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added a better message for the SO flag error in MergingSAMIterator2 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2685 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-01-25 22:57:18 +00:00
parent 24d4082925
commit 2e57bc7879
1 changed files with 3 additions and 1 deletions
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4
java/src/org/broadinstitute/sting/gatk/iterators/MergingSamRecordIterator2.java
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@ -100,7 +100,9 @@ public class MergingSamRecordIterator2 implements CloseableIterator<SAMRecord>,
*/
private void checkSortOrder(SAMFileReader reader) {
if (this.sortOrder != SAMFileHeader.SortOrder.unsorted && reader.getFileHeader().getSortOrder() != this.sortOrder) {
String msg = String.format("The GATK requires your bam have %s sort order, but your BAM file header %s. Continuing beyond this point is unsafe -- please update your BAM file to have a compatible sort order using samtools sort or Picard MergeBamFiles",
String msg = String.format("The GATK requires your bam have %s sort order, but your BAM file header %s. Continuing beyond this point is unsafe" +
"-- please update your BAM file to have a compatible sort order using samtools sort or Picard MergeBamFiles. You may overcome this error by " +
"passing the \'-U ALLOW_UNSET_BAM_SORT_ORDER\' on the command line; before doing so make sure that your input BAM is sorted even if it can't be marked as such.",
this.sortOrder, reader.getFileHeader().getAttribute("SO") == null ? "is missing the SO sort order flag" : "has an SO flag set to " + reader.getFileHeader().getAttribute("SO"));
if (!reads.getValidationExclusionList().contains(ValidationExclusion.TYPE.ALLOW_UNSET_BAM_SORT_ORDER)) {
throw new PicardException(msg);