From 32adbd614f9dc39b09fb3aa3fd9a2e910e3b4e24 Mon Sep 17 00:00:00 2001 From: Guillermo del Angel Date: Tue, 22 Nov 2011 22:48:46 -0500 Subject: [PATCH] Solve merge conflict --- .../sting/gatk/walkers/indels/PairHMMIndelErrorModel.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java index 95633c222..09968f47e 100755 --- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java +++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java @@ -561,7 +561,7 @@ public class PairHMMIndelErrorModel { System.out.format("indStart: %d indStop: %d WinStart:%d WinStop:%d start: %d stop: %d readLength: %d C:%s\n", indStart, indStop, ref.getWindow().getStart(), ref.getWindow().getStop(), start, stop, read.getReadLength(), read.getCigar().toString()); - if (indStart < 0 || indStop >= haplotype.getBasesAsBytes().length || indStart > indStop) { + if (indStart < 0 || indStop >= haplotype.getBases().length || indStart > indStop) { // read spanned more than allowed reference context: we currently can't deal with this readLikelihood =0; } else