">
+            <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> 
+        </param>
+    </xml>
+    <token name="@token_vcf_input_pre@" tokens="tag">
+<![CDATA[
+        ############################
+        ## create links to gVCF input files with correct extensions
+        ############################
+        #for $i, $variant in enumerate($analysis_type.input):
+            ln -s -f ${variant} variant_${i}.vcf &&
+        #end for
+]]>
+    </token>
+    <token name="@token_vcf_input@">
+<![CDATA[
+        #for $i, $variant in enumerate($analysis_type.input):
+            --variant variant_${i}.vcf
+        #end for
+        @token_reference_input@
+]]>
+    </token>
+
+
+    <xml name="macro_gvcf_input" tokens="tag">
+        <param name="input" type="data" format="vcf" multiple="true" label="Variant files (gVCF format)" help="-V, &#8209;&#8209;variant">
+            <validator type="unspecified_build" />
+            <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> 
+        </param>
+    </xml>
+    <token name="@token_gvcf_input_pre@" tokens="tag">
+<![CDATA[
+        ############################
+        ## create links to gVCF input files with correct extensions
+        ############################
+        #for $i, $variant in enumerate($analysis_type.input):
+            ln -s -f ${variant} variant_${i}.g.vcf &&
+        #end for
+]]>
+    </token>
+    <token name="@token_gvcf_input@">
+<![CDATA[
+        #for $i, $variant in enumerate($analysis_type.input):
+            --variant variant_${i}.g.vcf
+        #end for
+        @token_reference_input@
+]]>
+    </token>
+
+    <xml name="macro_bam_input">
+        <conditional name="cond_bam_input">
+            <param name="all_in_one" type="boolean" value="false" label="Input all BAM files in a single command" />
+            <when value="true">
+                <param name="input" type="data" format="bam" multiple="true" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
+                    <validator type="unspecified_build"/>
+                    <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
+                </param>
+            </when>
+            <when value="false">
+                <param name="input" type="data" format="bam" label="Input file containing sequence data (BAM)" help="-I, ‑‑input_file">
+                    <validator type="unspecified_build"/>
+                    <validator type="dataset_metadata_in_data_table" table_name="picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build."/>
+                </param>
+            </when>
+        </conditional>
+    </xml>
+    <token name="@token_bam_input_pre@">
+<![CDATA[
+        ############################
+        ## create links to bam input files with correct extensions
+        ############################
+        #if $analysis_type.cond_bam_input.all_in_one
+            #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
+                ln -s -f ${bam} input_${i}.bam &&
+                ln -s -f ${bam.metadata.bam_index} input_${i}.bam.bai &&
+            #end for
+        #else
+            ln -s -f ${analysis_type.cond_bam_input.input} input.bam &&
+            ln -s -f ${analysis_type.cond_bam_input.input.metadata.bam_index} input.bam.bai &&
+        #end if
+]]>
+    </token>
+    <token name="@token_bam_input@">
+<![CDATA[
+        #if $analysis_type.cond_bam_input.all_in_one
+            #for $i, $bam in enumerate($analysis_type.cond_bam_input.input):
+                --input_file input_${i}.bam
+            #end for
+        #else
+            --input_file            input.bam
+        #end if
+        @token_reference_input@
+]]>
+    </token>
+
+    <token name="@token_reference_input@">
+<![CDATA[
+]]>
+    </token>
+    <xml name="macro_input" tokens="tag">
+        <yield />
+    </xml>
+
+    <xml name="macro_optional_parameters">
+        <conditional name="optional_parameters">
+            <param name="optional_parameters_enabled" type="boolean" label="Configure Optional Parameters" />
+            <when value="true">
+                <yield />
+            </when>
+            <when value="false" />
+        </conditional>
+    </xml>
+
+    <xml name="macro_advanced_parameters">
+        <conditional name="advanced_parameters">
+            <param name="advanced_parameters_enabled" type="boolean" label="Configure Advanced Parameters" />
+            <when value="true">
+                <yield />
+            </when>
+            <when value="false" />
+        </conditional>
+    </xml>
+
+    <xml name="macro_tests">
+        <tests>
+            
+        </tests>
+    </xml>
+
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/generation/gatk.xsl	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,162 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform">
+<xsl:output
+    method="xml"
+    encoding="utf-8"
+    indent="yes"
+    cdata-section-elements="script style" />
+
+<xsl:template match="/">
+
+<tool id="gatk" name="GATK" version="@VERSION@.d9">
+    <description>tool collection Version @VERSION@</description>
+
+    <macros>
+        <import>gatk_macros.xml</import>
+        <xsl:for-each select="analyses/analysis">
+        <import><xsl:value-of select="macro_file" /></import>
+        </xsl:for-each>
+    </macros>
+
+    <expand macro="requirements" />
+
+    <stdio>
+        <regex match="^INFO" level="log" />
+        <regex match="^WARN" level="warning" />
+        <regex match="Using .* implementation of PairHMM" level="warning" />
+        <regex match="There is insufficient memory for the Java Runtime Environment to continue" level="fatal" />
+        <regex match="^##### ERROR" level="fatal" />
+        <exit_code range="1:" level="fatal"/>
+    </stdio>
+
+    <command>
+<xsl:text disable-output-escaping="yes">&lt;![CDATA[
+        ############################
+        ## import analysis specific preprocessings by using cheetahs internal searchList
+        ## if not defined, ignore
+        ############################
+        #if $analysis_type.analysis_type_selector + "Preprocessing" in vars()['SL'][2]
+            #set $analysisPreprocessing = vars()['SL'][2][$analysis_type.analysis_type_selector + "Preprocessing"]
+            #include source=$analysisPreprocessing
+        #end if
+        
+        ############################
+        ## GATK tool unspecific options
+        ############################
+        @GATK_EXEC@
+        
+        --analysis_type ${analysis_type.analysis_type_selector}
+        --reference_sequence    ${ref_file.fields.path}
+
+        --log_to_file           ${output_log}
+
+        #if $cond_intervals.cond_intervals_enabled
+            #for $interval in $cond_intervals.intervals:
+                --intervals ${interval.L}
+            #end for
+        #end if
+
+        #if $cond_BQSR.cond_BQSR_enabled
+          --BQSR $cond_BQSR.BQSR
+        #end if
+
+        ############################
+        ## import analysis specific options by using cheetahs internal searchList
+        ## if not defined throw raw python error until better idea
+        ############################
+        #if $analysis_type.analysis_type_selector + "Options" in vars()['SL'][2]
+            #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
+            #include source=$analysisOptions
+        #else
+            #set $analysisOptions = vars()['SL'][2][$analysis_type.analysis_type_selector + "Options"]
+        #end if
+        
+        ############################
+        ## only put ERROR or FATAL log messages into stderr
+        ## but keep full log for printing into log file
+        ############################
+        2>&amp;1 | awk '\$1 != "INFO" &amp;&amp; \$1 != "WARN"' >&amp;2
+]]&gt;</xsl:text>
+    </command>
+
+    <inputs>
+
+        <param name="ref_file" type="select" label="Using reference genome" help="-R,&#8209;&#8209;reference_sequence &amp;lt;reference_sequence&amp;gt;" >
+            <options from_data_table="picard_indexes">
+                <!--filter type="data_meta" key="dbkey" ref="@TAG@_input" column="dbkey" /-->
+            </options>
+            <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
+        </param>
+
+        <conditional name="cond_intervals">
+            <param name="cond_intervals_enabled" type="boolean" label="Select interval subset to operate on?" />
+            <when value="true">
+                <repeat name="intervals" title="genomic interval over which to operate" help="-L,&#8209;&#8209;intervals &amp;lt;intervals&amp;gt;">
+                    <param name="L" type="text" value="" />
+                </repeat>
+            </when>
+            <when value="false" />
+        </conditional>
+
+        <conditional name="cond_BQSR">
+            <param name="cond_BQSR_enabled" type="boolean" label="Select covariates for on-the-fly recalibration?" />
+            <when value="true">
+                <param name="BQSR" type="data" format="tabular" label="Input covariates table file for on-the-fly base quality score recalibration" help="-BQSR,&#8209;&#8209;BQSR &amp;lt;BQSR&amp;gt; intended primarily for use with BaseRecalibrator and PrintReads" />
+            </when>
+            <when value="false" />
+        </conditional>
+
+        <conditional name="cond_threads">
+            <param name="cond_threads_enabled" type="boolean" label="Set computational options (cpu, mem)?" />
+            <when value="true">
+                <param name="nt" type="integer" value="1" label="Number of data threads to allocate to this analysis" help="make sure, the option is available for the chosen tool" />
+                <param name="nct" type="integer" value="1" label="Number of CPU threads to allocate per data thread" help="make sure, the option is available for the chosen tool" />
+                <param name="mem" type="integer" value="0" label="Overwrite Memory in MB (0 = don't overwrite)" help="Overwrites all other defaults and might lead to crash the run. States mem per data thread" />
+            </when>
+            <when value="false" />
+        </conditional>
+
+        <conditional name="analysis_type">
+            <param name="analysis_type_selector" type="select" label="Analysis Type">
+                <xsl:for-each select="analyses/analysis">
+                <option value="{name}"><xsl:value-of select="name" /></option>
+                </xsl:for-each>
+            </param>
+            <xsl:for-each select="analyses/analysis">
+            <when value="{name}">
+                <!--xsl:choose>
+                    <xsl:when test="input_type = 'bam'">
+                        <expand macro="macro_bam_input" tag="{tag}" />
+                    </xsl:when>
+                    <xsl:when test="input_type = 'gvcf'">
+                        <expand macro="macro_gvcf_input" tag="{tag}" />
