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Add a MAX_READ_GROUPS sanity parameter. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@934 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-08 13:57:43 +00:00
parent 9f35a5aa32
commit e2ed56dc96
1 changed files with 7 additions and 0 deletions
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7
java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java
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@ -41,6 +41,9 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
@Argument(fullName="READ_GROUP", shortName="rg", required=false, doc="Only use reads with this read group (@RG)")
public String READ_GROUP = "none";
@Argument(fullName="MAX_READ_GROUPS", shortName="mrg", required=false, doc="Abort if number of read groups in input file exceeeds this count.")
public int MAX_READ_GROUPS = 100;
int NDINUCS = 16;
ArrayList<RecalData> flattenData = new ArrayList<RecalData>();
HashMap<String, RecalData[][][]> data = new HashMap<String, RecalData[][][]>();
@ -92,6 +95,10 @@ public class CovariateCounterWalker extends LocusWalker<Integer, Integer> {
}
public void initialize() {
if( getToolkit().getEngine().getSAMHeader().getReadGroups().size() > MAX_READ_GROUPS )
Utils.scareUser("Number of read groups in the specified file exceeds the number that can be processed in a reasonable amount of memory." +
"To override this limit, use the --MAX_READ_GROUPS (-mrg) parameter");
for (SAMReadGroupRecord readGroup : this.getToolkit().getEngine().getSAMHeader().getReadGroups()) {
if( readGroup.getAttribute("PL") == null )
Utils.warnUser(String.format("PL attribute for read group %s is unset; assuming all reads are illumina",readGroup.getReadGroupId()));