From 63a0ef68c2189b22428c14317bbb5c247587f432 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 8 Dec 2014 15:58:33 +0100
Subject: [PATCH] Fix for #95
---
.../main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
index 9c6677dc9..c96731b0c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfFilter.scala
@@ -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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