Commit 7729de26 authored by Peter van 't Hof's avatar Peter van 't Hof Committed by GitHub

Merge pull request #79 from biopet/fix-BIOPET-656

Adding new option to haplotypecaller
parents 5e2ceed3 e0b92056
......@@ -56,6 +56,8 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
@Argument(fullName = "maxGGAARExtension", shortName = "maxGGAARExtension", doc = "the maximum extent into the full active region extension that we're willing to go in genotyping our events for GGA mode", required = false, exclusiveOf = "", validation = "")
var maxGGAARExtension: Option[Int] = config("maxGGAARExtension")
var useNewAFCalculator: Boolean = config("useNewAFCalculator", default = false)
/** Include at least this many bases around an event for calling indels */
@Argument(fullName = "paddingAroundIndels", shortName = "paddingAroundIndels", doc = "Include at least this many bases around an event for calling indels", required = false, exclusiveOf = "", validation = "")
var paddingAroundIndels: Option[Int] = config("paddingAroundIndels")
......@@ -441,6 +443,7 @@ class HaplotypeCaller(val parent: Configurable) extends CommandLineGATK with Sca
optional("-paddingAroundSNPs", paddingAroundSNPs, spaceSeparated = true, escape = true, format = "%s") +
repeat("-comp", comp, formatPrefix = TaggedFile.formatCommandLineParameter, spaceSeparated = true, escape = true, format = "%s") +
repeat("-A", annotation, spaceSeparated = true, escape = true, format = "%s") +
conditional(useNewAFCalculator, "--useNewAFCalculator") +
repeat("-XA", excludeAnnotation, spaceSeparated = true, escape = true, format = "%s") +
repeat("-G", group, spaceSeparated = true, escape = true, format = "%s") +
conditional(debug, "-debug", escape = true, format = "%s") +
......
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