changeset 1:c8752e31f496 draft

Uploaded
author bgruening
date Tue, 26 Nov 2013 06:10:20 -0500
parents 9ad15075b9fa
children 28b85e2409ce
files base_recalibrator.xml haplotype_caller.xml indel_realigner.xml print_reads.xml realigner_target_creator.xml reduce_reads.xml test-data/gatk/fake_phiX_reads_1.bam test-data/gatk/fake_phiX_variant_locations.bed test-data/gatk/fake_phiX_variant_locations.vcf test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.html test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.log.contains test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_cumulative_coverage_counts_sample.tabular test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_output_cumulative_coverage_proportions_sample.tabular test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains test-data/gatk/gatk_print_reads/gatk_print_reads_out_1.log.contains test-data/gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval test-data/gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf test-data/gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains test-data/gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf unified_genotyper.xml variant_annotator.xml variant_apply_recalibration.xml variant_combine.xml variant_eval.xml variant_filtration.xml variant_recalibrator.xml variant_select.xml variant_validate.xml
diffstat 48 files changed, 6138 insertions(+), 143 deletions(-) [+]
line wrap: on
line diff
--- a/base_recalibrator.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/base_recalibrator.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,15 +4,15 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-   #end if
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+    #end if
+    -p '
+    @JAR_PATH@
     -T "BaseRecalibrator"
     \$GATK2_SITE_OPTIONS
 
@@ -21,7 +21,6 @@
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/haplotype_caller.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/haplotype_caller.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,22 +4,22 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-   #end if
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+    #end if
+    -p '
+    @JAR_PATH@
     -T "HaplotypeCaller"
     -o "${output_vcf}"
 
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/indel_realigner.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/indel_realigner.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,15 +4,15 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-   #end if
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+    #end if
+    -p '
+    @JAR_PATH@
     -T "IndelRealigner"
     -o "${output_bam}"
 
@@ -23,7 +23,6 @@
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/print_reads.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/print_reads.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,15 +4,15 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-   #end if
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+    #end if
+    -p '
+    @JAR_PATH@
     -T "PrintReads"
     -o "${output_bam}"
     \$GATK2_SITE_OPTIONS
@@ -21,7 +21,7 @@
     --num_cpu_threads_per_data_thread 8
 
     @THREADS@
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/realigner_target_creator.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/realigner_target_creator.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,15 +4,15 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-   #end if
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+    #end if
+    -p '
+    @JAR_PATH@
     -T "RealignerTargetCreator"
     -o "${output_interval}"
 
@@ -23,7 +23,6 @@
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/reduce_reads.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/reduce_reads.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,15 +4,15 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-   #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-       -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-   #end if
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+    #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+        -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+    #end if
+    -p '
+    @JAR_PATH@
     -T "ReduceReads"
     -o "${output_bam}"
 
@@ -22,7 +22,7 @@
     --num_cpu_threads_per_data_thread 1
 
     @THREADS@
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
Binary file test-data/gatk/fake_phiX_reads_1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/fake_phiX_variant_locations.bed	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,2 @@
+phiX174	1442	1443
+phiX174	1445	1446
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/fake_phiX_variant_locations.vcf	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,70 @@
+##fileformat=VCFv4.1
+##samtoolsVersion=0.1.18 (r982:295)
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
+##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
+##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
+##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
+##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
+##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
+##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
+##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
+##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
+##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
+##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
+##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
+##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
+##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
+##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
+##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
+##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
+##INFO=<ID=VDB,Number=1,Type=Float,Description="Variant Distance Bias">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
+##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="List of Phred-scaled genotype likelihoods">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
+phiX174	1411	.	A	.	28.2	.	DP=1;;AC1=2;FQ=-30	PL	0
+phiX174	1412	.	G	.	28.2	.	DP=3;;AC1=2;FQ=-30	PL	0
+phiX174	1413	.	C	.	28.2	.	DP=5;;AC1=2;FQ=-30	PL	0
+phiX174	1414	.	G	.	28.2	.	DP=6;;AC1=2;FQ=-30	PL	0
+phiX174	1415	.	C	.	28.2	.	DP=7;;AC1=2;FQ=-30	PL	0
+phiX174	1416	.	C	.	28.2	.	DP=8;;AC1=2;FQ=-30	PL	0
+phiX174	1417	.	G	.	28.2	.	DP=9;;AC1=2;FQ=-30	PL	0
+phiX174	1418	.	T	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1419	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1420	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1421	.	A	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1422	.	T	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1423	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1424	.	C	.	28.2	.	DP=10;VDB=0.0005;;AC1=2;FQ=-30	PL	0
+phiX174	1425	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1426	.	T	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1427	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1428	.	A	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1429	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1430	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1431	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1432	.	T	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1433	.	A	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1434	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1435	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1436	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1437	.	A	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1438	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1439	.	G	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1440	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1441	.	T	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1442	.	A	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1443	.	A	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1444	.	C	.	28.2	.	DP=7;;AC1=2;FQ=-30	PL	0
+phiX174	1445	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1446	.	C	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1447	.	T	.	28.2	.	DP=10;;AC1=2;FQ=-30	PL	0
+phiX174	1448	.	A	.	28.2	.	DP=8;;AC1=2;FQ=-30	PL	0
+phiX174	1449	.	A	.	28.2	.	DP=6;;AC1=2;FQ=-30	PL	0
+phiX174	1450	.	T	.	28.2	.	DP=4;;AC1=2;FQ=-30	PL	0
+phiX174	1451	.	G	.	28.2	.	DP=3;;AC1=2;FQ=-30	PL	0
+phiX174	1452	.	A	.	28.2	.	DP=2;;AC1=2;FQ=-30	PL	0
+phiX174	1453	.	G	.	28.2	.	DP=1;;AC1=2;FQ=-30	PL	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.html	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,34 @@
+<html>
+<head>
+<title>Galaxy - GATK Output</title>
+</head>
+<body>
+<p/>
+<ul>
+<li><a href="A Fake phiX Sample.CycleCovariate.dat">A Fake phiX Sample.CycleCovariate.dat</a></li>
+<li><a href="A Fake phiX Sample.CycleCovariate.dat.Cycle_hist.pdf">A Fake phiX Sample.CycleCovariate.dat.Cycle_hist.pdf</a></li>
+<li><a href="A Fake phiX Sample.CycleCovariate.dat.qual_diff_v_Cycle.pdf">A Fake phiX Sample.CycleCovariate.dat.qual_diff_v_Cycle.pdf</a></li>
+<li><a href="A Fake phiX Sample.CycleCovariate.dat.reported_qual_v_Cycle.pdf">A Fake phiX Sample.CycleCovariate.dat.reported_qual_v_Cycle.pdf</a></li>
+<li><a href="A Fake phiX Sample.DinucCovariate.dat">A Fake phiX Sample.DinucCovariate.dat</a></li>
+<li><a href="A Fake phiX Sample.DinucCovariate.dat.Dinuc_hist.pdf">A Fake phiX Sample.DinucCovariate.dat.Dinuc_hist.pdf</a></li>
+<li><a href="A Fake phiX Sample.DinucCovariate.dat.qual_diff_v_Dinuc.pdf">A Fake phiX Sample.DinucCovariate.dat.qual_diff_v_Dinuc.pdf</a></li>
+<li><a href="A Fake phiX Sample.DinucCovariate.dat.reported_qual_v_Dinuc.pdf">A Fake phiX Sample.DinucCovariate.dat.reported_qual_v_Dinuc.pdf</a></li>
+<li><a href="A Fake phiX Sample.HomopolymerCovariate.dat">A Fake phiX Sample.HomopolymerCovariate.dat</a></li>
+<li><a href="A Fake phiX Sample.HomopolymerCovariate.dat.Homopolymer_hist.pdf">A Fake phiX Sample.HomopolymerCovariate.dat.Homopolymer_hist.pdf</a></li>
+<li><a href="A Fake phiX Sample.HomopolymerCovariate.dat.qual_diff_v_Homopolymer.pdf">A Fake phiX Sample.HomopolymerCovariate.dat.qual_diff_v_Homopolymer.pdf</a></li>
+<li><a href="A Fake phiX Sample.HomopolymerCovariate.dat.reported_qual_v_Homopolymer.pdf">A Fake phiX Sample.HomopolymerCovariate.dat.reported_qual_v_Homopolymer.pdf</a></li>
+<li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat">A Fake phiX Sample.MinimumNQSCovariate.dat</a></li>
+<li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat.MinimumNQS_hist.pdf">A Fake phiX Sample.MinimumNQSCovariate.dat.MinimumNQS_hist.pdf</a></li>
+<li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat.qual_diff_v_MinimumNQS.pdf">A Fake phiX Sample.MinimumNQSCovariate.dat.qual_diff_v_MinimumNQS.pdf</a></li>
+<li><a href="A Fake phiX Sample.MinimumNQSCovariate.dat.reported_qual_v_MinimumNQS.pdf">A Fake phiX Sample.MinimumNQSCovariate.dat.reported_qual_v_MinimumNQS.pdf</a></li>
+<li><a href="A Fake phiX Sample.PositionCovariate.dat">A Fake phiX Sample.PositionCovariate.dat</a></li>
+<li><a href="A Fake phiX Sample.PositionCovariate.dat.Position_hist.pdf">A Fake phiX Sample.PositionCovariate.dat.Position_hist.pdf</a></li>
+<li><a href="A Fake phiX Sample.PositionCovariate.dat.qual_diff_v_Position.pdf">A Fake phiX Sample.PositionCovariate.dat.qual_diff_v_Position.pdf</a></li>
+<li><a href="A Fake phiX Sample.PositionCovariate.dat.reported_qual_v_Position.pdf">A Fake phiX Sample.PositionCovariate.dat.reported_qual_v_Position.pdf</a></li>
+<li><a href="A Fake phiX Sample.QualityScoreCovariate.dat">A Fake phiX Sample.QualityScoreCovariate.dat</a></li>
+<li><a href="A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_hist.pdf">A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_hist.pdf</a></li>
+<li><a href="A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_v_stated.pdf">A Fake phiX Sample.QualityScoreCovariate.dat.quality_emp_v_stated.pdf</a></li>
+<li><a href="A Fake phiX Sample.QualityScoreCovariate.dat.quality_rep_hist.pdf">A Fake phiX Sample.QualityScoreCovariate.dat.quality_rep_hist.pdf</a></li>
+</ul>
+</body>
+</html>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_analyze_covariates/gatk_analyze_covariates_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,9 @@
+Program Name: org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates
+Reading in input csv file...
+...Done!
+Writing out intermediate tables for R...
+Writing out data tables for read group: A Fake phiX Sample	with 340 observations	and aggregate residual error = -9.136
+...Done!
+Calling analysis R scripts and writing out figures...
+Analyzing read group: A Fake phiX Sample
+...Done!
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.csv	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,246 @@
+# Counted Sites    41
+# Counted Bases    340
+# Skipped Sites    2
+# Fraction Skipped 1 / 21 bp
+ReadGroup,QualityScore,Cycle,Dinuc,Homopolymer,MinimumNQS,Position,nObservations,nMismatches,Qempirical
+A Fake phiX Sample,26,1,NN,0,26,0,9,0,40
+A Fake phiX Sample,26,1,NN,1,26,0,1,0,40
+A Fake phiX Sample,26,2,AG,0,26,1,1,0,40
+A Fake phiX Sample,26,2,CC,0,26,1,1,0,40
+A Fake phiX Sample,26,2,CG,0,26,1,3,0,40
+A Fake phiX Sample,26,2,GC,0,26,1,2,0,40
+A Fake phiX Sample,26,2,GC,1,26,1,1,0,40
+A Fake phiX Sample,26,2,GT,0,26,1,1,0,40
+A Fake phiX Sample,26,2,TG,1,26,1,1,0,40
+A Fake phiX Sample,26,3,CC,0,26,2,1,0,40
+A Fake phiX Sample,26,3,CG,0,26,2,3,0,40
+A Fake phiX Sample,26,3,GC,0,26,2,1,0,40
+A Fake phiX Sample,26,3,GC,1,26,2,2,0,40
+A Fake phiX Sample,26,3,GG,0,26,2,1,0,40
+A Fake phiX Sample,26,3,GT,0,26,2,1,0,40
+A Fake phiX Sample,26,3,TG,1,26,2,1,0,40
+A Fake phiX Sample,26,4,CC,0,26,3,2,0,40
+A Fake phiX Sample,26,4,CG,0,26,3,2,0,40
+A Fake phiX Sample,26,4,GA,0,26,3,1,0,40
+A Fake phiX Sample,26,4,GC,1,26,3,2,0,40
+A Fake phiX Sample,26,4,GG,0,26,3,1,0,40
+A Fake phiX Sample,26,4,GT,0,26,3,1,0,40
+A Fake phiX Sample,26,4,TG,1,26,3,1,0,40
+A Fake phiX Sample,26,5,AT,0,26,4,1,0,40
+A Fake phiX Sample,26,5,CC,0,26,4,2,0,40
+A Fake phiX Sample,26,5,CG,0,26,4,2,0,40
+A Fake phiX Sample,26,5,GA,0,26,4,1,0,40
+A Fake phiX Sample,26,5,GC,1,26,4,1,0,40
+A Fake phiX Sample,26,5,GG,0,26,4,1,0,40
+A Fake phiX Sample,26,5,GT,0,26,4,1,0,40
+A Fake phiX Sample,26,5,TG,1,26,4,1,0,40
+A Fake phiX Sample,26,6,AT,0,26,5,1,0,40
+A Fake phiX Sample,26,6,CC,0,26,5,1,0,40
+A Fake phiX Sample,26,6,CG,0,26,5,2,0,40
+A Fake phiX Sample,26,6,GA,0,26,5,1,0,40
+A Fake phiX Sample,26,6,GG,0,26,5,1,0,40
+A Fake phiX Sample,26,6,GT,0,26,5,2,0,40
+A Fake phiX Sample,26,6,TG,0,26,5,1,0,40
+A Fake phiX Sample,26,6,TG,1,26,5,1,0,40
+A Fake phiX Sample,26,7,AT,0,26,6,1,0,40
+A Fake phiX Sample,26,7,CG,0,26,6,1,0,40
+A Fake phiX Sample,26,7,GA,0,26,6,2,1,3
+A Fake phiX Sample,26,7,GG,0,26,6,1,0,40
+A Fake phiX Sample,26,7,GT,0,26,6,2,0,40
+A Fake phiX Sample,26,7,TG,0,26,6,1,0,40
+A Fake phiX Sample,26,7,TG,1,26,6,2,0,40
+A Fake phiX Sample,26,8,AC,0,26,7,1,0,40
+A Fake phiX Sample,26,8,AT,0,26,7,1,0,40
+A Fake phiX Sample,26,8,GA,0,26,7,2,1,3
+A Fake phiX Sample,26,8,GG,0,26,7,2,0,40
+A Fake phiX Sample,26,8,GT,0,26,7,1,0,40
+A Fake phiX Sample,26,8,TG,0,26,7,1,0,40
+A Fake phiX Sample,26,8,TG,1,26,7,2,0,40
+A Fake phiX Sample,26,9,AC,0,26,8,1,0,40
+A Fake phiX Sample,26,9,AT,0,26,8,1,0,40
+A Fake phiX Sample,26,9,CT,0,26,8,1,0,40
+A Fake phiX Sample,26,9,GA,0,26,8,3,1,5
+A Fake phiX Sample,26,9,GG,0,26,8,2,0,40
+A Fake phiX Sample,26,9,TG,0,26,8,1,0,40
+A Fake phiX Sample,26,9,TG,1,26,8,1,0,40
+A Fake phiX Sample,26,10,AC,0,26,9,1,0,40
+A Fake phiX Sample,26,10,AT,0,26,9,2,0,40
+A Fake phiX Sample,26,10,CT,0,26,9,1,0,40
+A Fake phiX Sample,26,10,GA,0,26,9,3,1,5
+A Fake phiX Sample,26,10,GG,0,26,9,1,0,40
+A Fake phiX Sample,26,10,TG,0,26,9,2,0,40
+A Fake phiX Sample,26,11,AC,0,26,10,1,0,40
+A Fake phiX Sample,26,11,AT,0,26,10,2,0,40
+A Fake phiX Sample,26,11,CT,0,26,10,1,0,40
+A Fake phiX Sample,26,11,GA,0,26,10,3,1,5
+A Fake phiX Sample,26,11,TG,0,26,10,3,0,40
+A Fake phiX Sample,26,12,AC,0,26,11,1,0,40
+A Fake phiX Sample,26,12,AC,1,26,11,1,0,40
+A Fake phiX Sample,26,12,AT,0,26,11,1,0,40
+A Fake phiX Sample,26,12,CT,0,26,11,1,0,40
+A Fake phiX Sample,26,12,GA,0,26,11,2,1,3
+A Fake phiX Sample,26,12,GC,1,26,11,1,0,40
+A Fake phiX Sample,26,12,TG,0,26,11,3,0,40
+A Fake phiX Sample,26,13,AC,0,26,12,1,0,40
+A Fake phiX Sample,26,13,AC,1,26,12,1,0,40
+A Fake phiX Sample,26,13,CC,0,26,12,2,0,40
+A Fake phiX Sample,26,13,CT,0,26,12,1,0,40
+A Fake phiX Sample,26,13,GA,0,26,12,2,1,3
+A Fake phiX Sample,26,13,GC,1,26,12,1,0,40
+A Fake phiX Sample,26,13,TG,0,26,12,2,0,40
+A Fake phiX Sample,26,14,AC,0,26,13,1,0,40
+A Fake phiX Sample,26,14,AC,1,26,13,1,0,40
+A Fake phiX Sample,26,14,CC,0,26,13,2,0,40
+A Fake phiX Sample,26,14,CG,0,26,13,1,0,40
+A Fake phiX Sample,26,14,CT,0,26,13,2,0,40
+A Fake phiX Sample,26,14,GA,0,26,13,1,0,40
+A Fake phiX Sample,26,14,GC,1,26,13,1,0,40
+A Fake phiX Sample,26,14,TG,0,26,13,1,0,40
+A Fake phiX Sample,26,15,AC,1,26,14,1,0,40
+A Fake phiX Sample,26,15,CC,0,26,14,2,0,40
+A Fake phiX Sample,26,15,CG,0,26,14,1,0,40
+A Fake phiX Sample,26,15,CT,0,26,14,2,0,40
+A Fake phiX Sample,26,15,GA,0,26,14,1,0,40
+A Fake phiX Sample,26,15,GT,0,26,14,1,0,40
+A Fake phiX Sample,26,15,TG,0,26,14,2,0,40
+A Fake phiX Sample,26,16,AC,1,26,15,1,0,40
+A Fake phiX Sample,26,16,CC,0,26,15,1,0,40
+A Fake phiX Sample,26,16,CG,0,26,15,1,0,40
+A Fake phiX Sample,26,16,CT,0,26,15,1,0,40
+A Fake phiX Sample,26,16,GA,0,26,15,2,0,40
+A Fake phiX Sample,26,16,GT,0,26,15,1,0,40
+A Fake phiX Sample,26,16,TA,0,26,15,1,0,40
+A Fake phiX Sample,26,16,TG,0,26,15,2,0,40
+A Fake phiX Sample,26,17,AC,1,26,16,3,0,40
+A Fake phiX Sample,26,17,CC,0,26,16,1,0,40
+A Fake phiX Sample,26,17,CG,0,26,16,1,0,40
+A Fake phiX Sample,26,17,GA,0,26,16,2,0,40
+A Fake phiX Sample,26,17,GT,0,26,16,1,0,40
+A Fake phiX Sample,26,17,TA,0,26,16,1,0,40
+A Fake phiX Sample,26,17,TG,0,26,16,1,0,40
+A Fake phiX Sample,26,18,AC,1,26,17,3,0,40
+A Fake phiX Sample,26,18,CC,0,26,17,3,0,40
+A Fake phiX Sample,26,18,CG,0,26,17,1,0,40
+A Fake phiX Sample,26,18,GA,0,26,17,1,0,40
+A Fake phiX Sample,26,18,GT,0,26,17,1,0,40
+A Fake phiX Sample,26,18,TA,0,26,17,1,0,40
+A Fake phiX Sample,26,19,AC,1,26,18,2,0,40
+A Fake phiX Sample,26,19,CC,0,26,18,3,0,40
+A Fake phiX Sample,26,19,CG,0,26,18,3,0,40
+A Fake phiX Sample,26,19,GT,0,26,18,1,0,40
+A Fake phiX Sample,26,19,TA,0,26,18,1,0,40
+A Fake phiX Sample,26,20,AC,1,26,19,1,0,40
+A Fake phiX Sample,26,20,CC,0,26,19,2,0,40
+A Fake phiX Sample,26,20,CG,0,26,19,3,0,40
+A Fake phiX Sample,26,20,GA,0,26,19,1,0,40
+A Fake phiX Sample,26,20,GT,0,26,19,2,0,40
+A Fake phiX Sample,26,20,TA,0,26,19,1,0,40
+A Fake phiX Sample,26,21,AC,1,26,20,1,0,40
+A Fake phiX Sample,26,21,AG,1,26,20,1,0,40
+A Fake phiX Sample,26,21,CC,0,26,20,1,0,40
+A Fake phiX Sample,26,21,CG,0,26,20,2,0,40
+A Fake phiX Sample,26,21,GA,0,26,20,1,0,40
+A Fake phiX Sample,26,21,GT,0,26,20,2,0,40
+A Fake phiX Sample,26,21,TA,0,26,20,2,0,40
+A Fake phiX Sample,26,22,AC,1,26,21,2,0,40
+A Fake phiX Sample,26,22,AG,1,26,21,1,0,40
+A Fake phiX Sample,26,22,CC,0,26,21,1,0,40
+A Fake phiX Sample,26,22,CG,0,26,21,1,0,40
+A Fake phiX Sample,26,22,GA,0,26,21,1,0,40
+A Fake phiX Sample,26,22,GG,0,26,21,1,0,40
+A Fake phiX Sample,26,22,GT,0,26,21,1,0,40
+A Fake phiX Sample,26,22,TA,0,26,21,2,0,40
+A Fake phiX Sample,26,23,AC,1,26,22,2,0,40
+A Fake phiX Sample,26,23,AG,1,26,22,1,0,40
+A Fake phiX Sample,26,23,CC,0,26,22,2,0,40
+A Fake phiX Sample,26,23,CG,0,26,22,1,0,40
+A Fake phiX Sample,26,23,GA,0,26,22,1,0,40
+A Fake phiX Sample,26,23,GC,0,26,22,1,0,40
+A Fake phiX Sample,26,23,GG,0,26,22,1,0,40
+A Fake phiX Sample,26,23,TA,0,26,22,1,0,40
+A Fake phiX Sample,26,24,AC,1,26,23,1,0,40
+A Fake phiX Sample,26,24,AG,1,26,23,1,0,40
+A Fake phiX Sample,26,24,CC,0,26,23,2,0,40
+A Fake phiX Sample,26,24,CG,0,26,23,2,0,40
+A Fake phiX Sample,26,24,CT,0,26,23,1,0,40
+A Fake phiX Sample,26,24,GA,0,26,23,1,0,40
+A Fake phiX Sample,26,24,GC,0,26,23,1,0,40
+A Fake phiX Sample,26,24,GG,0,26,23,1,0,40
+A Fake phiX Sample,26,25,AG,1,26,24,1,0,40
+A Fake phiX Sample,26,25,CC,0,26,24,1,0,40
+A Fake phiX Sample,26,25,CG,0,26,24,2,0,40
+A Fake phiX Sample,26,25,CT,0,26,24,1,0,40
+A Fake phiX Sample,26,25,GA,0,26,24,2,0,40
+A Fake phiX Sample,26,25,GC,0,26,24,1,0,40
+A Fake phiX Sample,26,25,GG,0,26,24,1,0,40
+A Fake phiX Sample,26,25,TA,1,26,24,1,0,40
+A Fake phiX Sample,26,26,AG,1,26,25,2,0,40
+A Fake phiX Sample,26,26,CG,0,26,25,1,0,40
+A Fake phiX Sample,26,26,CT,0,26,25,1,0,40
+A Fake phiX Sample,26,26,GA,0,26,25,2,0,40
+A Fake phiX Sample,26,26,GC,0,26,25,1,0,40
+A Fake phiX Sample,26,26,GG,0,26,25,1,0,40
+A Fake phiX Sample,26,26,TA,1,26,25,1,0,40
+A Fake phiX Sample,26,27,AC,2,26,26,1,0,40
+A Fake phiX Sample,26,27,AG,1,26,26,2,0,40
+A Fake phiX Sample,26,27,CT,0,26,26,1,0,40
+A Fake phiX Sample,26,27,GA,0,26,26,1,0,40
+A Fake phiX Sample,26,27,GC,0,26,26,1,0,40
+A Fake phiX Sample,26,27,GG,0,26,26,2,0,40
+A Fake phiX Sample,26,27,TA,1,26,26,1,0,40
+A Fake phiX Sample,26,28,AC,2,26,27,1,0,40
+A Fake phiX Sample,26,28,AG,1,26,27,1,0,40
+A Fake phiX Sample,26,28,CC,1,26,27,1,0,40
+A Fake phiX Sample,26,28,CT,0,26,27,1,0,40
+A Fake phiX Sample,26,28,GC,0,26,27,2,0,40
+A Fake phiX Sample,26,28,GG,0,26,27,2,0,40
+A Fake phiX Sample,26,28,TA,1,26,27,1,0,40
+A Fake phiX Sample,26,29,AC,2,26,28,1,0,40
+A Fake phiX Sample,26,29,CC,1,26,28,1,0,40
+A Fake phiX Sample,26,29,CT,0,26,28,2,0,40
+A Fake phiX Sample,26,29,GC,0,26,28,2,0,40
+A Fake phiX Sample,26,29,GG,0,26,28,1,0,40
+A Fake phiX Sample,26,29,TA,1,26,28,1,0,40
+A Fake phiX Sample,26,30,AC,2,26,29,1,0,40
+A Fake phiX Sample,26,30,CC,1,26,29,1,0,40
+A Fake phiX Sample,26,30,CT,0,26,29,3,0,40
+A Fake phiX Sample,26,30,GC,0,26,29,1,0,40
+A Fake phiX Sample,26,30,TA,1,26,29,2,0,40
+A Fake phiX Sample,26,31,AC,2,26,30,1,0,40
+A Fake phiX Sample,26,31,CC,1,26,30,1,0,40
+A Fake phiX Sample,26,31,CT,0,26,30,2,0,40
+A Fake phiX Sample,26,31,TA,1,26,30,3,0,40
+A Fake phiX Sample,26,32,AA,0,26,31,1,0,40
+A Fake phiX Sample,26,32,AC,1,26,31,1,0,40
+A Fake phiX Sample,26,32,AC,2,26,31,1,0,40
+A Fake phiX Sample,26,32,CC,1,26,31,1,0,40
+A Fake phiX Sample,26,32,CT,0,26,31,1,0,40
+A Fake phiX Sample,26,32,TA,1,26,31,2,0,40
+A Fake phiX Sample,26,33,AA,0,26,32,1,0,40
+A Fake phiX Sample,26,33,AC,1,26,32,1,0,40
+A Fake phiX Sample,26,33,AC,2,26,32,1,0,40
+A Fake phiX Sample,26,33,AT,0,26,32,1,0,40
+A Fake phiX Sample,26,33,CC,1,26,32,1,0,40
+A Fake phiX Sample,26,33,CT,0,26,32,1,0,40
+A Fake phiX Sample,26,33,TA,1,26,32,1,0,40
+A Fake phiX Sample,26,34,AA,0,26,33,1,0,40
+A Fake phiX Sample,26,34,AC,1,26,33,1,0,40
+A Fake phiX Sample,26,34,AT,0,26,33,1,0,40
+A Fake phiX Sample,26,34,CC,1,26,33,1,0,40
+A Fake phiX Sample,26,34,CT,0,26,33,2,0,40
+A Fake phiX Sample,26,34,TA,1,26,33,1,0,40
+A Fake phiX Sample,26,34,TG,0,26,33,1,0,40
+A Fake phiX Sample,26,35,AA,0,26,34,1,0,40
+A Fake phiX Sample,26,35,AT,0,26,34,1,0,40
+A Fake phiX Sample,26,35,CT,0,26,34,2,0,40
+A Fake phiX Sample,26,35,GA,0,26,34,1,0,40
+A Fake phiX Sample,26,35,TA,1,26,34,2,0,40
+A Fake phiX Sample,26,35,TG,0,26,34,1,0,40
+A Fake phiX Sample,26,36,AA,0,26,35,2,0,40
+A Fake phiX Sample,26,36,AG,0,26,35,1,0,40
+A Fake phiX Sample,26,36,AT,0,26,35,1,0,40
+A Fake phiX Sample,26,36,CT,0,26,35,2,0,40
+A Fake phiX Sample,26,36,GA,0,26,35,1,0,40
+A Fake phiX Sample,26,36,TA,0,26,35,2,0,40
+A Fake phiX Sample,26,36,TG,0,26,35,1,0,40
+EOF
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_count_covariates/gatk_count_covariates_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,13 @@
+GenomeAnalysisEngine - Strictness is SILENT
+CountCovariatesWalker - The covariates being used here:
+CountCovariatesWalker - 	ReadGroupCovariate
+CountCovariatesWalker - 	QualityScoreCovariate
+CountCovariatesWalker - 	CycleCovariate
+CountCovariatesWalker - 	DinucCovariate
+CountCovariatesWalker - 	HomopolymerCovariate
+CountCovariatesWalker - 	MinimumNQSCovariate
+CountCovariatesWalker - 	PositionCovariate
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
+CountCovariatesWalker - Writing raw recalibration data...
+CountCovariatesWalker - ...done!
