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* added ability to load multiple BAM files from command line 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@489 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kcibul 2009-04-22 00:28:08 +00:00
parent 5b8502745a
commit b820130dce
1 changed files with 5 additions and 1 deletions
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6
java/src/org/broadinstitute/sting/gatk/executive/MicroManager.java
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@ -29,7 +29,7 @@ import java.util.List;
* *
*/ */
public class MicroManager { public class MicroManager {
private static long SHARD_SIZE = 5L; private static long SHARD_SIZE = 100000L;
private File reads; private File reads;
private FastaSequenceFile2 ref; private FastaSequenceFile2 ref;
@ -86,6 +86,10 @@ public class MicroManager {
fl.add(new File(line)); fl.add(new File(line));
} }
} }
} else if (reads.getCanonicalPath().indexOf(",") > 0) {
for (String bamFile : reads.getCanonicalPath().split(",")) {
fl.add(new File(bamFile));
}
} else { } else {
fl.add(reads); fl.add(reads);