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Warning for possibly mismatched reads / reference was very aggressive. Relax 

the criteria a bit.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1234 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-14 16:21:22 +00:00
parent 12b5d9c70c
commit 99f9cd84ed
1 changed files with 4 additions and 3 deletions
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7
java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java
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@ -326,9 +326,10 @@ public abstract class MicroScheduler {
Utils.scareUser("No overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference.");
}
// If one data source isn't a strict subset of the other or the match is of fewer than x% of the smaller,
// issue a warning.
if( !readsSequenceNames.equals(referenceSequenceNames) ) {
// If the two datasets are not equal and neither is a strict subset of the other, warn the user.
if( !readsSequenceNames.equals(referenceSequenceNames) &&
!readsSequenceNames.containsAll(referenceSequenceNames) &&
!referenceSequenceNames.containsAll(readsSequenceNames)) {
StringBuilder warning = new StringBuilder();
warning.append("Limited overlap exists between sequence dictionary of the reads and the sequence dictionary of the reference. Perhaps you're using the wrong reference?\n");
warning.append(System.getProperty("line.separator"));