+                    </xsl:when>
+                </xsl:choose-->
+                <expand macro="{name}Parameters" tag="{tag}" />
+            </when>
+            </xsl:for-each>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <xsl:for-each select="analyses/analysis">
+        <expand macro="{name}Output" tag="{tag}">
+            <filter>analysis_type['analysis_type_selector'] == '<xsl:value-of select="name" />'</filter>
+        </expand>
+        </xsl:for-each>
+        <data format="txt" name="output_log" label="${{tool.name}} - ${{analysis_type.analysis_type_selector}} on ${{on_string}} (log)" />
+    </outputs>
+
+    <expand macro="macro_tests" />
+
+    <citations>
+        <citation type="doi">10.1101/gr.107524.110</citation>
+        <citation type="doi">10.1038/ng.806</citation>
+        <citation type="doi">10.1002/0471250953.bi1110s43</citation>
+    </citations>
+</tool>
+
+</xsl:template>
+</xsl:stylesheet>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/generation/gatk.xsldb.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<analyses>
+    <analysis>
+	    <name>RealignerTargetCreator</name>
+	    <input_type>bam</input_type>
+	    <tag>rtc</tag>
+	    <macro_file>realigner_target_creator.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>IndelRealigner</name>
+	    <input_type>bam</input_type>
+	    <tag>ir</tag>
+	    <macro_file>indel_realigner.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>BaseRecalibrator</name>
+	    <input_type>bam</input_type>
+	    <tag>br</tag>
+	    <macro_file>base_recalibrator.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>AnalyzeCovariates</name>
+	    <input_type>bam</input_type>
+	    <tag>ac</tag>
+	    <macro_file>analyze_covariates.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>PrintReads</name>
+	    <input_type>bam</input_type>
+	    <tag>pr</tag>
+	    <macro_file>print_reads.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>HaplotypeCaller</name>
+	    <input_type>bam</input_type>
+	    <tag>hc</tag>
+	    <macro_file>haplotype_caller.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>GenotypeGVCFs</name>
+	    <input_type>gvcf</input_type>
+	    <tag>gg</tag>
+	    <macro_file>genotype_gvcfs.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>CombineGVCFs</name>
+	    <input_type>gvcf</input_type>
+	    <tag>cg</tag>
+	    <macro_file>combine_gvcfs.xml</macro_file>
+    </analysis>
+    <analysis>
+	    <name>CombineVariants</name>
+	    <input_type>vcf</input_type>
+	    <tag>cv</tag>
+	    <macro_file>combine_variants.xml</macro_file>
+    </analysis>
+</analyses>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/genotype_gvcfs.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,43 @@
+<macros>
+    <xml name="GenotypeGVCFsParameters" tokens="tag">
+        
+        <expand macro="macro_gvcf_input" tag="@TAG@" />
+
+        <expand macro="macro_optional_parameters">
+
+
+            <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,&#8209;&#8209;sample_ploidy &amp;lt;sample_ploidy&amp;gt;" />
+
+        </expand>
+
+    </xml>
+
+    <xml name="GenotypeGVCFsOutput">
+        <data format="vcf" name="gg_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (gVCF)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="GenotypeGVCFsPreprocessing">
+<![CDATA[
+        @token_gvcf_input_pre@
+]]>
+    </template>
+
+    <template name="GenotypeGVCFsOptions">
+<![CDATA[
+        --out output.g.vcf
+
+        @token_gvcf_input@
+
+        #set $optionals = $analysis_type.optional_parameters
+        #if $optionals.optional_parameters_enabled
+            --sample_ploidy $optionals.sample_ploidy
+        #end if
+]]>
+    </template>
+
+
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/haplotype_caller.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,65 @@
+<macros>
+    <xml name="HaplotypeCallerParameters" tokens="tag">
+        
+        <expand macro="macro_bam_input" tag="@TAG@" />
+
+        <conditional name="cond_usage">
+            <param name="cond_usage_selector" type="select" label="Select usage">
+                <option value="GVCF">Single-sample all-sites calling on DNAseq (GVCF mode)</option>
+            </param>
+            <when value="GVCF">
+                <expand macro="HaplotypeCallerGVCF" />
+            </when>
+        </conditional>
+
+        <expand macro="macro_optional_parameters">
+
+            <param name="sample_ploidy" type="integer" value="2" label="Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)" help="-ploidy,&#8209;&#8209;sample_ploidy &amp;lt;sample_ploidy&amp;gt;" />
+
+        </expand>
+
+    </xml>
+
+    <xml name="HaplotypeCallerOutput">
+        <data format="vcf" name="hc_output_gvcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string} (gVCF)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="HaplotypeCallerPreprocessing">
+<![CDATA[
+        @token_bam_input_pre@
+]]>
+    </template>
+
+    <template name="HaplotypeCallerOptions">
+<![CDATA[
+        --out output.g.vcf
+
+        @token_bam_input@
+
+        #set $optionals = $analysis_type.optional_parameters
+        #if $optionals.optional_parameters_enabled
+            --sample_ploidy $optionals.sample_ploidy
+        #end if
+
+        #set $usage_selector = $analysis_type.cond_usage.cond_usage_selector
+        #set $usage = $analysis_type.cond_usage
+
+        #if str($usage_selector) == 'GVCF'
+            --emitRefConfidence "GVCF"
+        #end if
+]]>
+    </template>
+
+
+
+    <xml name="HaplotypeCallerGVCF">
+        <param name="emitRefConfidence" type="select" optional="true" label="Mode for emitting reference confidence scores" help="-ERC,‑‑emitRefConfidence &amp;lt;emitRefConfidence&amp;gt;">
+              <option value="GVCF">GVCF (Reference model emitted with condensed non-variant blocks)</option>
+        </param>
+    </xml>
+
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/indel_realigner.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,90 @@
+<macros>
+    <xml name="IndelRealignerParameters" tokens="tag">
+        
+        <expand macro="macro_bam_input" tag="@TAG@" />
+
+        <param name="targetIntervals" type="data" format="gatk_interval" label="Intervals file output from RealignerTargetCreator" help="-targetIntervals,--targetIntervals &amp;lt;targetIntervals&amp;gt;" />
+
+        <expand macro="macro_optional_parameters">
+            <repeat name="knownAlleles" title="Input VCF file(s) with known indels" help="-known,&#8209;&#8209;knownAlleles &amp;lt;knownAlleles&amp;gt;">
+                <param name="knownAllele" type="data" format="vcf" label="Variant file (VCF format)" />
+            </repeat>
+            
+            <param name="consensusDeterminationModel" type="select" label="minimum reads at a locus to enable using the entropy calculation" help="-model,&#8209;&#8209;consensusDeterminationModel &amp;lt;consensusDeterminationModel&amp;gt;">
+                <option value="USE_READS">USE_READS - Additionally uses indels already present in the original alignments of the reads</option>
+                <option value="KNOWNS_ONLY">KNOWNS_ONLYS - Uses only indels from a provided ROD of known indels</option>
+                <option value="USE_SW">USE_SW - Additionally uses 'Smith-Waterman' to generate alternate consenses</option>
+            </param>
+            <param name="LODThresholdForCleaning" type="float" value="5.0" label="LOD threshold above which the cleaner will clean" help="-LOD,&#8209;&#8209;LODThresholdForCleaning &amp;lt;LODThresholdForCleaning&amp;gt;" />
+            <!--param name="nWayOut" type="float" value="5.0" label="Generate one output file for each input (-I) bam file (not compatible with -output)" help="-nWayOut,&#45;&#45;nWayOut &amp;lt;nWayOut&amp;gt;" /-->
+        </expand>
+
+
+        <expand macro="macro_advanced_parameters">
+            <param name="entropyThreshold" type="float" value="0.15" label="Percentage of mismatches at a locus to be considered having high entropy (0.0 &lt; entropy &lt;= 1.0)" help="-entropy,&#8209;&#8209;entropyThreshold &amp;lt;entropyThreshold&amp;gt;" />
+
+            <param name="maxConsensuses" type="integer" value="30" label="Max alternate consensuses to try (necessary to improve performance in deep coverage)" help="-maxConsensuses,&#8209;&#8209;maxConsensuses &amp;lt;maxConsensuses&amp;gt;" />
+
+            <param name="maxIsizeForMovement" type="integer" value="3000" label="maximum insert size of read pairs that we attempt to realign" help="-maxIsize,&#8209;&#8209;maxIsizeForMovement &amp;lt;maxIsizeForMovement&amp;gt;" />
+
+            <param name="maxPositionalMoveAllowed" type="integer" value="200" label="Maximum positional move in basepairs that a read can be adjusted during realignment" help="-maxPosMove,&#8209;&#8209;maxPositionalMoveAllowed &amp;lt;maxPositionalMoveAllowed&amp;gt;" />
+
+            <param name="maxReadsForConsensuses" type="integer" value="120" label="Max reads used for finding the alternate consensuses (necessary to improve performance in deep coverage)" help="-greedy,&#8209;&#8209;maxReadsForConsensuses &amp;lt;maxReadsForConsensuses&amp;gt;" />
+
+            <param name="maxReadsForRealignment" type="integer" value="20000" label="Max reads allowed at an interval for realignment" help="-maxReads,&#8209;&#8209;maxReadsForRealignment &amp;lt;maxReadsForRealignment&amp;gt;" />
+
+            <param name="maxReadsInMemory" type="integer" value="150000" label="max reads allowed to be kept in memory at a time by the SAMFileWriter" help="-maxInMemory,&#8209;&#8209;maxReadsInMemory &amp;lt;maxReadsInMemory&amp;gt;" />
+
+            <param name="noOriginalAlignmentTags" type="boolean" truevalue="--noOriginalAlignmentTags" falsevalue="" label="Don't output the original cigar or alignment start tags for each realigned read in the output bam" help="-noTags,&#8209;&#8209;noOriginalAlignmentTags" />
+        </expand>
+
+    </xml>
+
+    <xml name="IndelRealignerOutput">
+        <data format="bam" name="ir_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="IndelRealignerPreprocessing">
+<![CDATA[
+        @token_bam_input_pre@
+
+        ln -s -f ${analysis_type.targetIntervals} target.intervals &&
+
+        #if $analysis_type.optional_parameters.optional_parameters_enabled
+            #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles):
+                ln -s -f ${knownAllele.knownAllele} knownAllele_${i}.vcf &&
+            #end for
+        #end if
+]]>
+    </template>
+
+    <template name="IndelRealignerOptions">
+<![CDATA[
+        --out                   ${ir_output_bam}
+
+        @token_bam_input@
+        --targetIntervals       target.intervals
+
+        #if $analysis_type.optional_parameters.optional_parameters_enabled
+            #for $i, $knownAllele in enumerate($analysis_type.optional_parameters.knownAlleles):
