From fb6d7d19f9ac9a9e24c229c896df7bc9f1f3c56c Mon Sep 17 00:00:00 2001 From: depristo Date: Wed, 15 Sep 2010 20:40:56 +0000 Subject: [PATCH] Better window size error message git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4290 348d0f76-0448-11de-a6fe-93d51630548a --- .../sting/gatk/walkers/indels/IndelGenotyperV2Walker.java | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java index 954157005..7a3b05f1b 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelGenotyperV2Walker.java @@ -425,11 +425,10 @@ public class IndelGenotyperV2Walker extends ReadWalker { // let's double check now that the read fits after the shift if ( read.getAlignmentEnd() > normal_context.getStop()) { // ooops, looks like the read does not fit into the window even after the latter was shifted!! - throw new UserException.MissortedBAM(SAMFileHeader.SortOrder.coordinate, read, "Read "+read.getReadName()+": out of coverage window bounds. Probably window is too small.\n"+ + throw new UserException.BadArgumentValue("window_size", "Read "+read.getReadName()+": out of coverage window bounds. Probably window is too small, so increase the value of the window_size argument.\n"+ "Read length="+read.getReadLength()+"; cigar="+read.getCigarString()+"; start="+ read.getAlignmentStart()+"; end="+read.getAlignmentEnd()+ - "; window start (after trying to accomodate the read)="+normal_context.getStart()+ - "; window end="+normal_context.getStop()); + "; window start (after trying to accomodate the read)="+normal_context.getStart()+"; window end="+normal_context.getStop()); } }