+TraversalEngine - Total runtime
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,6 @@
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
+TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining 
+DepthOfCoverageWalker - Printing summary info 
+DepthOfCoverageWalker - Printing locus summary 
+TraversalEngine - Total runtime
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%)
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_cumulative_coverage_counts_sample.tabular	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,2 @@
+	gte_0	gte_1	gte_2	gte_3	gte_4	gte_5	gte_6	gte_7	gte_8	gte_9	gte_10	gte_11	gte_12	gte_13	gte_14	gte_15	gte_16	gte_17	gte_18	gte_19	gte_20	gte_21	gte_22	gte_23	gte_24	gte_25	gte_26	gte_27	gte_28	gte_29	gte_30	gte_31	gte_32	gte_33	gte_34	gte_35	gte_36	gte_37	gte_38	gte_39	gte_40	gte_41	gte_42	gte_43	gte_44	gte_45	gte_46	gte_47	gte_48	gte_49	gte_50	gte_51	gte_52	gte_53	gte_54	gte_55	gte_56	gte_57	gte_58	gte_59	gte_60	gte_61	gte_62	gte_63	gte_64	gte_65	gte_66	gte_67	gte_68	gte_69	gte_70	gte_71	gte_72	gte_73	gte_74	gte_75	gte_76	gte_77	gte_78	gte_79	gte_80	gte_81	gte_82	gte_83	gte_84	gte_85	gte_86	gte_87	gte_88	gte_89	gte_90	gte_91	gte_92	gte_93	gte_94	gte_95	gte_96	gte_97	gte_98	gte_99	gte_100	gte_101	gte_102	gte_103	gte_104	gte_105	gte_106	gte_107	gte_108	gte_109	gte_110	gte_111	gte_112	gte_113	gte_114	gte_115	gte_116	gte_117	gte_118	gte_119	gte_120	gte_121	gte_122	gte_123	gte_124	gte_125	gte_126	gte_127	gte_128	gte_129	gte_130	gte_131	gte_132	gte_133	gte_134	gte_135	gte_136	gte_137	gte_138	gte_139	gte_140	gte_141	gte_142	gte_143	gte_144	gte_145	gte_146	gte_147	gte_148	gte_149	gte_150	gte_151	gte_152	gte_153	gte_154	gte_155	gte_156	gte_157	gte_158	gte_159	gte_160	gte_161	gte_162	gte_163	gte_164	gte_165	gte_166	gte_167	gte_168	gte_169	gte_170	gte_171	gte_172	gte_173	gte_174	gte_175	gte_176	gte_177	gte_178	gte_179	gte_180	gte_181	gte_182	gte_183	gte_184	gte_185	gte_186	gte_187	gte_188	gte_189	gte_190	gte_191	gte_192	gte_193	gte_194	gte_195	gte_196	gte_197	gte_198	gte_199	gte_200	gte_201	gte_202	gte_203	gte_204	gte_205	gte_206	gte_207	gte_208	gte_209	gte_210	gte_211	gte_212	gte_213	gte_214	gte_215	gte_216	gte_217	gte_218	gte_219	gte_220	gte_221	gte_222	gte_223	gte_224	gte_225	gte_226	gte_227	gte_228	gte_229	gte_230	gte_231	gte_232	gte_233	gte_234	gte_235	gte_236	gte_237	gte_238	gte_239	gte_240	gte_241	gte_242	gte_243	gte_244	gte_245	gte_246	gte_247	gte_248	gte_249	gte_250	gte_251	gte_252	gte_253	gte_254	gte_255	gte_256	gte_257	gte_258	gte_259	gte_260	gte_261	gte_262	gte_263	gte_264	gte_265	gte_266	gte_267	gte_268	gte_269	gte_270	gte_271	gte_272	gte_273	gte_274	gte_275	gte_276	gte_277	gte_278	gte_279	gte_280	gte_281	gte_282	gte_283	gte_284	gte_285	gte_286	gte_287	gte_288	gte_289	gte_290	gte_291	gte_292	gte_293	gte_294	gte_295	gte_296	gte_297	gte_298	gte_299	gte_300	gte_301	gte_302	gte_303	gte_304	gte_305	gte_306	gte_307	gte_308	gte_309	gte_310	gte_311	gte_312	gte_313	gte_314	gte_315	gte_316	gte_317	gte_318	gte_319	gte_320	gte_321	gte_322	gte_323	gte_324	gte_325	gte_326	gte_327	gte_328	gte_329	gte_330	gte_331	gte_332	gte_333	gte_334	gte_335	gte_336	gte_337	gte_338	gte_339	gte_340	gte_341	gte_342	gte_343	gte_344	gte_345	gte_346	gte_347	gte_348	gte_349	gte_350	gte_351	gte_352	gte_353	gte_354	gte_355	gte_356	gte_357	gte_358	gte_359	gte_360	gte_361	gte_362	gte_363	gte_364	gte_365	gte_366	gte_367	gte_368	gte_369	gte_370	gte_371	gte_372	gte_373	gte_374	gte_375	gte_376	gte_377	gte_378	gte_379	gte_380	gte_381	gte_382	gte_383	gte_384	gte_385	gte_386	gte_387	gte_388	gte_389	gte_390	gte_391	gte_392	gte_393	gte_394	gte_395	gte_396	gte_397	gte_398	gte_399	gte_400	gte_401	gte_402	gte_403	gte_404	gte_405	gte_406	gte_407	gte_408	gte_409	gte_410	gte_411	gte_412	gte_413	gte_414	gte_415	gte_416	gte_417	gte_418	gte_419	gte_420	gte_421	gte_422	gte_423	gte_424	gte_425	gte_426	gte_427	gte_428	gte_429	gte_430	gte_431	gte_432	gte_433	gte_434	gte_435	gte_436	gte_437	gte_438	gte_439	gte_440	gte_441	gte_442	gte_443	gte_444	gte_445	gte_446	gte_447	gte_448	gte_449	gte_450	gte_451	gte_452	gte_453	gte_454	gte_455	gte_456	gte_457	gte_458	gte_459	gte_460	gte_461	gte_462	gte_463	gte_464	gte_465	gte_466	gte_467	gte_468	gte_469	gte_470	gte_471	gte_472	gte_473	gte_474	gte_475	gte_476	gte_477	gte_478	gte_479	gte_480	gte_481	gte_482	gte_483	gte_484	gte_485	gte_486	gte_487	gte_488	gte_489	gte_490	gte_491	gte_492	gte_493	gte_494	gte_495	gte_496	gte_497	gte_498	gte_499	gte_500
+NSamples_1	5386	43	41	40	38	37	36	34	32	30	29	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_output_cumulative_coverage_proportions_sample.tabular	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,2 @@
+	gte_0	gte_1	gte_2	gte_3	gte_4	gte_5	gte_6	gte_7	gte_8	gte_9	gte_10	gte_11	gte_12	gte_13	gte_14	gte_15	gte_16	gte_17	gte_18	gte_19	gte_20	gte_21	gte_22	gte_23	gte_24	gte_25	gte_26	gte_27	gte_28	gte_29	gte_30	gte_31	gte_32	gte_33	gte_34	gte_35	gte_36	gte_37	gte_38	gte_39	gte_40	gte_41	gte_42	gte_43	gte_44	gte_45	gte_46	gte_47	gte_48	gte_49	gte_50	gte_51	gte_52	gte_53	gte_54	gte_55	gte_56	gte_57	gte_58	gte_59	gte_60	gte_61	gte_62	gte_63	gte_64	gte_65	gte_66	gte_67	gte_68	gte_69	gte_70	gte_71	gte_72	gte_73	gte_74	gte_75	gte_76	gte_77	gte_78	gte_79	gte_80	gte_81	gte_82	gte_83	gte_84	gte_85	gte_86	gte_87	gte_88	gte_89	gte_90	gte_91	gte_92	gte_93	gte_94	gte_95	gte_96	gte_97	gte_98	gte_99	gte_100	gte_101	gte_102	gte_103	gte_104	gte_105	gte_106	gte_107	gte_108	gte_109	gte_110	gte_111	gte_112	gte_113	gte_114	gte_115	gte_116	gte_117	gte_118	gte_119	gte_120	gte_121	gte_122	gte_123	gte_124	gte_125	gte_126	gte_127	gte_128	gte_129	gte_130	gte_131	gte_132	gte_133	gte_134	gte_135	gte_136	gte_137	gte_138	gte_139	gte_140	gte_141	gte_142	gte_143	gte_144	gte_145	gte_146	gte_147	gte_148	gte_149	gte_150	gte_151	gte_152	gte_153	gte_154	gte_155	gte_156	gte_157	gte_158	gte_159	gte_160	gte_161	gte_162	gte_163	gte_164	gte_165	gte_166	gte_167	gte_168	gte_169	gte_170	gte_171	gte_172	gte_173	gte_174	gte_175	gte_176	gte_177	gte_178	gte_179	gte_180	gte_181	gte_182	gte_183	gte_184	gte_185	gte_186	gte_187	gte_188	gte_189	gte_190	gte_191	gte_192	gte_193	gte_194	gte_195	gte_196	gte_197	gte_198	gte_199	gte_200	gte_201	gte_202	gte_203	gte_204	gte_205	gte_206	gte_207	gte_208	gte_209	gte_210	gte_211	gte_212	gte_213	gte_214	gte_215	gte_216	gte_217	gte_218	gte_219	gte_220	gte_221	gte_222	gte_223	gte_224	gte_225	gte_226	gte_227	gte_228	gte_229	gte_230	gte_231	gte_232	gte_233	gte_234	gte_235	gte_236	gte_237	gte_238	gte_239	gte_240	gte_241	gte_242	gte_243	gte_244	gte_245	gte_246	gte_247	gte_248	gte_249	gte_250	gte_251	gte_252	gte_253	gte_254	gte_255	gte_256	gte_257	gte_258	gte_259	gte_260	gte_261	gte_262	gte_263	gte_264	gte_265	gte_266	gte_267	gte_268	gte_269	gte_270	gte_271	gte_272	gte_273	gte_274	gte_275	gte_276	gte_277	gte_278	gte_279	gte_280	gte_281	gte_282	gte_283	gte_284	gte_285	gte_286	gte_287	gte_288	gte_289	gte_290	gte_291	gte_292	gte_293	gte_294	gte_295	gte_296	gte_297	gte_298	gte_299	gte_300	gte_301	gte_302	gte_303	gte_304	gte_305	gte_306	gte_307	gte_308	gte_309	gte_310	gte_311	gte_312	gte_313	gte_314	gte_315	gte_316	gte_317	gte_318	gte_319	gte_320	gte_321	gte_322	gte_323	gte_324	gte_325	gte_326	gte_327	gte_328	gte_329	gte_330	gte_331	gte_332	gte_333	gte_334	gte_335	gte_336	gte_337	gte_338	gte_339	gte_340	gte_341	gte_342	gte_343	gte_344	gte_345	gte_346	gte_347	gte_348	gte_349	gte_350	gte_351	gte_352	gte_353	gte_354	gte_355	gte_356	gte_357	gte_358	gte_359	gte_360	gte_361	gte_362	gte_363	gte_364	gte_365	gte_366	gte_367	gte_368	gte_369	gte_370	gte_371	gte_372	gte_373	gte_374	gte_375	gte_376	gte_377	gte_378	gte_379	gte_380	gte_381	gte_382	gte_383	gte_384	gte_385	gte_386	gte_387	gte_388	gte_389	gte_390	gte_391	gte_392	gte_393	gte_394	gte_395	gte_396	gte_397	gte_398	gte_399	gte_400	gte_401	gte_402	gte_403	gte_404	gte_405	gte_406	gte_407	gte_408	gte_409	gte_410	gte_411	gte_412	gte_413	gte_414	gte_415	gte_416	gte_417	gte_418	gte_419	gte_420	gte_421	gte_422	gte_423	gte_424	gte_425	gte_426	gte_427	gte_428	gte_429	gte_430	gte_431	gte_432	gte_433	gte_434	gte_435	gte_436	gte_437	gte_438	gte_439	gte_440	gte_441	gte_442	gte_443	gte_444	gte_445	gte_446	gte_447	gte_448	gte_449	gte_450	gte_451	gte_452	gte_453	gte_454	gte_455	gte_456	gte_457	gte_458	gte_459	gte_460	gte_461	gte_462	gte_463	gte_464	gte_465	gte_466	gte_467	gte_468	gte_469	gte_470	gte_471	gte_472	gte_473	gte_474	gte_475	gte_476	gte_477	gte_478	gte_479	gte_480	gte_481	gte_482	gte_483	gte_484	gte_485	gte_486	gte_487	gte_488	gte_489	gte_490	gte_491	gte_492	gte_493	gte_494	gte_495	gte_496	gte_497	gte_498	gte_499	gte_500