+                --knownAlleles knownAllele_${i}.vcf
+            #end for
+            --consensusDeterminationModel       ${analysis_type.consensusDeterminationModel}
+            --LODThresholdForCleaning           ${analysis_type.LODThresholdForCleaning}
+        #end if
+
+        #if $analysis_type.advanced_parameters.advanced_parameters_enabled
+            --entropyThreshold          ${analysis_type.advanced_parameters.entropyThreshold}
+            --maxConsensuses            ${analysis_type.advanced_parameters.maxConsensuses}
+            --maxIsizeForMovement       ${analysis_type.advanced_parameters.maxIsizeForMovement}
+            --maxPositionalMoveAllowed  ${analysis_type.advanced_parameters.maxPositionalMoveAllowed}
+            --maxReadsForConsensuses    ${analysis_type.advanced_parameters.maxReadsForConsensuses}
+            --maxReadsForRealignment    ${analysis_type.advanced_parameters.maxReadsForRealignment}
+            --maxReadsInMemory          ${analysis_type.advanced_parameters.maxReadsInMemory}
+            ${analysis_type.advanced_parameters.noOriginalAlignmentTags}
+        #end if
+]]>
+    </template>
+</macros>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/print_reads.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,71 @@
+<macros>
+    <xml name="PrintReadsParameters" tokens="tag">
+        
+        <expand macro="macro_bam_input" tag="@TAG@" />
+
+        <!-- BQSR in main config -->
+
+        <expand macro="macro_optional_parameters">
+
+            <param name="number" type="integer" value="" optional="true" label="Print the first n reads from the file, discarding the rest" help="-n,&#8209;&#8209;number &amp;lt;number&amp;gt;" />
+
+            <param name="platform" type="text" value="" optional="true" label="Exclude all reads with this platform from the output" help="-platform,&#8209;&#8209;platform &amp;lt;platform&amp;gt;" />
+
+            <param name="readGroup" type="text" value="" optional="true" label="Exclude all reads with this read group from the output" help="-readGroup,&#8209;&#8209;readGroup &amp;lt;readGroup&amp;gt;" />
+
+            <param name="sample_file" type="data" format="txt" optional="true" label="File containing a list of samples (one per line). Can be specified multiple times" help="-sf,&#8209;&#8209;sample_file &amp;lt;sample_file&amp;gt;" />
+
+            <repeat name="sample_names" title="Sample names to be included in the analysis" help="-sn,‑‑sample_name &amp;lt;sample_name&amp;gt;">
+                <param name="sample_name" type="text" value="" title="Sample name to be included in the analysis" />
+            </repeat>
+            
+            <param name="simplify" type="text" truevalue="-s" falsevalue="" label="Erase all extra attributes in the read but keep the read group information" help="-s,&#8209;&#8209;simplify" />
+
+        </expand>
+
+    </xml>
+
+    <xml name="PrintReadsOutput">
+        <data format="bam" name="pr_output_bam" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (BAM)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="PrintReadsPreprocessing">
+<![CDATA[
+        @token_bam_input_pre@
+]]>
+    </template>
+
+    <template name="PrintReadsOptions">
+<![CDATA[
+        --out                   ${pr_output_bam}
+
+        @token_bam_input@
+
+        #set $optionals = $analysis_type.optional_parameters
+        #if $optionals.optional_parameters_enabled
+            #if int($optionals.number) > 0
+                --number $optionals.number
+            #end if
+            #if str($optionals.platform)
+                --platform $optionals.platform
+            #end if
+            #if str($optionals.readGroup)
+                --readGroup $optionals.readGroup
+            #end if
+            #if $optionals.sample_file
+                --sample_file $optionals.sample_file
+            #end if
+            #if $optionals.sample_names
+                #for $sample in $optionals.sample_names:
+                    --intervals ${sample.sample_name}
+                #end for
+            #end if
+            $optionals.simplify
+        #end if
+]]>
+    </template>
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/realigner_target_creator.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,57 @@
+<macros>
+    <xml name="RealignerTargetCreatorParameters" tokens="tag">
+        
+        <expand macro="macro_bam_input" tag="@TAG@" />
+
+        <expand macro="macro_optional_parameters">
+            <param name="maxIntervalSize" type="integer" value="500" label="maximum interval size; any intervals larger than this value will be dropped" help="-maxInterval,&#8209;&#8209;maxIntervalSize &amp;lt;maxIntervalSize&amp;gt;" />
+            <param name="minReadsAtLocus" type="integer" value="4" label="minimum reads at a locus to enable using the entropy calculation" help="-minReads,&#8209;&#8209;minReadsAtLocus &amp;lt;minReadsAtLocus&amp;gt;" />
+            <param name="windowSize" type="integer" value="10" label="window size for calculating entropy or SNP clusters" help="-window,&#8209;&#8209;windowSize &amp;lt;windowSize&amp;gt;" />
+
+            <param name="mismatchFraction" type="float" value="0.0" label="fraction of base qualities needing to mismatch for a position to have high entropy" help="-mismatch,&#8209;&#8209;mismatchFraction &amp;lt;mismatchFraction&amp;gt;" />
+            <repeat name="rod_bindings" title="Input VCF files with known indels" help="-known,&#8209;&#8209;known &amp;lt;known&amp;gt;">
+                <param name="input_rod" type="data" format="vcf" label="Variant file (VCF format)" />
+            </repeat>
+        </expand>
+        
+    </xml>
+
+    <xml name="RealignerTargetCreatorOutput">
+        <data format="gatk_interval" name="rtc_output_intervals" label="${tool.name} - ${analysis_type.analysis_type_selector} on ${on_string} (GATK intervals)">
+            <yield />
+        </data>
+    </xml>
+
+    <template name="RealignerTargetCreatorPreprocessing">
+<![CDATA[
+        @token_bam_input_pre@
+
+        #if $analysis_type.optional_parameters.optional_parameters_enabled
+            #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
+                ln -s -f ${rod_binding.input_rod} rod_binding_${i}.vcf &&
+            #end for
+        #end if
+]]>
+    </template>
+
+    <template name="RealignerTargetCreatorOptions">
+<![CDATA[
+        --out                   ${rtc_output_intervals}
+
+        @token_bam_input@
+
+        #if $analysis_type.optional_parameters.optional_parameters_enabled
+            --maxIntervalSize       ${analysis_type.optional_parameters.maxIntervalSize}
+            --minReadsAtLocus       ${analysis_type.optional_parameters.minReadsAtLocus}
+            --windowSize            ${analysis_type.optional_parameters.windowSize}
+            --mismatchFraction      ${analysis_type.optional_parameters.mismatchFraction}
+
+            #for $i, $rod_binding in enumerate($analysis_type.optional_parameters.rod_bindings):
+                --known rod_binding_${i}.vcf
+            #end for
+        #end if
+]]>
+    </template>
+</macros>
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool-data/destinations.py	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,62 @@
+from galaxy.jobs import JobDestination
+import os
+import sys
+import json
+import cStringIO
+import logging
+
+log = logging.getLogger( __name__ )
+
+
+def dump(obj, nested_level=0, output=sys.stdout):
+    spacing = '   '
+    if type(obj) == dict:
+        print >> output, '%s{' % ((nested_level) * spacing)
+        for k, v in obj.items():
+            if hasattr(v, '__iter__'):
+                print >> output, '%s%s:' % ((nested_level + 1) * spacing, k)
+                dump(v, nested_level + 1, output)
+            else:
+                print >> output, '%s%s: %s' % ((nested_level + 1) * spacing, k, v)
+        print >> output, '%s}' % (nested_level * spacing)
+    elif type(obj) == list:
+        print >> output, '%s[' % ((nested_level) * spacing)
+        for v in obj:
+            if hasattr(v, '__iter__'):
+                dump(v, nested_level + 1, output)
+            else:
+                print >> output, '%s%s' % ((nested_level + 1) * spacing, v)
+        print >> output, '%s]' % ((nested_level) * spacing)
+    else:
+        print >> output, '%s%s' % (nested_level * spacing, obj)
+
+
+def dynamic_slurm_cluster_gatk(job, tool_id):
+    # Allocate extra time
+    inp_data = dict( [ ( da.name, da.dataset ) for da in job.input_datasets ] )
+    inp_data.update( [ ( da.name, da.dataset ) for da in job.input_library_datasets ] )
+    inp_data.update( [ ( da.name, json.loads(da.value) ) for da in job.parameters ] )
+    out = cStringIO.StringIO()
+    dump(inp_data, 1, out)
+    log.debug(out.getvalue())
+    
+    nativeSpecs = '--nodes=1 --ntasks=1'
+    
+    # runner doesn't allow to specify --cpus-per-task
+    # thus the mem calculation gets messy with more than 1 node
+    # --> translate nt ==> nodes, nct ==> ntasks
+    
+    if 'cond_threads' not in inp_data:
+        return JobDestination(runner="slurm")
+    
+    if inp_data['cond_threads']['cond_threads_enabled'] == "True":
+        nNodes = int(inp_data['cond_threads']['nt'])
+        nCPU   = int(inp_data['cond_threads']['nct'])
+        nMEM   = int(inp_data['cond_threads']['mem'])
+        if nMEM > 0:
+            nativeSpecs = '--nodes=%d --ntasks=%d --mem=%d' % (nNodes, nCPU*nNodes, nMEM)
+        else:
+            nativeSpecs = '--nodes=%d --ntasks=%d' % (nNodes, nCPU*nNodes)
+        
+    return JobDestination(runner="slurm", params={"nativeSpecification": nativeSpecs})
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool-data/picard_index.loc.sample	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,26 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Picard dict and associated files. You will need
+#to create these data files and then create a picard_index.loc file 
+#similar to this one (store it in this directory) that points to 
+#the directories in which those files are stored. The picard_index.loc 
+#file has this format (longer white space is the TAB character):
+#
+#<unique_build_id>	<dbkey>		<display_name>		<fasta_file_path>
+#
+#So, for example, if you had hg18 indexed and stored in 
+#/depot/data2/galaxy/srma/hg18/,
+#then the srma_index.loc entry would look like this:
+#
+#hg18	hg18	hg18 Pretty		/depot/data2/galaxy/picard/hg18/hg18.fa
+#
+#and your /depot/data2/galaxy/srma/hg18/ directory
+#would contain the following three files:
+#hg18.fa
+#hg18.dict
+#hg18.fa.fai
+#
+#The dictionary file for each reference (ex. hg18.dict) must be 
+#created via Picard (http://picard.sourceforge.net). Note that
+#the dict file does not have the .fa extension although the
+#path list in the loc file does include it.
