Commit 85639636 authored by Sander Bollen's avatar Sander Bollen Committed by GitHub
Browse files

Merge pull request #19 from biopet/fix-BIOPET-560

Fixing GATK 3.7 compatible extensions
parents cefa43a5 4ac25c6a
......@@ -137,7 +137,6 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) +
optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) +
optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) +
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat) +
optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") +
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
......@@ -146,7 +145,12 @@ class GenotypeGVCFs(val root: Configurable) extends CommandLineGATK with Scatter
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")
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") +
(this.getVersion match {
case Some(s) if s.contains("3.0") | s.contains("3.1") | s.contains("3.2") | s.contains("3.3") | s.contains("3.4") | s.contains("3.5") | s.contains("3.6") =>
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat)
case _ => ""
})
}
object GenotypeGVCFs {
......
......@@ -453,7 +453,6 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) +
optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) +
optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) +
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat) +
optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") +
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
......@@ -512,7 +511,12 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
optional("-mmq", min_mapping_quality_score, 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")
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") +
(this.getVersion match {
case Some(s) if s.contains("3.0") | s.contains("3.1") | s.contains("3.2") | s.contains("3.3") | s.contains("3.4") | s.contains("3.5") | s.contains("3.6") =>
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat)
case _ => ""
})
}
object HaplotypeCaller {
......
......@@ -300,7 +300,6 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
optional("-hets", heterozygosity, spaceSeparated = true, escape = true, format = heterozygosityFormat) +
optional("-indelHeterozygosity", indel_heterozygosity, spaceSeparated = true, escape = true, format = indel_heterozygosityFormat) +
optional("-stand_call_conf", standard_min_confidence_threshold_for_calling, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_callingFormat) +
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat) +
optional("-maxAltAlleles", max_alternate_alleles, spaceSeparated = true, escape = true, format = "%s") +
repeat("-inputPrior", input_prior, spaceSeparated = true, escape = true, format = "%s") +
optional("-ploidy", sample_ploidy, spaceSeparated = true, escape = true, format = "%s") +
......@@ -323,7 +322,12 @@ class UnifiedGenotyper(val root: Configurable) extends CommandLineGATK with Scat
repeat("-G", group, 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")
conditional(filter_bases_not_stored, "-filterNoBases", escape = true, format = "%s") +
(this.getVersion match {
case Some(s) if s.contains("3.0") | s.contains("3.1") | s.contains("3.2") | s.contains("3.3") | s.contains("3.4") | s.contains("3.5") | s.contains("3.6") =>
optional("-stand_emit_conf", standard_min_confidence_threshold_for_emitting, spaceSeparated = true, escape = true, format = standard_min_confidence_threshold_for_emittingFormat)
case _ => ""
})
}
object UnifiedGenotyper {
......
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