+A Fake phiX Sample	1.00	0.01	0.01	0.01	0.01	0.01	0.01	0.01	0.01	0.01	0.01	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00	0.00
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_per_locus_coverage.tabular	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,5387 @@
+Locus	Total_Depth	Average_Depth_sample	Depth_for_A Fake phiX Sample
+phiX174:1	0	0.00	0
+phiX174:2	0	0.00	0
+phiX174:3	0	0.00	0
+phiX174:4	0	0.00	0
+phiX174:5	0	0.00	0
+phiX174:6	0	0.00	0
+phiX174:7	0	0.00	0
+phiX174:8	0	0.00	0
+phiX174:9	0	0.00	0
+phiX174:10	0	0.00	0
+phiX174:11	0	0.00	0
+phiX174:12	0	0.00	0
+phiX174:13	0	0.00	0
+phiX174:14	0	0.00	0
+phiX174:15	0	0.00	0
+phiX174:16	0	0.00	0
+phiX174:17	0	0.00	0
+phiX174:18	0	0.00	0
+phiX174:19	0	0.00	0
+phiX174:20	0	0.00	0
+phiX174:21	0	0.00	0
+phiX174:22	0	0.00	0
+phiX174:23	0	0.00	0
+phiX174:24	0	0.00	0
+phiX174:25	0	0.00	0
+phiX174:26	0	0.00	0
+phiX174:27	0	0.00	0
+phiX174:28	0	0.00	0
+phiX174:29	0	0.00	0
+phiX174:30	0	0.00	0
+phiX174:31	0	0.00	0
+phiX174:32	0	0.00	0
+phiX174:33	0	0.00	0
+phiX174:34	0	0.00	0
+phiX174:35	0	0.00	0
+phiX174:36	0	0.00	0
+phiX174:37	0	0.00	0
+phiX174:38	0	0.00	0
+phiX174:39	0	0.00	0
+phiX174:40	0	0.00	0
+phiX174:41	0	0.00	0
+phiX174:42	0	0.00	0
+phiX174:43	0	0.00	0
+phiX174:44	0	0.00	0
+phiX174:45	0	0.00	0
+phiX174:46	0	0.00	0
+phiX174:47	0	0.00	0
+phiX174:48	0	0.00	0
+phiX174:49	0	0.00	0
+phiX174:50	0	0.00	0
+phiX174:51	0	0.00	0
+phiX174:52	0	0.00	0
+phiX174:53	0	0.00	0
+phiX174:54	0	0.00	0
+phiX174:55	0	0.00	0
+phiX174:56	0	0.00	0
+phiX174:57	0	0.00	0
+phiX174:58	0	0.00	0
+phiX174:59	0	0.00	0
+phiX174:60	0	0.00	0
+phiX174:61	0	0.00	0
+phiX174:62	0	0.00	0
+phiX174:63	0	0.00	0
+phiX174:64	0	0.00	0
+phiX174:65	0	0.00	0
+phiX174:66	0	0.00	0
+phiX174:67	0	0.00	0
+phiX174:68	0	0.00	0
+phiX174:69	0	0.00	0
+phiX174:70	0	0.00	0
+phiX174:71	0	0.00	0
+phiX174:72	0	0.00	0
+phiX174:73	0	0.00	0
+phiX174:74	0	0.00	0
+phiX174:75	0	0.00	0
+phiX174:76	0	0.00	0
+phiX174:77	0	0.00	0
+phiX174:78	0	0.00	0
+phiX174:79	0	0.00	0
+phiX174:80	0	0.00	0
+phiX174:81	0	0.00	0
+phiX174:82	0	0.00	0
+phiX174:83	0	0.00	0
+phiX174:84	0	0.00	0
+phiX174:85	0	0.00	0
+phiX174:86	0	0.00	0
+phiX174:87	0	0.00	0
+phiX174:88	0	0.00	0
+phiX174:89	0	0.00	0
+phiX174:90	0	0.00	0
+phiX174:91	0	0.00	0
+phiX174:92	0	0.00	0
+phiX174:93	0	0.00	0
+phiX174:94	0	0.00	0
+phiX174:95	0	0.00	0
+phiX174:96	0	0.00	0
+phiX174:97	0	0.00	0
+phiX174:98	0	0.00	0
+phiX174:99	0	0.00	0
+phiX174:100	0	0.00	0
+phiX174:101	0	0.00	0
+phiX174:102	0	0.00	0
+phiX174:103	0	0.00	0
+phiX174:104	0	0.00	0
+phiX174:105	0	0.00	0
+phiX174:106	0	0.00	0
+phiX174:107	0	0.00	0
+phiX174:108	0	0.00	0
+phiX174:109	0	0.00	0
+phiX174:110	0	0.00	0
+phiX174:111	0	0.00	0
+phiX174:112	0	0.00	0
+phiX174:113	0	0.00	0
+phiX174:114	0	0.00	0
+phiX174:115	0	0.00	0
+phiX174:116	0	0.00	0
+phiX174:117	0	0.00	0
+phiX174:118	0	0.00	0
+phiX174:119	0	0.00	0
+phiX174:120	0	0.00	0
+phiX174:121	0	0.00	0
+phiX174:122	0	0.00	0
+phiX174:123	0	0.00	0
+phiX174:124	0	0.00	0
+phiX174:125	0	0.00	0
+phiX174:126	0	0.00	0
+phiX174:127	0	0.00	0
+phiX174:128	0	0.00	0
+phiX174:129	0	0.00	0
+phiX174:130	0	0.00	0
+phiX174:131	0	0.00	0
+phiX174:132	0	0.00	0
+phiX174:133	0	0.00	0
+phiX174:134	0	0.00	0
+phiX174:135	0	0.00	0
+phiX174:136	0	0.00	0
+phiX174:137	0	0.00	0
+phiX174:138	0	0.00	0
+phiX174:139	0	0.00	0
+phiX174:140	0	0.00	0
+phiX174:141	0	0.00	0
+phiX174:142	0	0.00	0
+phiX174:143	0	0.00	0
+phiX174:144	0	0.00	0
+phiX174:145	0	0.00	0
+phiX174:146	0	0.00	0
+phiX174:147	0	0.00	0
+phiX174:148	0	0.00	0
+phiX174:149	0	0.00	0
+phiX174:150	0	0.00	0
+phiX174:151	0	0.00	0
+phiX174:152	0	0.00	0
+phiX174:153	0	0.00	0
+phiX174:154	0	0.00	0
+phiX174:155	0	0.00	0
+phiX174:156	0	0.00	0
+phiX174:157	0	0.00	0
+phiX174:158	0	0.00	0
+phiX174:159	0	0.00	0
+phiX174:160	0	0.00	0
+phiX174:161	0	0.00	0
+phiX174:162	0	0.00	0
+phiX174:163	0	0.00	0
+phiX174:164	0	0.00	0
+phiX174:165	0	0.00	0
+phiX174:166	0	0.00	0
+phiX174:167	0	0.00	0
+phiX174:168	0	0.00	0
+phiX174:169	0	0.00	0
+phiX174:170	0	0.00	0
+phiX174:171	0	0.00	0
+phiX174:172	0	0.00	0
+phiX174:173	0	0.00	0
+phiX174:174	0	0.00	0
+phiX174:175	0	0.00	0
+phiX174:176	0	0.00	0
+phiX174:177	0	0.00	0
+phiX174:178	0	0.00	0
+phiX174:179	0	0.00	0
+phiX174:180	0	0.00	0
+phiX174:181	0	0.00	0
+phiX174:182	0	0.00	0
+phiX174:183	0	0.00	0
+phiX174:184	0	0.00	0
+phiX174:185	0	0.00	0
+phiX174:186	0	0.00	0
+phiX174:187	0	0.00	0
+phiX174:188	0	0.00	0
+phiX174:189	0	0.00	0
+phiX174:190	0	0.00	0
+phiX174:191	0	0.00	0
+phiX174:192	0	0.00	0
+phiX174:193	0	0.00	0
+phiX174:194	0	0.00	0
+phiX174:195	0	0.00	0
+phiX174:196	0	0.00	0
+phiX174:197	0	0.00	0
+phiX174:198	0	0.00	0
+phiX174:199	0	0.00	0
+phiX174:200	0	0.00	0
+phiX174:201	0	0.00	0
+phiX174:202	0	0.00	0
+phiX174:203	0	0.00	0
+phiX174:204	0	0.00	0
+phiX174:205	0	0.00	0
+phiX174:206	0	0.00	0
+phiX174:207	0	0.00	0
+phiX174:208	0	0.00	0
+phiX174:209	0	0.00	0
+phiX174:210	0	0.00	0
+phiX174:211	0	0.00	0
+phiX174:212	0	0.00	0
+phiX174:213	0	0.00	0
+phiX174:214	0	0.00	0
+phiX174:215	0	0.00	0
+phiX174:216	0	0.00	0
+phiX174:217	0	0.00	0
+phiX174:218	0	0.00	0
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_statistics_sample.tabular	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,2 @@
+Source_of_reads	from_0_to_1)	from_1_to_2)	from_2_to_3)	from_3_to_4)	from_4_to_5)	from_5_to_6)	from_6_to_7)	from_7_to_8)	from_8_to_9)	from_9_to_10)	from_10_to_11)	from_11_to_12)	from_12_to_13)	from_13_to_14)	from_14_to_15)	from_15_to_16)	from_16_to_17)	from_17_to_18)	from_18_to_19)	from_19_to_20)	from_20_to_21)	from_21_to_22)	from_22_to_23)	from_23_to_24)	from_24_to_25)	from_25_to_26)	from_26_to_27)	from_27_to_28)	from_28_to_29)	from_29_to_30)	from_30_to_31)	from_31_to_32)	from_32_to_33)	from_33_to_34)	from_34_to_35)	from_35_to_36)	from_36_to_37)	from_37_to_38)	from_38_to_39)	from_39_to_40)	from_40_to_41)	from_41_to_42)	from_42_to_43)	from_43_to_44)	from_44_to_45)	from_45_to_46)	from_46_to_47)	from_47_to_48)	from_48_to_49)	from_49_to_50)	from_50_to_51)	from_51_to_52)	from_52_to_53)	from_53_to_54)	from_54_to_55)	from_55_to_56)	from_56_to_57)	from_57_to_58)	from_58_to_59)	from_59_to_60)	from_60_to_61)	from_61_to_62)	from_62_to_63)	from_63_to_64)	from_64_to_65)	from_65_to_66)	from_66_to_67)	from_67_to_68)	from_68_to_69)	from_69_to_70)	from_70_to_71)	from_71_to_72)	from_72_to_73)	from_73_to_74)	from_74_to_75)	from_75_to_76)	from_76_to_77)	from_77_to_78)	from_78_to_79)	from_79_to_80)	from_80_to_81)	from_81_to_82)	from_82_to_83)	from_83_to_84)	from_84_to_85)	from_85_to_86)	from_86_to_87)	from_87_to_88)	from_88_to_89)	from_89_to_90)	from_90_to_91)	from_91_to_92)	from_92_to_93)	from_93_to_94)	from_94_to_95)	from_95_to_96)	from_96_to_97)	from_97_to_98)	from_98_to_99)	from_99_to_100)	from_100_to_101)	from_101_to_102)	from_102_to_103)	from_103_to_104)	from_104_to_105)	from_105_to_106)	from_106_to_107)	from_107_to_108)	from_108_to_109)	from_109_to_110)	from_110_to_111)	from_111_to_112)	from_112_to_113)	from_113_to_114)	from_114_to_115)	from_115_to_116)	from_116_to_117)	from_117_to_118)	from_118_to_119)	from_119_to_120)	from_120_to_121)	from_121_to_122)	from_122_to_123)	from_123_to_124)	from_124_to_125)	from_125_to_126)	from_126_to_127)	from_127_to_128)	from_128_to_129)	from_129_to_130)	from_130_to_131)	from_131_to_132)	from_132_to_133)	from_133_to_134)	from_134_to_135)	from_135_to_136)	from_136_to_137)	from_137_to_138)	from_138_to_139)	from_139_to_140)	from_140_to_141)	from_141_to_142)	from_142_to_143)	from_143_to_144)	from_144_to_145)	from_145_to_146)	from_146_to_147)	from_147_to_148)	