+#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool_data_table_conf.xml.sample	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Location of Picard dict files valid for GATK -->
+    <table name="picard_indexes" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/picard_index.loc" />
+    </table>
+</tables>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/gatk/tool_dependencies.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,19 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="GATK_PATH">/mnt/galaxy/tools/GATK/3.4-0</environment_variable>
+    </set_environment>
+    <!--
+    Use GATK_SITE_OPTIONS to set additional parameters that should be inserted in every GATK call.
+    The intended use case was to prohibit GATK to collect and send data.
+    For example:
+
+    -et "NO_ET" -K "/data/gatk_key_file" ##ET no phone home
+    -->
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="GATK_SITE_OPTIONS"> </environment_variable>
+    </set_environment>
+    <package name="package_r_for_gatk_3_4_0" version="3.1.2.1">
+        <repository changeset_revision="49c62e9b71ad" name="package_r_for_gatk_3_4_0" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/package_picard_1_135/tool_dependencies.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="picard" version="1.135">
+        <install version="1.0">
+            <actions_group>
+                <actions architecture="x86_64" os="linux">
+                    <action type="download_by_url">https://github.com/broadinstitute/picard/releases/download/1.135/picard-tools-1.135.zip</action>
+                    <action type="move_directory_files">
+                        <source_directory>.</source_directory>
+                        <destination_directory>$INSTALL_DIR</destination_directory>
+                    </action>       
+                </actions>                
+                <action type="set_environment">
+                    <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions_group>
+        </install>
+        <readme>
+This picard package dependency is retrieved directly from https://github.com/broadinstitute/picard/releases
+        </readme>
+    </package>
+</tool_dependency>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GATK/package_r_for_gatk_3_4_0/tool_dependencies.xml	Thu Sep 12 06:50:21 2019 -0400
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R" version="3.1.2">
+        <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="package_r_for_gatk_3_4_0" version="3.1.2.1">
+        <install version="1.0">
+            <actions>
+                <action type="setup_r_environment">
+
+                    <repository changeset_revision="9f2fddb9d6e2" name="package_r_3_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+                        <package name="R" version="3.1.2" />
+                    </repository>
+                    <package>https://github.com/cran/stringi/archive/0.5-5.tar.gz</package>
+                    <package>https://github.com/cran/magrittr/archive/1.5.tar.gz</package>
+                    <package>https://github.com/cran/stringr/archive/1.0.0.tar.gz</package>
+                    <package>https://github.com/cran/RColorBrewer/archive/1.1-2.tar.gz</package>
+                    <package>https://github.com/cran/dichromat/archive/2.0-0.tar.gz</package>
+                    <package>https://github.com/cran/colorspace/archive/1.2-6.tar.gz</package>
+                    <package>https://github.com/cran/munsell/archive/0.4.2.tar.gz</package>
+                    <package>https://github.com/cran/labeling/archive/0.3.tar.gz</package>
+                    <package>https://github.com/cran/Rcpp/archive/0.11.6.tar.gz</package>
+                    <package>https://github.com/cran/digest/archive/0.6.8.tar.gz</package>
+                    <package>https://github.com/cran/gtable/archive/0.1.2.tar.gz</package>
+                    <package>https://github.com/cran/bitops/archive/1.0-6.tar.gz</package>
+                    <package>https://github.com/cran/caTools/archive/1.17.1.tar.gz</package>
+                    <package>https://github.com/cran/gtools/archive/3.5.0.tar.gz</package>
+                    <package>https://github.com/cran/gdata/archive/2.17.0.tar.gz</package>
+                    <package>https://github.com/cran/gsalib/archive/2.1.tar.gz</package>
+                    <package>https://github.com/cran/gplots/archive/2.17.0.tar.gz</package>
+                    <package>https://github.com/cran/plyr/archive/1.8.3.tar.gz</package>
+                    <package>https://github.com/cran/reshape/archive/0.8.5.tar.gz</package>
+                    <package>https://github.com/cran/reshape2/archive/1.4.1.tar.gz</package>
+                    <package>https://github.com/cran/scales/archive/0.2.5.tar.gz</package>
+                    <package>https://github.com/cran/proto/archive/0.3-10.tar.gz</package>
+                    <package>https://github.com/cran/MASS/archive/7.3-43.tar.gz</package>
