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adding a check to the RodVCF to ensure that records are in-order in the underlying VCF file. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2403 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-12-18 15:24:45 +00:00
parent 38563bbc2d
commit 9971a8da9a
1 changed files with 17 additions and 1 deletions
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18
java/src/org/broadinstitute/sting/gatk/refdata/RodVCF.java
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@ -340,7 +340,23 @@ public class RodVCF extends BasicReferenceOrderedDatum implements VariationRod,
*/
public RodVCF next() {
if (!this.hasNext()) throw new NoSuchElementException("RodVCF next called on iterator with no more elements");
return new RodVCF(name, mReader.next(), mReader);
// get the next record
VCFRecord rec = mReader.next();
// make sure the next VCF record isn't before the current record (we'll accept at the same location, the
// spec doesn't indicate, and it seems like a valid use case)
GenomeLoc curPosition = null;
if (mCurrentRecord != null) curPosition = mCurrentRecord.getLocation();
if (curPosition != null && rec != null && curPosition.compareTo(rec.getLocation()) > 0)
throw new StingException("The next VCF record appears to be before the current (current location => " + curPosition.toString() +
", the next record position => " + rec.getLocation().toString() + " with line : " + rec.toStringEncoding(mReader.getHeader()) + "). " +
"Check to make sure the input VCF file is correctly sorted.");
// save off the previous record. This is needed given how iterators are used in the ROD system;
// we need to save off the last record
mCurrentRecord = rec;
return new RodVCF(name, rec, mReader);
}
public void remove() {