From 99f9cd84ed73fcccbe6755ea6937c8068ab11127 Mon Sep 17 00:00:00 2001 From: hanna Date: Tue, 14 Jul 2009 16:21:22 +0000 Subject: [PATCH] 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 --- .../sting/gatk/executive/MicroScheduler.java | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java index 89720b8cc..c2ac3c528 100755 --- a/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java +++ b/java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java @@ -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"));