from_148_to_149)	from_149_to_150)	from_150_to_151)	from_151_to_152)	from_152_to_153)	from_153_to_154)	from_154_to_155)	from_155_to_156)	from_156_to_157)	from_157_to_158)	from_158_to_159)	from_159_to_160)	from_160_to_161)	from_161_to_162)	from_162_to_163)	from_163_to_164)	from_164_to_165)	from_165_to_166)	from_166_to_167)	from_167_to_168)	from_168_to_169)	from_169_to_170)	from_170_to_171)	from_171_to_172)	from_172_to_173)	from_173_to_174)	from_174_to_175)	from_175_to_176)	from_176_to_177)	from_177_to_178)	from_178_to_179)	from_179_to_180)	from_180_to_181)	from_181_to_182)	from_182_to_183)	from_183_to_184)	from_184_to_185)	from_185_to_186)	from_186_to_187)	from_187_to_188)	from_188_to_189)	from_189_to_190)	from_190_to_191)	from_191_to_192)	from_192_to_193)	from_193_to_194)	from_194_to_195)	from_195_to_196)	from_196_to_197)	from_197_to_198)	from_198_to_199)	from_199_to_200)	from_200_to_201)	from_201_to_202)	from_202_to_203)	from_203_to_204)	from_204_to_205)	from_205_to_206)	from_206_to_207)	from_207_to_208)	from_208_to_209)	from_209_to_210)	from_210_to_211)	from_211_to_212)	from_212_to_213)	from_213_to_214)	from_214_to_215)	from_215_to_216)	from_216_to_217)	from_217_to_218)	from_218_to_219)	from_219_to_220)	from_220_to_221)	from_221_to_222)	from_222_to_223)	from_223_to_224)	from_224_to_225)	from_225_to_226)	from_226_to_227)	from_227_to_228)	from_228_to_229)	from_229_to_230)	from_230_to_231)	from_231_to_232)	from_232_to_233)	from_233_to_234)	from_234_to_235)	from_235_to_236)	from_236_to_237)	from_237_to_238)	from_238_to_239)	from_239_to_240)	from_240_to_241)	from_241_to_242)	from_242_to_243)	from_243_to_244)	from_244_to_245)	from_245_to_246)	from_246_to_247)	from_247_to_248)	from_248_to_249)	from_249_to_250)	from_250_to_251)	from_251_to_252)	from_252_to_253)	from_253_to_254)	from_254_to_255)	from_255_to_256)	from_256_to_257)	from_257_to_258)	from_258_to_259)	from_259_to_260)	from_260_to_261)	from_261_to_262)	from_262_to_263)	from_263_to_264)	from_264_to_265)	from_265_to_266)	from_266_to_267)	from_267_to_268)	from_268_to_269)	from_269_to_270)	from_270_to_271)	from_271_to_272)	from_272_to_273)	from_273_to_274)	from_274_to_275)	from_275_to_276)	from_276_to_277)	from_277_to_278)	from_278_to_279)	from_279_to_280)	from_280_to_281)	from_281_to_282)	from_282_to_283)	from_283_to_284)	from_284_to_285)	from_285_to_286)	from_286_to_287)	from_287_to_288)	from_288_to_289)	from_289_to_290)	from_290_to_291)	from_291_to_292)	from_292_to_293)	from_293_to_294)	from_294_to_295)	from_295_to_296)	from_296_to_297)	from_297_to_298)	from_298_to_299)	from_299_to_300)	from_300_to_301)	from_301_to_302)	from_302_to_303)	from_303_to_304)	from_304_to_305)	from_305_to_306)	from_306_to_307)	from_307_to_308)	from_308_to_309)	from_309_to_310)	from_310_to_311)	from_311_to_312)	from_312_to_313)	from_313_to_314)	from_314_to_315)	from_315_to_316)	from_316_to_317)	from_317_to_318)	from_318_to_319)	from_319_to_320)	from_320_to_321)	from_321_to_322)	from_322_to_323)	from_323_to_324)	from_324_to_325)	from_325_to_326)	from_326_to_327)	from_327_to_328)	from_328_to_329)	from_329_to_330)	from_330_to_331)	from_331_to_332)	from_332_to_333)	from_333_to_334)	from_334_to_335)	from_335_to_336)	from_336_to_337)	from_337_to_338)	from_338_to_339)	from_339_to_340)	from_340_to_341)	from_341_to_342)	from_342_to_343)	from_343_to_344)	from_344_to_345)	from_345_to_346)	from_346_to_347)	from_347_to_348)	from_348_to_349)	from_349_to_350)	from_350_to_351)	from_351_to_352)	from_352_to_353)	from_353_to_354)	from_354_to_355)	from_355_to_356)	from_356_to_357)	from_357_to_358)	from_358_to_359)	from_359_to_360)	from_360_to_361)	from_361_to_362)	from_362_to_363)	from_363_to_364)	from_364_to_365)	from_365_to_366)	from_366_to_367)	from_367_to_368)	from_368_to_369)	from_369_to_370)	from_370_to_371)	from_371_to_372)	from_372_to_373)	from_373_to_374)	from_374_to_375)	from_375_to_376)	from_376_to_377)	from_377_to_378)	from_378_to_379)	from_379_to_380)	from_380_to_381)	from_381_to_382)	from_382_to_383)	from_383_to_384)	from_384_to_385)	from_385_to_386)	from_386_to_387)	from_387_to_388)	from_388_to_389)	from_389_to_390)	from_390_to_391)	from_391_to_392)	from_392_to_393)	from_393_to_394)	from_394_to_395)	from_395_to_396)	from_396_to_397)	from_397_to_398)	from_398_to_399)	from_399_to_400)	from_400_to_401)	from_401_to_402)	from_402_to_403)	from_403_to_404)	from_404_to_405)	from_405_to_406)	from_406_to_407)	from_407_to_408)	from_408_to_409)	from_409_to_410)	from_410_to_411)	from_411_to_412)	from_412_to_413)	from_413_to_414)	from_414_to_415)	from_415_to_416)	from_416_to_417)	from_417_to_418)	from_418_to_419)	from_419_to_420)	from_420_to_421)	from_421_to_422)	from_422_to_423)	from_423_to_424)	from_424_to_425)	from_425_to_426)	from_426_to_427)	from_427_to_428)	from_428_to_429)	from_429_to_430)	from_430_to_431)	from_431_to_432)	from_432_to_433)	from_433_to_434)	from_434_to_435)	from_435_to_436)	from_436_to_437)	from_437_to_438)	from_438_to_439)	from_439_to_440)	from_440_to_441)	from_441_to_442)	from_442_to_443)	from_443_to_444)	from_444_to_445)	from_445_to_446)	from_446_to_447)	from_447_to_448)	from_448_to_449)	from_449_to_450)	from_450_to_451)	from_451_to_452)	from_452_to_453)	from_453_to_454)	from_454_to_455)	from_455_to_456)	from_456_to_457)	from_457_to_458)	from_458_to_459)	from_459_to_460)	from_460_to_461)	from_461_to_462)	from_462_to_463)	from_463_to_464)	from_464_to_465)	from_465_to_466)	from_466_to_467)	from_467_to_468)	from_468_to_469)	from_469_to_470)	from_470_to_471)	from_471_to_472)	from_472_to_473)	from_473_to_474)	from_474_to_475)	from_475_to_476)	from_476_to_477)	from_477_to_478)	from_478_to_479)	from_479_to_480)	from_480_to_481)	from_481_to_482)	from_482_to_483)	from_483_to_484)	from_484_to_485)	from_485_to_486)	from_486_to_487)	from_487_to_488)	from_488_to_489)	from_489_to_490)	from_490_to_491)	from_491_to_492)	from_492_to_493)	from_493_to_494)	from_494_to_495)	from_495_to_496)	from_496_to_497)	from_497_to_498)	from_498_to_499)	from_499_to_500)	from_500_to_inf
+sample_A Fake phiX Sample	5343	2	1	2	1	1	2	2	2	1	29	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_depth_of_coverage/gatk_depth_of_coverage_out_1_output_summary_sample.tabular	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,3 @@
+sample_id	total	mean	granular_third_quartile	granular_median	granular_first_quartile	%_bases_above_15
+A Fake phiX Sample	360	0.07	1	1	1	0.0
+Total	360	0.07	N/A	N/A	N/A
Binary file test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,4 @@
+GenomeAnalysisEngine - Strictness is SILENT 
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
+TraversalEngine - Total runtime
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%) 
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_print_reads/gatk_print_reads_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,5 @@
+SAMDataSource$SAMReaders - Initializing SAMRecords in serial
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
+TraversalEngine -        Location processed.reads  runtime per.1M.reads completed total.runtime remaining 
+Walker - [REDUCE RESULT] Traversal result is: org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%)
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.gatk_interval	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,1 @@
+phiX174:1446-1447
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_realigner_target_creator/gatk_realigner_target_creator_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,4 @@
+GenomeAnalysisEngine - Strictness is SILENT
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
+TraversalEngine - Total runtime
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%)
\ No newline at end of file
Binary file test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.bam has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_table_recalibration/gatk_table_recalibration_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,16 @@
+GenomeAnalysisEngine - Strictness is SILENT
+TableRecalibrationWalker - Reading in the data from input csv file...
