From 1fbfd4082ecab5844f63717ec6cde23bda65578e Mon Sep 17 00:00:00 2001 From: carneiro Date: Mon, 7 Feb 2011 17:14:55 +0000 Subject: [PATCH] Cycle covariate now works with pacbio reads. No need to override the platform anymore. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5210 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/recalibration/CycleCovariate.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java index 56eca09e4..64e0864c0 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java @@ -160,6 +160,7 @@ public class CycleCovariate implements StandardCovariate { */ // todo -- this should be put into a common place in the code base + private static List PACBIO_NAMES = Arrays.asList("PACBIO"); private static List ILLUMINA_NAMES = Arrays.asList("ILLUMINA", "SLX", "SOLEXA"); private static List SOLID_NAMES = Arrays.asList("SOLID"); private static List LS454_NAMES = Arrays.asList("454"); @@ -180,7 +181,7 @@ public class CycleCovariate implements StandardCovariate { //----------------------------- - if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) ) { + if( isPlatform(read, ILLUMINA_NAMES) || isPlatform(read, SOLID_NAMES) || isPlatform(read, PACBIO_NAMES)) { final int init; final int increment; if( !read.getReadNegativeStrandFlag() ) {