Commit 63a0ef68 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix for #95

parent b2a02952
......@@ -97,13 +97,13 @@ object VcfFilter extends ToolCommand {
} text ("Min value of AD field in genotype fields")
opt[Int]("minSamplesPass") unbounded () valueName ("<int>") action { (x, c) =>
c.copy(minSamplesPass = x)
} text ("Min number opf samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth")
} text ("Min number off samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth")
opt[Int]("minBamAlternateDepth") unbounded () valueName ("<int>") action { (x, c) =>
c.copy(minBamAlternateDepth = x)
} // TODO: Convert this to more generic filter
opt[String]("denovoInSample") maxOccurs (1) unbounded () valueName ("<sample>") action { (x, c) =>
c.copy(denovoInSample = x)
} text ("Only show variants that contain unique alleles in compete set for given sample")
} text ("Only show variants that contain unique alleles in complete set for given sample")
opt[String]("mustHaveVariant") unbounded () valueName ("<sample>") action { (x, c) =>
c.copy(mustHaveVariant = x :: c.mustHaveVariant)
} text ("Given sample must have 1 alternative allele")
......@@ -114,7 +114,7 @@ object VcfFilter extends ToolCommand {
opt[String]("filterHetVarToHomVar") unbounded () valueName ("<sample:sample>") action { (x, c) =>
c.copy(filterHetVarToHomVar = (x.split(":")(0), x.split(":")(1)) :: c.filterHetVarToHomVar)
} validate { x => if (x.split(":").length == 2) success else failure("--filterHetVarToHomVar should be in this format: sample:sample")
} text ("If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filterd")
} text ("If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filtered")
opt[Unit]("filterRefCalls") unbounded () action { (x, c) =>
c.copy(filterRefCalls = true)
} text ("Filter when there are only ref calls")
......
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