+                    <package>https://github.com/cran/ggplot2/archive/1.0.1.tar.gz</package>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and none of the bad parts.
+            It takes care of many of the fiddly details that make plotting a hassle (like drawing legends) as well as providing a powerful model of graphics that makes it easy to produce complex multi-layered graphics.
+
+            http://ggplot2.org/
+        </readme>
+    </package>
+</tool_dependency>
--- a/ebola.len	Sun Mar 04 00:49:57 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-1	Chr1	18959
-
-
--- a/ebolamutant.fasta	Sun Mar 04 00:49:57 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,273 +0,0 @@
->Chr1
-CGGACACACAAAAAGAAAGAAGAATTTTTAGGATCTTTTGTGTGCGAATAACTATGAGGAAGATTAATAA
-TTTTCCTCTCATTGAAATTTATATCGGAATTTAAATTGAAATTGTTACTGTAATCACACCTGGTTTGTTT
-CAGAGCCACATCACAAAGATAGAGAACAACCTAGGTCTCCGAAGGGAGCAAGGGCATCAGTGTGCTCAGT
-TGAAAATCCCTTGTCAACACCTAGGTCTTATCACATCACAAGTTCCACCTCAGACTCTGCAGGGTGATCC
-AACAACCTTAATAGAAACATTATTGTTAAAGGACAGCATTAGTTCACAGTCAAACAAGCAAGATTGAGAA
-TTAACCTTGGTTTTGAACTTGAACACTTAGGGGATTGAAGATTCAACAACCCTAAAGCTTGGGGTAAAAC
-ATTGGAAATAGTTAAAAGACAAATTGCTCGGAATCACAAAATTCCGAGTATGGATTCTCGTCCTCAGAAA
-ATCTGGATGGCGCCGAGTCTCACTGAATCTGACATGGATTACCACAAGATCTTGACAGCAGGTCTGTCCG
-TTCAACAGGGGATTGTTCGGCAAAGAGTCATCCCAGTGTATCAAGTAAACAATCTTGAAGAAATTTGCCA
-ACTTATCATACAGGCCTTTGAAGCAGGTGTTGATTTTCAAGAGAGTGCGGACAGTTTCCTTCTCATGCTT
-TGTCTTCATCATGCGTACCAGGGAGATTACAAACTTTTCTTGGAAAGTGGCGCAGTCAAGTATTTGGAAG
-GGCACGGGTTCCGTTTTGAAGTCAAGAAGCGTGATGGAGTGAAGCGCCTTGAGGAATTGCTGCCAGCAGT
-ATCTAGTGGAAAAAACATTAAGAGAACACTTGCTGCCATGCCGGAAGAGGAGACAACTGAAGCTAATGCC
-GGTCAGTTTCTCTCCTTTGCAAGTCTATTCCTTCCGAAATTGGTAGTAGGAGAAAAGGCTTGCCTTGAGA
-AGGTTCAAAGGCAAATTCAAGTACATGCAGAGCAAGGACTGATACAATATCCAACAGCTTGGCAATCAGT
-AGGACACATGATGGTGATTTTCCGTTTGATGCGAACAAATTTTCTGATCAAATTTCTCCTAATACACCAA
-GGGATGCACATGGTTGCCGGGCATGATGCCAACGATGCTGTGATTTCAAATTCAGTGGCTCAAGCTCGTT
-TTTCAGGCTTATTGATTGTCAAAACAGTACTTGATCATATCCTACAAAAGACAGAACGAGGAGTTCGTCT
-CCATCCTCTTGCAAGGACCGCCAAGGTAAAAAATGAGGTGAACTCCTTTAAGGCTGCACTCAGCTCCCTG
-GCCAAGCATGGAGAGTATGCTCCTTTCGCCCGACTTTTGAACCTTTCTGGAGTAAATAATCTTGAGCATG
-GTCTTTTCCCTCAACTATCGGCAATTGCACTCGGAGTCGCCACAGCACACGGGAGTACCCTCGCAGGAGT
-AAATGTTGGAGAACAGTATCAACAACTCAGAGAGGCTGCCACTGAGGCTGAGAAGCAACTCCAACAATAT
-GCAGAGTCTCGCGAACTTGACCATCTTGGACTTGATGATCAGGAAAAGAAAATTCTTATGAACTTCCATC
-AGAAAAAGAACGAAATCAGCTTCCAGCAAACAAACGCTATGGTAACTCTAAGAAAAGAGCGCCTGGCCAA
-GCTGACAGAAGCTATCACTGCTGCGTCACTGCCCAAAACAAGTGGACATTACGATGATGATGACGACATT
-CCCTTTCCAGGACCCATCAATGATGACGACAATCCTGGCCATCAAGATGATGATCCGACTGACTCACAGG
-ATACGACCATTCCCGATGTGGTGGTTGATCCCGATGATGGAAGCTACGGCGAATACCAGAGTTACTCGGA
-AAACGGCATGAATGCACCAGATGACTTGGTCCTATTCGATCTAGACGAGGACGACGAGGACACTAAGCCA
-GTGCCTAATAGATCGACCAAGGGTGGACAACAGAAGAACAGTCAAAAGGGCCAGCATATAGAGGGCAGAC
-AGACACAATCCAGGCCAATTCAAAATGTCCCAGGCCCTCACAGAACAATCCACCACGCCAGTGCGCCACT
-CACGGACAATGACAGAAGAAATGAACCCTCCGGCTCAACCAGCCCTCGCATGCTGACACCAATTAACGAA
-GAGGCAGACCCACTGGACGATGCCGACGACGAGACGTCTAGCCTTCCGCCCTTGGAGTCAGATGATGAAG
-AGCAGGACAGGGACGGAACTTCCAACCGCACACCCACTGTCGCCCCACCGGCTCCCGTATACAGAGATCA
-CTCTGAAAAGAAAGAACTCCCGCAAGACGAGCAACAAGATCAGGACCACACTCAAGAGGCCAGGAACCAG
-GACAGTGACAACACCCAGTCAGAACACTCTTTTGAGGAGATGTATCGCCACATTCTAAGATCACAGGGGC
-CATTTGATGCTGTTTTGTATTATCATATGATGAAGGATGAGCCTGTAGTTTTCAGTACCAGTGATGGCAA
-AGAGTACACGTATCCAGACTCCCTTGAAGAGGAATATCCACCATGGCTCACTGAAAAAGAGGCTATGAAT
-GAAGAGAATAGATTTGTTACATTGGATGGTCAACAATTTTATTGGCCGGTGATGAATCACAAGAATAAAT
-TCATGGCAATCCTGCAACATCATCAGTGAATGAGCATGGAACAATGGGATGATTCAACCGACAAATAGCT
-AACATTAAGTAGTCAAGGAACGAAAACAGGAAGAATTTTTGATGTCTAAGGTGTGAATTATTATCACAAT
-AAAAGTGATTCTTATTTTTGAATTTAAAGCTAGCTTATTATTACTAGCCGTTTTTCAAAGTTCAATTTGA
-GTCTTAATGCAAATAGGCGTTAAGCCACAGTTATAGCCATAATTGTAACTCAATATTCTAACTAGCGATT
-TATCTAAATTAAATTACATTATGCTTTTATAACTTACCTACTAGCCTGCCCAACATTTACACGATCGTTT
-TATAATTAAGAAAAAACTAATGATGAAGATTAAAACCTTCATCATCCTTACGTCAATTGAATTCTCTAGC
-ACTCGAAGCTTATTGTCTTCAATGTAAAAGAAAAGCTGGTCTAACAAGATGACAACTAGAACAAAGGGCA
-GGGGCCATACTGCGGCCACGACTCAAAACGACAGAATGCCAGGCCCTGAGCTTTCGGGCTGGATCTCTGA
-GCAGCTAATGACCGGAAGAATTCCTGTAAGCGACATCTTCTGTGATATTGAGAACAATCCAGGATTATGC
-TACGCATCCCAAATGCAACAAACGAAGCCAAACCCGAAGACGCGCAACAGTCAAACCCAAACGGACCCAA
-TTTGCAATCATAGTTTTGAGGAGGTAGTACAAACATTGGCTTCATTGGCTACTGTTGTGCAACAACAAAC
-CATCGCATCAGAATCATTAGAACAACGCATTACGAGTCTTGAGAATGGTCTAAAGCCAGTTTATGATATG
-GCAAAAACAATCTCCTCATTGAACAGGGTTTGTGCTGAGATGGTTGCAAAATATGATCTTCTGGTGATGA
-CAACCGGTCGGGCAACAGCAACCGCTGCGGCAACTGAGGCTTATTGGGCCGAACATGGTCAACCACCACC
-TGGACCATCACTTTATGAAGAAAGTGCGATTCGGGGTAAGATTGAATCTAGAGATGAGACCGTCCCTCAA
-AGTGTTAGGGAGGCATTCAACAATCTAAACAGTACCACTTCACTAACTGAGGAAAATTTTGGGAAACCTG
-ACATTTCGGCAAAGGATTTGAGAAACATTATGTATGATCACTTGCCTGGTTTTGGAACTGCTTTCCACCA
-ATTAGTACAAGTGATTTGTAAATTGGGAAAAGATAGCAACTCATTGGACATCATTCATGCTGAGTTCCAG
-GCCAGCCTGGCTGAAGGAGACTCTCCTCAATGTGCCCTAATTCAAATTACAAAAAGAGTTCCAATCTTCC
-AAGATGCTGCTCCACCTGTCATCCACATCCGCTCTCGAGGTGACATTCCCCGAGCTTGCCAGAAAAGCTT
-GCGTCCAGTCCCACCATCGCCCAAGATTGATCGAGGTTGGGTATGTGTTTTTCAGCTTCAAGATGGTAAA
-ACACTTGGACTCAAAATTTGAGCCAATCTCCCTTCCCTCCGAAAGAGGCGAATAATAGCAGAGGCTTCAA
-CTGCTGAACTATAGGGTACGTTACATTAATGATACACTTGTGAGTATCAGCCCTGGATAATATAAGTCAA
