Commit bffd796d authored by bow's avatar bow
Browse files

Merge branch 'fix-tagged_files' into 'develop'

Fixed tagged files

Fixes #339 

See merge request !394
parents 59c78525 e7aeabf3
......@@ -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") +
......
......@@ -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")
......
......@@ -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") +
......
......@@ -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") +
......
......@@ -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") +
......
......@@ -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") +
......
......@@ -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") +
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment