From 38914384d1a1523b3ed9d3b8d5cf9b0106d42bd0 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Tue, 12 Mar 2013 15:41:28 -0400 Subject: [PATCH] Changing CALLED_IN_DB_UNKNOWN_STATUS to count as TRUE_POSITIVEs in the simplified stats for AssessNA12878. --- .../sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java | 2 +- .../sting/utils/activeregion/ActivityProfile.java | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java index 3f3d7123a..1f72fd82f 100644 --- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java +++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java @@ -149,7 +149,7 @@ public class HaplotypeCaller extends ActiveRegionWalker implem * The assembled haplotypes will be written as BAM to this file if requested. Really for debugging purposes only. * Note that the output here does not include uninformative reads so that not every input read is emitted to the bam. * - * Turning on this mode may result in serious performance cost for the HC. It's really only approprate to + * Turning on this mode may result in serious performance cost for the HC. It's really only appropriate to * use in specific areas where you want to better understand why the HC is making specific calls. * * The reads are written out containing a HC tag (integer) that encodes which haplotype each read best matches diff --git a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java index 25948a857..39509e9df 100644 --- a/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java +++ b/public/java/src/org/broadinstitute/sting/utils/activeregion/ActivityProfile.java @@ -259,7 +259,7 @@ public class ActivityProfile { * Can be overridden by subclasses to transform states in any way * * There's no particular contract for the output states, except that they can never refer to states - * beyond the current end of the stateList unless the explictly include preceding states before + * beyond the current end of the stateList unless the explicitly include preceding states before * the reference. So for example if the current state list is [1, 2, 3] this function could return * [1,2,3,4,5] but not [1,2,3,5]. *