From fccba7e8dd5e0bd98840c6dffa9c3f5059cff2d5 Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Mon, 3 Jun 2019 15:33:59 -0700 Subject: [PATCH 1/2] Update CollectSamErrorMetrics.java @yfarjoun care to take a look at this? Happy for there to be a test for it, but it ain't my bug. --- .../java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java b/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java index 4f7b34f256..32b054b24a 100644 --- a/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java +++ b/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java @@ -137,7 +137,7 @@ public class CollectSamErrorMetrics extends CommandLineProgram { public ReadBaseStratification.Stratifier STRATIFIER_VALUE; @Argument(shortName = "V", doc = "VCF of known variation for sample. program will skip over polymorphic sites in this VCF and " + - "avoid collecting data on these loci.") + "avoid collecting data on these loci.", , optional = true) public File VCF; @Argument(shortName = "L", doc = "Region(s) to limit analysis to. Supported formats are VCF or interval_list. Will intersect inputs if multiple are given. ", optional = true) From ca9d0001ba117a6a69dfdb9d42b97823ebecfd3a Mon Sep 17 00:00:00 2001 From: Nils Homer Date: Mon, 3 Jun 2019 15:34:35 -0700 Subject: [PATCH 2/2] Update CollectSamErrorMetrics.java --- .../java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java b/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java index 32b054b24a..579d7742a5 100644 --- a/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java +++ b/src/main/java/picard/sam/SamErrorMetric/CollectSamErrorMetrics.java @@ -137,7 +137,7 @@ public class CollectSamErrorMetrics extends CommandLineProgram { public ReadBaseStratification.Stratifier STRATIFIER_VALUE; @Argument(shortName = "V", doc = "VCF of known variation for sample. program will skip over polymorphic sites in this VCF and " + - "avoid collecting data on these loci.", , optional = true) + "avoid collecting data on these loci.", optional = true) public File VCF; @Argument(shortName = "L", doc = "Region(s) to limit analysis to. Supported formats are VCF or interval_list. Will intersect inputs if multiple are given. ", optional = true)