+TableRecalibrationWalker - ...done!
+TableRecalibrationWalker - The covariates being used here:
+TableRecalibrationWalker - 	ReadGroupCovariate
+TableRecalibrationWalker - 	QualityScoreCovariate
+TableRecalibrationWalker - 	CycleCovariate
+TableRecalibrationWalker - 	DinucCovariate
+TableRecalibrationWalker - 	HomopolymerCovariate
+TableRecalibrationWalker - 	MinimumNQSCovariate
+TableRecalibrationWalker - 	PositionCovariate
+TableRecalibrationWalker - Generating tables of empirical qualities for use in sequential calculation...
+TableRecalibrationWalker - ...done!
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
+TraversalEngine - Total runtime
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%)
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,12 @@
+Program Args: -T UnifiedGenotyper
+GenomeAnalysisEngine - Strictness is SILENT
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
+TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
+UnifiedGenotyper - Visited bases                                5387
+UnifiedGenotyper - Callable bases                               5344
+UnifiedGenotyper - Confidently called bases                     5344
+UnifiedGenotyper - % callable bases of all loci                 99.202
+UnifiedGenotyper - % confidently called bases of all loci       99.202
+UnifiedGenotyper - % confidently called bases of callable loci  100.000
+UnifiedGenotyper - Actual calls made                            1
+TraversalEngine - Total runtime
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.metrics	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,7 @@
+Visited bases                                5387
+Callable bases                               5344
+Confidently called bases                     5344
+% callable bases of all loci                 99.202
+% confidently called bases of all loci       99.202
+% confidently called bases of callable loci  100.000
+Actual calls made                            1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]"
+##contig=<ID=phiX174,length=5386>
+##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
+phiX174	1443	.	AC	.	0	.	DB;DP=10;MQ=37.74;MQ0=0	GT	./.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_validate_variants/gatk_validate_variants_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,1 @@
+Found 1 records with failures.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,5 @@
+GenomeAnalysisEngine - Strictness is SILENT 
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
+TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining 
+VariantAnnotator - Processed 1 loci.
+TraversalEngine - 0 reads were filtered out during traversal out of 10 total (0.00%) 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,31 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]"
+##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_variant.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_dbsnp_dbsnp.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub annotation=[SpanningDeletions, MappingQualityZero, AlleleBalance, RMSMappingQuality, HaplotypeScore, HomopolymerRun, DepthOfCoverage, MappingQualityRankSumTest, BaseQualityRankSumTest, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
+##contig=<ID=phiX174,length=5386>
+##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta
+##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
+phiX174	1443	.	AC	.	0	.	DB;DP=10;MQ=37.74;MQ0=0	GT	./.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,5 @@
+HelpFormatter - Program Args: -T CombineVariants
+GenomeAnalysisEngine - Strictness is SILENT
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING]
+TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
+TraversalEngine - Total runtime
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,33 @@
+##fileformat=VCFv4.1
+##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=from_variant_annotator source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/input_variant_from_variant_annotator.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=from_variant_annotator printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 mergeInfoWithMaxAC=false"
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]"
+##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_variant.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_dbsnp_dbsnp.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub annotation=[SpanningDeletions, MappingQualityZero, AlleleBalance, RMSMappingQuality, HaplotypeScore, HomopolymerRun, DepthOfCoverage, MappingQualityRankSumTest, BaseQualityRankSumTest, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
+##contig=<ID=phiX174,length=5386>
+##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta
+##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
+phiX174	1443	.	AC	.	.	PASS	AC=0;AF=0.00;AN=0;DB;DP=10;MQ=37.74;MQ0=0;set=ReferenceInAll	GT	./.
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.gatk_report	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,30 @@
+##:GATKReport.v0.2 CompOverlap : The overlap between eval and comp sites
+CompOverlap  CompRod  EvalRod  JexlExpression  Novelty  nEvalVariants  novelSites  nVariantsAtComp  compRate  nConcordant  concordantRate
+CompOverlap  dbsnp    input_0  none            all                  0           0                0      0.00            0            0.00
+CompOverlap  dbsnp    input_0  none            known                0           0                0      0.00            0            0.00
+CompOverlap  dbsnp    input_0  none            novel                0           0                0      0.00            0            0.00
+
+##:GATKReport.v0.2 CountVariants : Counts different classes of variants in the sample
+CountVariants  CompRod  EvalRod  JexlExpression  Novelty  nProcessedLoci  nCalledLoci  nRefLoci  nVariantLoci  variantRate  variantRatePerBp  nSNPs  nMNPs  nInsertions  nDeletions  nComplex  nSymbolic  nMixed  nNoCalls  nHets  nHomRef  nHomVar  nSingletons  nHomDerived  heterozygosity  heterozygosityPerBp  hetHomRatio  indelRate  indelRatePerBp  deletionInsertionRatio
+CountVariants  dbsnp    input_0  none            all                5386            1         1             0   0.00000000        0.00000000      0      0            0           0         0          0       0         1      0        0        0            0            0        0.00e+00                 0.00         0.00   0.00e+00            0.00                    0.00
+CountVariants  dbsnp    input_0  none            known              5386            1         1             0   0.00000000        0.00000000      0      0            0           0         0          0       0         1      0        0        0            0            0        0.00e+00                 0.00         0.00   0.00e+00            0.00                    0.00
+CountVariants  dbsnp    input_0  none            novel              5386            0         0             0   0.00000000        0.00000000      0      0            0           0         0          0       0         0      0        0        0            0            0        0.00e+00                 0.00         0.00   0.00e+00            0.00                    0.00
+
+##:GATKReport.v0.2 TiTvVariantEvaluator : Ti/Tv Variant Evaluator
+TiTvVariantEvaluator  CompRod  EvalRod  JexlExpression  Novelty  nTi  nTv  tiTvRatio  nTiInComp  nTvInComp  TiTvRatioStandard  nTiDerived  nTvDerived  tiTvDerivedRatio
+TiTvVariantEvaluator  dbsnp    input_0  none            all        0    0       0.00          0          0               0.00           0           0              0.00
+TiTvVariantEvaluator  dbsnp    input_0  none            known      0    0       0.00          0          0               0.00           0           0              0.00
+TiTvVariantEvaluator  dbsnp    input_0  none            novel      0    0       0.00          0          0               0.00           0           0              0.00
+
+##:GATKReport.v0.2 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay
+ValidationReport  CompRod  EvalRod  JexlExpression  Novelty  nComp  TP  FP  FN  TN  sensitivity  specificity  PPV  FDR  CompMonoEvalNoCall  CompMonoEvalFiltered  CompMonoEvalMono  CompMonoEvalPoly  CompPolyEvalNoCall  CompPolyEvalFiltered  CompPolyEvalMono  CompPolyEvalPoly  CompFiltered  nDifferentAlleleSites
+ValidationReport  dbsnp    input_0  none            all         43   0   0   0  43          NaN       100.00  NaN  NaN                  42                     0                 1                 0                   0                     0                 0                 0             0                      0
+ValidationReport  dbsnp    input_0  none            known        1   0   0   0   1          NaN       100.00  NaN  NaN                   0                     0                 1                 0                   0                     0                 0                 0             0                      0
+ValidationReport  dbsnp    input_0  none            novel       42   0   0   0  42          NaN       100.00  NaN  NaN                  42                     0                 0                 0                   0                     0                 0                 0             0                      0
+
+##:GATKReport.v0.2 VariantSummary : 1000 Genomes Phase I summary of variants table
+VariantSummary  CompRod  EvalRod  JexlExpression  Novelty  nSamples  nProcessedLoci  nSNPs  TiTvRatio  SNPNoveltyRate  nSNPsPerSample  TiTvRatioPerSample  SNPDPPerSample  nIndels  IndelNoveltyRate  nIndelsPerSample  IndelDPPerSample  nSVs  SVNoveltyRate  nSVsPerSample
+VariantSummary  dbsnp    input_0  none            all             1            5386      0       0.00              NA               0                0.00             0.0        0                NA                 0               0.0     0             NA              0
+VariantSummary  dbsnp    input_0  none            known           1            5386      0       0.00              NA               0                0.00             0.0        0                NA                 0               0.0     0             NA              0
+VariantSummary  dbsnp    input_0  none            novel           1            5386      0       0.00              NA               0                0.00             0.0        0                NA                 0               0.0     0             NA              0
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,5 @@
+HelpFormatter - Program Args: -T VariantEval
+GenomeAnalysisEngine - Strictness is SILENT
+TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
+VariantEvalWalker - Finalizing variant report
+TraversalEngine - Total runtime
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_filtration/gatk_variant_filtration_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,4 @@
+GenomeAnalysisEngine - Strictness is SILENT 
+TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] 
+TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining 
+TraversalEngine - Total runtime 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.log.contains	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,4 @@
+GenomeAnalysisEngine - Strictness is SILENT 
+SelectVariants - Including sample 'A Fake phiX Sample' 
+TraversalEngine -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining 
+SelectVariants - 1 records processed. 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf	Tue Nov 26 06:10:20 2013 -0500
@@ -0,0 +1,32 @@
+##fileformat=VCFv4.1
+##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
+##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
+##INFO=<ID=AB,Number=1,Type=Float,Description="Allele Balance for hets (ref/(ref+alt))">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
+##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
+##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
+##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
+##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
+##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
+##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
+##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
+##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
+##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
+##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
+##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
+##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input_0.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_ALL_CONFIDENT_SITES standard_min_confidence_threshold_for_calling=0.0 standard_min_confidence_threshold_for_emitting=4.0 computeSLOD=false alleles=(RodBinding name= source=UNBOUND) assume_single_sample_reads=null abort_at_too_much_coverage=-1 min_base_quality_score=17 min_mapping_quality_score=20 max_deletion_fraction=-1.0 min_indel_count_for_genotyping=2 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10.0 indelGapOpenPenalty=3.0 indelHaplotypeSize=80 doContextDependentGapPenalties=true getGapPenaltiesFromData=false indel_recal_file=indel.recal_data.csv indelDebug=false dovit=false GSA_PRODUCTION_ONLY=false exactCalculation=LINEAR_EXPERIMENTAL ignoreSNPAlleles=false output_all_callable_bases=false genotype=false dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/input_dbsnp_0.vcf) out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null annotation=[]"
+##VariantAnnotator="analysis_type=VariantAnnotator input_file=[/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.bam] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=(RodBinding name=variant source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_variant.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name=dbsnp source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/input_dbsnp_dbsnp.vcf) comp=[] resource=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub annotation=[SpanningDeletions, MappingQualityZero, AlleleBalance, RMSMappingQuality, HaplotypeScore, HomopolymerRun, DepthOfCoverage, MappingQualityRankSumTest, BaseQualityRankSumTest, QualByDepth] group=[] expression=[] useAllAnnotations=false list=false assume_single_sample_reads=null vcfContainsOnlyIndels=false"
+##contig=<ID=phiX174,length=5386>
+##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta
+##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta
+##source=SelectVariants
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	A Fake phiX Sample
+phiX174	1443	.	AC	.	0	.	AC=0;AF=0.00;AN=0;DB;DP=0;MQ=37.74;MQ0=0	GT	./.
