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()); } }