-TTAAACGACCAAGATAAAATTGTTCATATCTCGCTAGCAGCTTAAAATATAAATGTAATAGGAGCTATAT
-CTCTGACAGTATTATAATCAATTGTTATTAAGTAACCCAAACCAAAAGTGATGAAGATTAAGAAAAACCT
-ACCTCGGCTGAGAGAGTGTTTTTTCATTAACCTTCATCTTGTAAACGTTGAGCAAAATTGTTAAAAATAT
-GAGGCGGGTTATATTGCCTACTGCTCCTCCTGAATATATGGAGGCCATATACCCTGTCAGGTCAAATTCA
-ACAATTGCTAGAGGTGGCAACAGCAATACAGGCTTCCTGACACCGGAGTCAGTCAATGGGGACACTCCAT
-CGAATCCACTCAGGCCAATTGCCGATGACACCATCGACCATGCCAGCCACACACCAGGCAGTGTGTCATC
-AGCATTCATCCTTGAAGCTATGGTGAATGTCATATCGGGCCCCAAAGTGCTAATGAAGCAAATTCCAATT
-TGGCTTCCTCTAGGTGTCGCTGATCAAAAGACCTACAGCTTTGACTCAACTACGGCCGCCATCATGCTTG
-CTTCATACACTATCACCCATTTCGGCAAGGCAACCAATCCACTTGTCAGAGTCAATCGGCTGGGTCCTGG
-AATCCCGGATCATCCCCTCAGGCTCCTGCGAATTGGAAACCAGGCTTTCCTCCAGGAGTTCGTTCTTCCG
-CCAGTCCAACTACCCCAGTATTTCACCTTTGATTTGACAGCACTCAAACTGATCACCCAACCACTGCCTG
-CTGCAACATGGACCGATGACACTCCAACAGGATCAAATGGAGCGTTGCGTCCAGGAATTTCATTTCATCC
-AAAACTTCGCCCCATTCTTTTACCCAACAAAAGTGGGAAGAAGGGGAACAGTGCCGATCTAACATCTCCG
-GAGAAAATCCAAGCAATAATGACTTCACTCCAGGACTTTAAGATCGTTCCAATTGATCCAACCAAAAATA
-TCATGGGAATCGAAGTGCCAGAAACTCTGGTCCACAAGCTGACCGGTAAGAAGGTGACTTCTAAAAATGG
-ACAACCAATCATCCCTGTTCTTTTGCCAAAGTACATTGGGTTGGACCCGGTGGCTCCAGGAGACCTCACC
-ATGGTAATCACACAGGATTGTGACACGTGTCATTCTCCTGCAAGTCTTCCAGCTGTGATTGAGAAGTAAT
-TGCAATAATTGACTCAGATCCAGTTTTATAGAATCTTCTCAGGGATAGTGATAACATCTATTTAGTAATC
-CGTCCATTAGAGGAGACACTTTTAATTGATCAATATACTAAAGGTGCTTTACACCATTGTCTTTTTTCTC
-TCCTAAATGTAGAACTTAACAAAAGACTCATAATATACTTGTTTTTAAAGGATTGATTGATGAAAGATCA
-TAACTAATAACATTACAAATAATCCTACTATAATCAATACGGTGATTCAAATGTTAATCTTTCTCATTGC
-ACATACTTTTTGCCCTTATCCTCAAATTGCCTGCATGCTTACATCTGAGGATAGCCAGTGTGACTTGGAT
-TGGAAATGTGGAGAAAAAATCGGGACCCATTTCTAGGTTGTTCACAATCCAAGTACAGACATTGCCCTTC
-TAATTAAGAAAAAATCGGCGATGAAGATTAAGCCGACAGTGAGCGTAATCTTCATCTCTCTTAGATTATT
-TGTTTTCCAGAGTAGGGGTCGTCAGGTCCTTTTCAATCGTGTAACCAAAATAAACTCCACTAGAAGGATA
-TTGTGGGGCAACAACACAATGGGCGTTACAGGAATATTGCAGTTACCTCGTGATCGATTCAAGAGGACAT
-CATTCTTTCTTTGGGTAATTATCCTTTTCCAAAGAACATTTTCCATCCCACTTGGAGTCATCCACAATAG
-CACATTACAGGTTAGTGATGTCGACAAACTAGTTTGTCGTGACAAACTGTCATCCACAAATCAATTGAGA
-TCAGTTGGACTGAATCTCGAAGGGAATGGAGTGGCAACTGACGTGCCATCTGCAACTAAAAGATGGGGCT
-TCAGGTCCGGTGTCCCACCAAAGGTGGTCAATTATGAAGCTGGTGAATGGGCTGAAAACTGCTACAATCT
-TGAAATCAAAAAACCTGACGGGAGTGAGTGTCTACCAGCAGCGCCAGACGGGATTCGGGGCTTCCCCCGG
-TGCCGGTATGTGCACAAAGTATCAGGAACGGGACCGTGTGCCGGAGACTTTGCCTTCCATAAAGAGGGTG
-CTTTCTTCCTGTATGATCGACTTGCTTCCACAGTTATCTACCGAGGAACGACTTTCGCTGAAGGTGTCGT
-TGCATTTCTGATACTGCCCCAAGCTAAGAAGGACTTCTTCAGCTCACACCCCTTGAGAGAGCCGGTCAAT
-GCAACGGAGGACCCGTCTAGTGGCTACTATTCTACCACAATTAGATATCAGGCTACCGGTTTTGGAACCA
-ATGAGACAGAGTACTTGTTCGAGGTTGACAATTTGACCTACGTCCAACTTGAATCAAGATTCACACCACA
-GTTTCTGCTCCAGCTGAATGAGACAATATATACAAGTGGGAAAAGGAGCAATACCACGGGAAAACTAATT
-TGGAAGGTCAACCCCGAAATTGATACAACAATCGGGGAGTGGGCCTTCTGGGAAACTAAAAAAACCTCAC
-TAGAAAAATTCGCAGTGAAGAGTTGTCTTTCACAGTTGTATCAAACGGAGCCAAAAACATCAGTGGTCAG
-AGTCCGGCGCGAACTTCTTCCGACCCAGGGACCAACACAACAACTGAAGACCACAAAATCATGGCTTCAG
-AAAATTCCTCTGCAATGGTTCAAGTGCACAGTCAAGGAAGGGAAGCTGCAGTGTCGCATCTAACAACCCT
-TGCCACAATCTCCACGAGTCCCCAATCCCTCACAACCAAACCAGGTCCGGACAACAGCACCCATAATACA
-CCCGTGTATAAACTTGACATCTCTGAGGCAACTCAAGTTGAACAACATCACCGCAGAACAGACAACGACA
-GCACAGCCTCCGACACTCCCTCTGCCACGACCGCAGCCGGACCCCCAAAAGCAGAGAACACCAACACGAG
-CAAGAGCACTGACTTCCTGGACCCCGCCACCACAACAAGTCCCCAAAACCACAGCGAGACCGCTGGCAAC
-AACAACACTCATCACCAAGATACCGGAGAAGAGAGTGCCAGCAGCGGGAAGCTAGGCTTAATTACCAATA
-CTATTGCTGGAGTCGCAGGACTGATCACAGGCGGGAGAAGAACTCGAAGAGAAGCAATTGTCAATGCTCA
-ACCCAAATGCAACCCTAATTTACATTACTGGACTACTCAGGATGAAGGTGCTGCAATCGGACTGGCCTGG
-ATACCATATTTCGGGCCAGCAGCCGAGGGAATTTACATAGAGGGGCTAATGCACAATCAAGATGGTTTAA
-TCTGTGGGTTGAGACAGCTGGCCAACGAGACGACTCAAGCTCTTCAACTGTTCCTGAGAGCCACAACTGA
-GCTACGCACCTTTTCAATCCTCAACCGTAAGGCAATTGATTTCTTGCTGCAGCGATGGGGCGGCACATGC
-CACATTCTGGGACCGGACTGCTGTATCGAACCACATGATTGGACCAAGAACATAACAGACAAAATTGATC
-AGATTATTCATGATTTTGTTGATAAAACCCTTCCGGACCAGGGGGACAATGACAATTGGTGGACAGGATG
-GAGACAATGGATACCGGCAGGTATTGGAGTTACAGGCGTTATAATTGCAGTTATCGCTTTATTCTGTATA
-TGCAAATTTGTCTTTTAGTTTTTCTTCAGATTGCTTCATGGAAAAGCTCAGCCTCAAATCAATGAAACCA
-GGATTTAATTATATGGATTACTTGAATCTAAGATTACTTGACAAATGATAATATAATACACTGGAGCTTT
-AAACATAGCCAATGTGATTCTAACTCCTTTAAACTCACAGTTAATCATAAACAAGGTTTGACATCAATCT
-AGTTATCTCTTTGAGAATGATAAACTTGATGAAGATTAAGAAAAAGGTAATCTTTCGATTATCTTTAATC
-TTCATCCTTGATTCTACAATCATGACAGTTGTCTTTAGTGACAAGGGAAAGAAGCCTTTTTATTAAGTTG
-TAATAATCAGATCTGCGAACCGGTAGAGTTTAGTTGCAACCTAACACACATAAAGCATTGGTCAAAAAGT
-CAATAGAAATTTAAACAGTGAGTGGAGACAACTTTTAAATGGAAGCTTCATATGAGAGAGGACGCCCACG
-AGCTGCCAGACAGCATTCAAGGGATGGACACGACCACCATGTTCGAGCACGATCATCATCCAGAGAGAAT
-TATCGAGGTGAGTACCGTCAATCAAGGAGCGCCTCACAAGTGCGCGTTCCTACTGTATTTCATAAGAAGA
-GAGTTGAACCATTAACAGTTCCTCCAGCACCTAAAGACATATGTCCGACCTTGAAAAAAGGATTTTTGTG
-TGACAGTAGTTTTTGCAAAAAAGATCACCAGTTGGAGAGTTTAACTGATAGGGAATTACTCCTACTAATC
-GCCCGTAAGACTTGTGGATCAGTAGAACAACAATTAAATATAACTGCACCCAAGGACTCGCGCTTAGCAA
-ATCCAACGGCTGATGATTTCCAGCAAGAGGAAGGTCCAAAAATTACCTTGTTGACACTGATCAAGACGGC
-AGAACACTGGGCGAGACAAGACATCAGAACCATAGAGGATTCAAAATTAAGAGCATTGTTGACTCTATGT
-GCTGTGATGACGAGGAAATTCTCAAAATCCCAGCTGAGTCTTTTATGTGAGACACACCTAAGGCGCGAGG
-GGCTTGGGCAAGATCAGGCAGAACCCGTTCTCGAAGTATATCAACGATTACACAGTGATAAAGGAGGCAG
