From e7aeabf34029a1496161af1dce1b320c1fd97506 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 10 May 2016 17:38:40 +0200
Subject: [PATCH] Fixed tagged files
---
.../nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala | 2 +-
.../nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala | 2 +-
.../lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala | 4 ++--
.../lumc/sasc/biopet/extensions/gatk/SelectVariants.scala | 4 ++--
.../lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala | 6 +++---
.../lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala | 4 ++--
.../nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala | 4 ++--
7 files changed, 13 insertions(+), 13 deletions(-)
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
index ed0065e58..1460f3f6d 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CombineGVCFs.scala
@@ -69,7 +69,7 @@ class CombineGVCFs(val root: Configurable) extends CommandLineGATK with ScatterG
override def cmdLine = super.cmdLine +
repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
repeat("-V", variant, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
conditional(convertToBasePairResolution, "-bpResolution", escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
index b36bc2988..ac939b078 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/GenotypeGVCFs.scala
@@ -129,7 +129,7 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
conditional(filter_reads_with_N_cigar, "-filterRNC", escape = true, format = "%s") +
conditional(filter_mismatching_base_and_quals, "-filterMBQ", escape = true, format = "%s") +
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s")
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
index 9eac2ba9e..403bee79f 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/HaplotypeCaller.scala
@@ -419,7 +419,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
optional("-likelihoodEngine", likelihoodCalculationEngine, spaceSeparated = true, escape = true, format = "%s") +
optional("-hksr", heterogeneousKmerSizeResolution, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
conditional(dontTrimActiveRegions, "-dontTrimActiveRegions", escape = true, format = "%s") +
optional("-maxDiscARExtension", maxDiscARExtension, spaceSeparated = true, escape = true, format = "%s") +
optional("-maxGGAARExtension", maxGGAARExtension, spaceSeparated = true, escape = true, format = "%s") +
@@ -444,7 +444,7 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
optional("-gt_mode", genotyping_mode, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-alleles", alleles), alleles, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-alleles", alleles.getOrElse(null)), alleles, spaceSeparated = true, escape = true, format = "%s") +
optional("-contamination", contamination_fraction_to_filter, spaceSeparated = true, escape = true, format = contamination_fraction_to_filterFormat) +
optional("-contaminationFile", contamination_fraction_per_sample_file, spaceSeparated = true, escape = true, format = "%s") +
optional("-pnrm", p_nonref_model, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
index a1ed7b732..37885ac9c 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/SelectVariants.scala
@@ -218,8 +218,8 @@ class SelectVariants(val root: Configurable) extends CommandLineGATK with Scatte
override def cmdLine = super.cmdLine +
required(TaggedFile.formatCommandLineParameter("-V", variant), variant, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-disc", discordance), discordance, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-conc", concordance), concordance, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-disc", discordance.getOrElse(null)), discordance, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-conc", concordance.getOrElse(null)), concordance, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
repeat("-sn", sample_name, spaceSeparated = true, escape = true, format = "%s") +
repeat("-se", sample_expressions, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
index 0edfe5260..42daf5e64 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/UnifiedGenotyper.scala
@@ -276,7 +276,7 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
conditional(ignoreSNPAlleles, "-ignoreSNPAlleles", escape = true, format = "%s") +
conditional(allReadsSP, "-dl", escape = true, format = "%s") +
conditional(ignoreLaneInfo, "-ignoreLane", escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-referenceCalls", reference_sample_calls), reference_sample_calls, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-referenceCalls", reference_sample_calls.getOrElse(null)), reference_sample_calls, spaceSeparated = true, escape = true, format = "%s") +
optional("-refsample", reference_sample_name, spaceSeparated = true, escape = true, format = "%s") +
optional("-minqs", min_quality_score, spaceSeparated = true, escape = true, format = "%s") +
optional("-maxqs", max_quality_score, spaceSeparated = true, escape = true, format = "%s") +
@@ -291,14 +291,14 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
optional("-gt_mode", genotyping_mode, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-alleles", alleles), alleles, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-alleles", alleles.getOrElse(null)), alleles, spaceSeparated = true, escape = true, format = "%s") +
optional("-contamination", contamination_fraction_to_filter, spaceSeparated = true, escape = true, format = contamination_fraction_to_filterFormat) +
optional("-contaminationFile", contamination_fraction_per_sample_file, spaceSeparated = true, escape = true, format = "%s") +
optional("-pnrm", p_nonref_model, spaceSeparated = true, escape = true, format = "%s") +
optional("-logExactCalls", exactcallslog, spaceSeparated = true, escape = true, format = "%s") +
optional("-out_mode", output_mode, spaceSeparated = true, escape = true, format = "%s") +
conditional(allSitePLs, "-allSitePLs", escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
repeat("-onlyEmitSamples", onlyEmitSamples, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
index d98a55a49..0e35d9b81 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantAnnotator.scala
@@ -104,8 +104,8 @@ class VariantAnnotator(val root: Configurable) extends CommandLineGATK with Scat
override def cmdLine = super.cmdLine +
required(TaggedFile.formatCommandLineParameter("-V", variant), variant, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile), snpEffFile, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-snpEffFile", snpEffFile.getOrElse()), snpEffFile, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse()), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
repeat("-resource", resource, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
index cf1c362c7..182007076 100644
--- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
+++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/VariantEval.scala
@@ -135,8 +135,8 @@ class VariantEval(val root: Configurable) extends CommandLineGATK {
optional("-o", out, spaceSeparated = true, escape = true, format = "%s") +
repeat("-eval", eval, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-D", dbsnp), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
- optional(TaggedFile.formatCommandLineParameter("-gold", goldStandard), goldStandard, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-D", dbsnp.getOrElse(null)), dbsnp, spaceSeparated = true, escape = true, format = "%s") +
+ optional(TaggedFile.formatCommandLineParameter("-gold", goldStandard.getOrElse(null)), goldStandard, spaceSeparated = true, escape = true, format = "%s") +
repeat("-select", select_exps, spaceSeparated = true, escape = true, format = "%s") +
repeat("-selectName", select_names, spaceSeparated = true, escape = true, format = "%s") +
repeat("-sn", sample, spaceSeparated = true, escape = true, format = "%s") +
--
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