--- a/unified_genotyper.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/unified_genotyper.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,16 +4,16 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   #for $i, $input_bam in enumerate( $reference_source.input_bams ):
-       -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
-       #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
-           -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
-       #end if
-   #end for
-   -p '
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
+        -d "-I" "${input_bam.input_bam}" "${input_bam.input_bam.ext}" "gatk_input_${i}"
+        #if str( $input_bam.input_bam.metadata.bam_index ) != "None":
+            -d "" "${input_bam.input_bam.metadata.bam_index}" "bam_index" "gatk_input_${i}" ##hardcode galaxy ext type as bam_index
+        #end if
+    #end for
+    -p '
     @JAR_PATH@
     -T "UnifiedGenotyper"
     @THREADS@
@@ -24,7 +24,6 @@
     ## according to http://www.broadinstitute.org/gatk/guide/article?id=1975
     --num_cpu_threads_per_data_thread 6
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/variant_annotator.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_annotator.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,25 +4,23 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   #if str( $reference_source.input_bam ) != "None":
-       -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
-       #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
-           -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
-       #end if
-   #end if
-   -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
-   -p '
-   @JAR_PATH@
-    ##--list
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #if str( $reference_source.input_bam ) != "None":
+        -d "-I" "${reference_source.input_bam}" "${reference_source.input_bam.ext}" "gatk_input"
+        #if str( $reference_source.input_bam.metadata.bam_index ) != "None":
+            -d "" "${reference_source.input_bam.metadata.bam_index}" "bam_index" "gatk_input" ##hardcode galaxy ext type as bam_index
+        #end if
+    #end if
+    -d "--variant" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+    -p '
+    @JAR_PATH@
     -T "VariantAnnotator"
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
@@ -92,7 +90,7 @@
       <expand macro="reference_source_selector_param" />
       <when value="cached">
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
-        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="--intervals"/>
+        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files." help="-BTI variant"/>
         <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
           <validator type="unspecified_build" />
           <validator type="dataset_metadata_in_data_table" table_name="gatk2_picard_indexes" metadata_name="dbkey" metadata_column="dbkey" message="Sequences are not currently available for the specified build." /> <!-- fixme!!! this needs to be a select -->
@@ -106,9 +104,8 @@
       </when>
       <when value="history"> <!-- FIX ME!!!! -->
         <param name="input_variant" type="data" format="vcf" label="Variant file to annotate" help="-V,--variant &amp;lt;variant&amp;gt;"/>
-        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files."  help="--intervals"/>
-        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" >
-        </param>
+        <param name="input_variant_bti" type="boolean" truevalue="-BTI variant" falsevalue="" label="Increase efficiency for small variant files."  help="-BTI variant"/>
+        <param name="input_bam" type="data" format="bam" label="BAM file" optional="True" help="Not needed for all annotations. (-I,--input_file &amp;lt;input_file&amp;gt;)" />
         <param name="ref_file" type="data" format="fasta" label="Using reference file" help="-R,--reference_sequence &amp;lt;reference_sequence&amp;gt;" />
       </when>
     </conditional>
@@ -160,7 +157,7 @@
     </repeat>
     
     <conditional name="snpEff_rod_bind_type">
-      <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
+      <param name="snpEff_rod_bind_type_selector" type="select" label="Provide a snpEff reference-ordered data file (VCF)" help="-snpEffFile,--snpEffFile &amp;lt;snpEffFile&amp;gt;">
         <option value="set_snpEff">Set snpEff</option>
         <option value="exclude_snpEff" selected="True">Don't set snpEff</option>
       </param>
--- a/variant_apply_recalibration.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_apply_recalibration.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,12 +4,12 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   #for $var_count, $variant in enumerate( $reference_source.variants ):
-      -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
-   #end for
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #for $var_count, $variant in enumerate( $reference_source.variants ):
+        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+    #end for
    -p '
    @JAR_PATH@
     -T "ApplyRecalibration"
--- a/variant_combine.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_combine.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,26 +4,25 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   
-   #set $priority_order = []
-   #for $input_variant in $reference_source.input_variants:
-       -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
-       #set $input_variant_name = str( $input_variant.input_variant_name )
-       #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator
-       #silent $priority_order.append( $input_variant_name )
-   #end for
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+
+    #set $priority_order = []
+    #for $input_variant in $reference_source.input_variants:
+        -d "--variant:${input_variant.input_variant_name},%(file_type)s" "${input_variant.input_variant}" "${input_variant.input_variant.ext}" "input_variant_${input_variant.input_variant_name}"
+        #set $input_variant_name = str( $input_variant.input_variant_name )
+        #assert $input_variant_name not in $priority_order, "Variant Names must be unique" ##this should be handled by a validator
+        #silent $priority_order.append( $input_variant_name )
+    #end for
+    -p '
+    @JAR_PATH@
     -T "CombineVariants"
     --out "${output_variants}"
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/variant_eval.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_eval.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,22 +4,22 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
+  <command interpreter="python">
    #from binascii import hexlify
-   ##--max_jvm_heap_fraction "1"
+
+    gatk2_wrapper.py
    --stdout "${output_log}"
-   #for $var_count, $variant in enumerate( $reference_source.variants ):
-      -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}"
-   #end for
-   -p '
-   @JAR_PATH@
+    #for $var_count, $variant in enumerate( $reference_source.variants ):
+        -d "--eval:input_${var_count},%(file_type)s" "${variant.input_variant}" "${variant.input_variant.ext}" "input_variants_${var_count}"
+    #end for
+    -p '
+    @JAR_PATH@
     -T "VariantEval"
     --out "${output_report}"
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/variant_filtration.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_filtration.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,20 +4,21 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   #from binascii import hexlify
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    #from binascii import hexlify
+
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
+    -p '
+    @JAR_PATH@
     -T "VariantFiltration"
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
 
     -o "${output_vcf}"
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/variant_recalibrator.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_recalibrator.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,20 +4,19 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
-   --stdout "${output_log}"
-   #for $var_count, $variant in enumerate( $reference_source.variants ):
-      -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
-   #end for
-   -p '
-   @JAR_PATH@
+  <command interpreter="python">
+    gatk2_wrapper.py
+    --stdout "${output_log}"
+    #for $var_count, $variant in enumerate( $reference_source.variants ):
+        -d "--input:input_${var_count},%(file_type)s" "${variant.input_variants}" "${variant.input_variants.ext}" "input_variants_${var_count}"
+    #end for
+    -p '
+    @JAR_PATH@
     -T "VariantRecalibrator"
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
 
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
--- a/variant_select.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_select.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,9 +4,10 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   #from binascii import hexlify
-   ##--max_jvm_heap_fraction "1"
+  <command interpreter="python">
+    #from binascii import hexlify
+
+    gatk2_wrapper.py
    --stdout "${output_log}"
    -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
    -p '
@@ -38,7 +39,6 @@
     #for $sample_name in $sample_name_repeat:
         --sample_name "${sample_name.sample_name}"
     #end for
-    
     '
     
     #for $select_expressions in $select_expressions_repeat:
--- a/variant_validate.xml	Mon Nov 25 14:23:47 2013 -0500
+++ b/variant_validate.xml	Tue Nov 26 06:10:20 2013 -0500
@@ -4,8 +4,8 @@
   <macros>
     <import>gatk2_macros.xml</import>
   </macros>
-  <command interpreter="python">gatk2_wrapper.py
-   ##--max_jvm_heap_fraction "1"
+  <command interpreter="python">
+    gatk2_wrapper.py
    --stdout "${output_log}"
    -d "--variant:variant,%(file_type)s" "${reference_source.input_variant}" "${reference_source.input_variant.ext}" "input_variant"
    -p '
@@ -15,7 +15,7 @@
     \$GATK2_SITE_OPTIONS
 
     @THREADS@
-    ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout
+
     #if $reference_source.reference_source_selector != "history":
         -R "${reference_source.ref_file.fields.path}"
     #end if
@@ -27,7 +27,7 @@
         -d "--dbsnp:${dbsnp_rod_bind_type.dbsnp_rod_name},%(file_type)s" "${dbsnp_rod_bind_type.dbsnp_input_rod}" "${dbsnp_rod_bind_type.dbsnp_input_rod.ext}" "input_dbsnp_${dbsnp_rod_bind_type.dbsnp_rod_name}"
     #end if
    
-    #include source=$standard_gatk_options#    
+    #include source=$standard_gatk_options#
   </command>
   <inputs>