-TTTTGAAGCTGCACTATGGCAACAATGGGACCGACAATCCCTAATTATGTTTATCACTGCATTCTTGAAT
-ATTGCTCTCCAGTTACCGTGTGAAAGTTCTGCTGTCGTTGTTTCAGGGTTAAGAACATTGGTTCCTCAAT
-CAGATAATGAGGAAGCTTCAACCAACCCGGGGACATGCTCATGGTCTGATGAGGGTACCCCTTAATAAGG
-CTGACTAAAACACTATATAACCTTCTACTTGATCACAATACTCCGTATACCTATCATCATATATTTAATC
-AAGACGATATCCTTTAAAACTTATTCAGTACTATAATCACTCTCGTTTCAAATTAATAAGATGTGCATGA
-TTGCCCTAATATATGAAGAGGTATGATACAACCCTAACAGTGATCAAAGAAAATCATAATCTCGTATCGC
-TCGTAATATAACCTGCCAAGCATACCTCTTGCACAAAGTGATTCTTGTACACAAATAATGTTTTACTCTA
-CAGGAGGTAGCAACGATCCATCCCATCAAAAAATAAGTATTTCATGACTTACTAATGATCTCTTAAAATA
-TTAAGAAAAACTGACGGAACATAAATTCTTTATGCTTCAAGCTGTGGAGGAGGTGTTTGGTATTGGCTAT
-TGTTATATTACAATCAATAACAAGCTTGTAAAAATATTGTTCTTGTTTCAAGAGGTAGATTGTGACCGGA
-AATGCTAAACTAATGATGAAGATTAATGCGGAGGTCTGATAAGAATAAACCTTATTATTCAGATTAGGCC
-CCAAGAGGCATTCTTCATCTCCTTTTAGCAAAGTACTATTTCAGGGTAGTCCAATTAGTGGCACGTCTTT
-TAGCTGTATATCAGTCGCCCCTGAGATACGCCACAAAAGTGTCTCTAAGCTAAATTGGTCTGTACACATC
-CCATACATTGTATTAGGGGCAATAATATCTAATTGAACTTAGCCGTTTAAAATTTAGTGCATAAATCTGG
-GCTAACACCACCAGGTCAACTCCATTGGCTGAAAAGAAGCTTACCTACAACGAACATCACTTTGAGCGCC
-CTCACAATTAAAAAATAGGAACGTCGTTCCAACAATCGAGCGCAAGGTTTCAAGGTTGAACTGAGAGTGT
-CTAGACAACAAAATATTGATACTCCAGACACCAAGCAAGACCTGAGAAAAAACCATGGCTAAAGCTACGG
-GACGATACAATCTAATATCGCCCAAAAAGGACCTGGAGAAAGGGGTTGTCTTAAGCGACCTCTGTAACTT
-CTTAGTTAGCCAAACTATTCAGGGGTGGAAGGTTTATTGGGCTGGTATTGAGTTTGATGTGACTCACAAA
-GGAATGGCCCTATTGCATAGACTGAAAACTAATGACTTTGCCCCTGCATGGTCAATGACAAGGAATCTCT
-TTCCTCATTTATTTCAAAATCCGAATTCCACAATTGAATCACCGCTGTGGGCATTGAGAGTCATCCTTGC
-AGCAGGGATACAGGACCAGCTGATTGACCAGTCTTTGATTGAACCCTTAGCAGGAGCCCTTGGTCTGATC
-TCTGATTGGCTGCTAACAACCAACACTAACCATTTCAACATGCGAACACAACGTGTCAAGGAACAATTGA
-GCCTAAAAATGCTGTCGTTGATTCGATCCAATATTCTCAAGTTTATTAACAAATTGGATGCTCTACATGT
-CGTGAACTACAACGGATTGTTGAGCAGTATTGAAATTGGAACTCAAAATCATACAATCATCATAACTCGA
-ACTAACATGGGTTTTCTGGTGGAGCTCCAAGAACCCGACAAATCGGCAATGAACCGCATGAAGCCTGGGC
-CGGCGAAATTTTCCCTCCTTCATGAGTCCACACTGAAAGCATTTACACAAGGATCCTCGACACGAATGCA
-AAGTTTGATTCTTGAATTTAATAGCTCTCTTGCTATCTAACTAAGGTAGAATACTTCATATTGAGCTAAC
-TCATATATGCTGACTCAATAGTTATCTTGACATCTCTGCTTTCATAATCAGATATATAAGCATAATAAAT
-AAATACTCATATTTCTTGATAATTTGTTTAACCACAGATAAATCCTCACTGTAAGCCAGCTTCCAAGTTG
-ACACCCTTACAAAAACCAGGACTCAGAATCCCTCAAACAAGAGATTCCAAGACAACATCATAGAATTGCT
-TTATTATATGAATAAGCATTTTATCACCAGAAATCCTATATACTAAATGGTTAATTGTAACTGAACCCGC
-AGGTCACATGTGTTAGGTTTCACAGATTCTATATATTACTAACTCTATACTCGTAATTAACATTAGATAA
-GTAGATTAAGAAAAAAGCCTGAGGAAGATTAAGAAAAACTGCTTATTGGGTCTTTCCGTGTTTTAGATGA
-AGCAGTTGAAATTCTTCCTCTTGATATTAAATGGCTACACAACATACCCAATACCCAGACGCTAGGTTAT
-CATCACCAATTGTATTGGACCAATGTGACCTAGTCACTAGAGCTTGCGGGTTATATTCATCATACTCCCT
-TAATCCGCAACTACGCAACTGTAAACTCCCGAAACATATCTACCGTTTGAAATACGATGTAACTGTTACC
-AAGTTCTTGAGTGATGTACCAGTGGCGACATTGCCCATAGATTTCATAGTCCCAGTTCTTCTCAAGGCAC
-TGTCAGGCAATGGATTCTGTCCTGTTGAGCCGCGGTGCCAACAGTTCTTAGATGAAATCATTAAGTACAC
-AATGCAAGATGCTCTCTTCTTGAAATATTATCTCAAAAATGTGGGTGCTCAAGAAGACTGTGTTGATGAA
-CACTTTCAAGAGAAAATCTTATCTTCAATTCAGGGCAATGAATTTTTACATCAAATGTTTTTCTGGTATG
-ATCTGGCTATTTTAACTCGAAGGGGTAGATTAAATCGAGGAAACTCTAGATCAACATGGTTTGTTCATGA
-TGATTTAATAGACATCTTAGGCTATGGGGACTATGTTTTTTGGAAGATCCCAATTTCAATGTTACCACTG
-AACACACAAGGAATCCCCCATGCTGCTATGGACTGGTATCAGGCATCAGTATTCAAAGAAGCGGTTCAAG
-GGCATACACACATTGTTTCTGTTTCTACTGCCGACGTCTTGATAATGTGCAAAGATTTAATTACATGTCG
-ATTCAACACAACTCTAATCTCAAAAATAGCAGAGATTGAGGATCCAGTTTGTTCTGATTATCCCAATTTT
-AAGATTGTGTCTATGCTTTACCAGAGCGGAGATTACTTACTCTCCATATTAGGGTCTGATGGGTATAAAA
-TTATTAAGTTCCTCGAACCATTGTGCTTGGCCAAAATTCAATTATGCTCAAAGTACACTGAGAGGAAGGG
-CCGATTCTTAACACAAATGCATTTAGCTGTAAATCACACCCTAGAAGAAATTACAGAAATGCGTGCACTA
-AAGCCTTCACAGGCTCAAAAGATCCGTGAATTCCATAGAACATTGATAAGGCTGGAGATGACGCCACAAC
-AACTTTGTGAGCTATTTTCCATTCAAAAACACTGGGGGCATCCTGTGCTACATAGTGAAACAGCAATCCA
-AAAAGTTAAAAAACATGCTACGGTGCTAAAAGCATTACGCCCTATAGTGATTTTCGAGACATACTGTGTT
-TTTAAATATAGTATTGCCAAACATTATTTTGATAGTCAAGGATCTTGGTACAGTGTTACTTCAGATAGGA
-ATCTAACACCGGGTCTTAATTCTTATATCAAAAGAAATCAATTCCCTCCGTTGCCAATGATTAAAGAACT
-ACTATGGGAATTTTACCACCTTGACCACCCTCCACTTTTCTCAACCAAAATTATTAGTGACTTAAGTATT
-TTTATAAAAGACAGAGCTACCGCAGTAGAAAGGACATGCTGGGATGCAGTATTCGAGCCTAATGTTCTAG
-GATATAATCCACCTCACAAATTTAGTACTAAACGTGTACCGGAACAATTTTTAGAGCAAGAAAACTTTTC
-TATTGAGAATGTTCTTTCCTACGCACAAAAACTCGAGTATCTACTACCACAATATCGGAACTTTTCTTTC
-TCATTGAAAGAGAAAGAGTTGAATGTAGGTAGAACCTTCGGAAAATTGCCTTATCCGACTCGCAATGTTC
-AAACACTTTGTGAAGCTCTGTTAGCTGATGGTCTTGCTAAAGCATTTCCTAGCAATATGATGGTAGTTAC
-GGAACGTGAGCAAAAAGAAAGCTTATTGCATCAAGCATCATGGCACCACACAAGTGATGATTTTGGTGAA
-CATGCCACAGTTAGAGGGAGTAGCTTTGTAACTGATTTAGAGAAATACAATCTTGCATTTAGATATGAGT
-TTACAGCACCTTTTATAGAATATTGCAACCGTTGCTATGGTGTTAAGAATGTTTTTAATTGGATGCATTA
-TACAATCCCACAGTGTTATATGCATGTCAGTGATTATTATAATCCACCACATAACCTCACACTGGAGAAT
-CGAGACAACCCCCCCGAAGGGCCTAGTTCATACAGGGGTCATATGGGAGGGATTGAAGGACTGCAACAAA
-AACTCTGGACAAGTATTTCATGTGCTCAAATTTCTTTAGTTGAAATTAAGACTGGTTTTAAGTTACGCTC
-AGCTGTGATGGGTGACAATCAGTGCATTACTGTTTTATCAGTCTTCCCCTTAGAGACTGACGCAGACGAG
-CAGGAACAGAGCGCCGAAGACAATGCAGCGAGGGTGGCCGCCAGCCTAGCAAAAGTTACAAGTGCCTGTG
-GAATCTTTTTAAAACCTGATGAAACATTTGTACATTCAGGTTTTATCTATTTTGGAAAAAAACAATATTT
-GAATGGGGTCCAATTGCCTCAGTCCCTTAAAACGGCTACAAGAATGGCACCATTGTCTGATGCAATTTTT
