zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Fixed warnings in LAATV and ValidateVariants

This commit is contained in:
Geraldine Van der Auwera 2016-05-27 11:49:48 -04:00
parent c4a06ad20a
commit 81d4eaea29
2 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
View File

@ -249,7 +249,7 @@ public class LeftAlignAndTrimVariants extends RodWalker<Integer, Integer> {
// ignore if the reference length is greater than the reference window stop before and after expansion // ignore if the reference length is greater than the reference window stop before and after expansion
if ( refLength > MAX_INDEL_LENGTH && refLength > referenceWindowStop ) { if ( refLength > MAX_INDEL_LENGTH && refLength > referenceWindowStop ) {
logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d",
REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength)); REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getChr(), vc.getStart(), refLength));
return 0; return 0;
} }

2
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/variantutils/ValidateVariants.java
View File

@ -283,7 +283,7 @@ public class ValidateVariants extends RodWalker<GenomeLoc, GenomeLocSortedSet> {
// reference length is greater than the reference window stop before and after expansion // reference length is greater than the reference window stop before and after expansion
if ( refLength > 100 && refLength > referenceWindowStop ) { if ( refLength > 100 && refLength > referenceWindowStop ) {
logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --referenceWindowStop >= %d", logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --reference_window_stop >= %d",
REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getContig(), vc.getStart(), refLength)); REFERENCE_ALLELE_TOO_LONG_MSG, refLength, vc.getContig(), vc.getStart(), refLength));
return; return;
} }