-GATGATCTTCAAGGGACCCTGGCTAGTATAGGCACTGCTTTTGAGCGATCCATCTCTGAGACACGACATA
-TCTTTCCTTGCAGGATAACCGCAGCTTTCCATACGTTTTTTTCGGTGAGAATCTTGCAATATCATCATCT
-CGGGTTCAATAAAGGTTTTGACCTTGGACAGTTAACACTCGGCAAACCTCTGGATTTCGGAACAATATCA
-TTGGCACTAGCGGTACCGCAGGTGCTTGGAGGGTTATCCTTCTTGAATCCTGAGAAATGTTTCTACCGGA
-ATCTAGGAGATCCAGTTACCTCAGGCTTATTCCAGTTAAAAACTTATCTCCGAATGATTGAGATGGATGA
-TTTATTCTTACCTTTAATTGCGAAGAACCCTGGGAACTGCACTGCCATTGACTTTGTGCTAAATCCTAGC
-GGATTAAATGTCCCTGGGTCGCAAGACTTAACTTCATTTCTGCGCCAGATTGTACGCAGGACCATCACCC
-TAAGTGCGAAAAACAAACTTATTAATACCTTATTTCATGCGTCAGCTGACTTCGAAGACGAAATGGTTTG
-TAAATGGCTATTATCATCAACTCCTGTTATGAGTCGTTTTGCGGCCGATATCTTTTCACGCACGCCGAGC
-GGGAAGCGATTGCAAATTCTAGGATACCTGGAAGGAACACGCACATTATTAGCCTCTAAGATCATCAACA
-ATAATACAGAGACACCGGTTTTGGACAGACTGAGGAAAATAACATTGCAAAGGTGGAGCCTATGGTTTAG
-TTATCTTGATCATTGTGATAATATCCTGGCGGAGGCTTTAACCCAAATAACTTGCACAGTTGATTTAGCA
-CAGATTCTGAGGGAATATTCATGGGCTCATATTTTAGAGGGAAGACCTCTTATTGGAGCCACACTCCCAT
-GTATGATTGAGCAATTCAAAGTGTTTTGGCTGAAACCCTACGAACAATGTCCGCAGTGTTCAAATGCAAA
-GCAACCAGGTGGGAAACCATTCGTGTCAGTGGCAGTCAAGAAACATATTGTTAGTGCATGGCCGAACGCA
-TCCCGAATAAGCTGGACTATCGGGGATGGAATCCCATACATTGGATCAAGGACAGAAGATAAGATAGGAC
-AACCTGCTATTAAACCAAAATGTCCTTCCGCAGCCTTAAGAGAGGCCATTGAATTGGCGTCCCGTTTAAC
-ATGGGTAACTCAAGGCAGTTCGAACAGTGACTTGCTAATAAAACCATTTTTGGAAGCACGAGTAAATTTA
-AGTGTTCAAGAAATACTTCAAATGACCCCTTCACATTACTCAGGAAATATTGTTCACAGGTACAACGATC
-AATACAGTCCTCATTCTTTCATGGCCAATCGTATGAGTAATTCAGCAACGCGATTGATTGTTTCTACAAA
-CACTTTAGGTGAGTTTTCAGGAGGTGGCCAGTCTGCACGCGACAGCAATATTATTTTCCAGAATGTTATA
-AATTATGCAGTTGCACTGTTCGATATTAAATTTAGAAACACTGAGGCTACAGATATCCAATATAATCGTG
-CTCACCTTCATCTAACTAAGTGTTGCACCCGGGAAGTACCAGCTCAGTATTTAACATACACATCTACATT
-GGATTTAGATTTAACAAGATACCGAGAAAACGAATTGATTTATGACAGTAATCCTCTAAAAGGAGGACTC
-AATTGCAATATCTCATTCGATAATCCATTTTTCCAAGGTAAACGGCTGAACATTATAGAAGATGATCTTA
-TTCGACTGCCTCACTTATCTGGATGGGAGCTAGCCAAGACCATCATGCAATCAATTATTTCAGATAGCAA
-CAATTCATCTACAGACCCAATTAGCAGTGGAGAAACAAGATCATTCACTACCCATTTCTTAACTTATCCC
-AAGATAGGACTTCTGTACAGTTTTGGGGCCTTTGTAAGTTATTATCTTGGCAATACAATTCTTCGGACTA
-AGAAATTAACACTTGACAATTTTTTATATTACTTAACTACTCAAATTCATAATCTACCACATCGCTCATT
-GCGAATACTTAAGCCAACATTCAAACATGCAAGCGTTATGTCACGGTTAATGAGTATTGATCCTCATTTT
-TCTATTTACATAGGCGGTGCTGCAGGTGACAGAGGACTCTCAGATGCGGCCAGGTTATTTTTGAGAACGT
-CCATTTCATCTTTTCTTACATTTGTAAAAGAATGGATAATTAATCGCGGAACAATTGTCCCTTTATGGAT
-AGTATATCCGCTAGAGGGTCAAAACCCAACACCTGTGAATAATTTTCTCTATCAGATCGTAGAACTGCTG
-GTGCATGATTCATCAAGACAACAGGCTTTTAAAACTACCATAAGTGATCATGTACATCCTCACGACAATC
-TTGTTTACACATGTAAGAGTACAGCCAGCAATTTCTTCCATGCATCATTGGCGTACTGGAGGAGCAGACA
-CAGAAACAGCAACCGAAAATACTTGGCAAGAGACTCTTCAACTGGATCAAGCACAAACAACAGTGATGGT
-CATATTGAGAGAAGTCAAGAACAAACCACCAGAGATCCACATGATGGCACTGAACGGAATCTAGTCCTAC
-AAATGAGCCATGAAATAAAAAGAACGACAATTCCACAAGAAAACACGCACCAGGGTCCGTCGTTCCAGTC
-CTTTCTAAGTGACTCTGCTTGTGGTACAGCAAATCCAAAACTAAATTTCGATCGATCGAGACACAATGTG
-AAATTTCAGGATCATAACTCGGCATCCAAGAGGGAAGGTCATCAAATAATCTCACACCGTCTAGTCCTAC
-CTTTCTTTACATTATCTCAAGGGACACGCCAATTAACGTCATCCAATGAGTCACAAACCCAAGACGAGAT
-ATCAAAGTACTTACGGCAATTGAGATCCGTCATTGATACCACAGTTTATTGTAGATTTACCGGTATAGTC
-TCGTCCATGCATTACAAACTTGATGAGGTCCTTTGGGAAATAGAGAGTTTCAAGTCGGCTGTGACGCTAG
-CAGAGGGAGAAGGTGCTGGTGCCTTACTATTGATTCAGAAATACCAAGTTAAGACCTTATTTTTCAACAC
-GCTAGCTACTGAGTCCAGTATAGAGTCAGAAATAGTATCAGGAATGACTACTCCTAGGATGCTTCTACCT
-GTTATGTCAAAATTCCATAATGACCAAATTGAGATTATTCTTAACAACTCAGCAAGCCAAATAACAGACA
-TAACAAATCCTACTTGGTTTAAAGACCAAAGAGCAAGGCTACCTAAGCAAGTCGAGGTTATAACCATGGA
-TGCAGAGACAACAGAGAATATAAACAGATCGAAATTGTACGAAGCTGTATATAAATTGATCTTACACCAT
-ATTGATCCTAGCGTATTGAAAGCAGTGGTCCTTAAAGTCTTTCTAAGTGATACTGAGGGTATGTTATGGC
-TAAATGATAATTTAGCCCCGTTTTTTGCCACTGGTTATTTAATTAAGCCAATAACGTCAAGTGCTAGATC
-TAGTGAGTGGTATCTTTGTCTGACGAACTTCTTATCAACTACACGTAAGATGCCACACCAAAACCATCTC
-AGTTGTAAACAGGTAATACTTACGGCATTGCAACTGCAAATTCAACGAAGCCCATACTGGCTAAGTCATT
-TAACTCAGTATGCTGACTGTGAGTTACATTTAAGTTATATCCGCCTTGGTTTTCCATCATTAGAGAAAGT
-ACTATACCACAGGTATAACCTCGTCGATTCAAAAAGAGGTCCACTAGTCTCTATCACTCAGCACTTAGCA
-CATCTTAGAGCAGAGATTCGAGAATTAACTAATGATTATAATCAACAGCGACAAAGTCGGACTCAAACAT
-ATCACTTTATTCGTACTGCAAAAGGACGAATCACAAAACTAGTCAATGATTATTTAAAATTCTTTCTTAT
-TGTGCAAGCATTAAAACATAATGGGACATGGCAAGCTGAGTTTAAGAAATTACCAGAGTTGATTAGTGTG
-TGCAATAGGTTCTACCATATTAGAGATTGCAATTGTGAAGAACGTTTCTTAGTTCAAACCTTATATTTAC
-ATAGAATGCAGGATTCTGAAGTTAAGCTTATCGAAAGGCTGACAGGGCTTCTGAGTTTATTTCCGGATGG
-TCTCTACAGGTTTGATTGAATTACCGTGCATAGTATCCTGATACTTGCAAAGGTTGGTTATTAACATACA
-GATTATAAAAAACTCATAAATTGCTCTCATACATCATATTGATCTAATCTCAATAAACAACTATTTAAAT
-AACGAAAGGAGTCCCTATATTATATACTATATTTAGCCTCTCTCCCTGCGTGATAATCAAAAAATTCACA
-ATGCAGCATGTGTGACATATTACTGCCGCAATGAATTTAACGCAACATAATAAACTCTGCACTCTTTATA
-ATTAAGCTTTAACGAAAGGTCTGGGCTCATATTGTTATTGATATAATAATGTTGTATCAATATCCTGTCA
-GATGGAATAGTGTTTTGGTTGATAACACAACTTCTTAAAACAAAATTGATCTTTAAGATTAAGTTTTTTA
-TAATTATCATTACTTTAATTTGTCGTTTTAAAAACGGTGATAGCCTTAATCTTTGTGTAAAATAAGAGAT
-TAGGTGTAATAACCTTAACATTTTTGTCTAGTAAGCTACTATTTCATACAGAATGATAAAATTAAAAGAA
-AAGGCAGGACTGTAAAATCAGAAATACCTTCTTTACAATATAGCAGACTAGATAATAATCTTCGTGTTAA
-TGATAATTAAGACATTGACCACGCTCATCAGAAGGCTCGCCAGAATAAACGTTGCAAAAAGGATTCCTGG
-AAAAATGGTCGCACACAAAAATTTAAAAATAAATCTATTTCTTCTTTTTTGTGTGTCCA
-