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Validates intervals against sequence dictionary header bounds. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1900 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-10-22 19:31:15 +00:00
parent 54c61c663c
commit 2e552eb5a1
1 changed files with 18 additions and 2 deletions
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20
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -343,8 +343,9 @@ public class GenomeLocParser {
List<String> lines = reader.readLines(); List<String> lines = reader.readLines();
reader.close(); reader.close();
String locStr = Utils.join(";", lines); String locStr = Utils.join(";", lines);
logger.debug("locStr: " + locStr);
ret = parseGenomeLocs(locStr); ret = parseGenomeLocs(locStr);
for(GenomeLoc locus: ret)
verifyGenomeLocBounds(locus);
return ret; return ret;
} catch (Exception e2) { } catch (Exception e2) {
logger.error("Attempt to parse interval file in GATK format failed: " + e2.getMessage()); logger.error("Attempt to parse interval file in GATK format failed: " + e2.getMessage());
@ -447,8 +448,9 @@ public class GenomeLocParser {
/** /**
* verify the specified genome loc is valid, if it's not, throw an exception * verify the specified genome loc is valid, if it's not, throw an exception
* Will not verify the location against contig bounds.
* *
* @param toReturn teh genome loc we're about to return * @param toReturn the genome loc we're about to return
* *
* @return the genome loc if it's valid, otherwise we throw an exception * @return the genome loc if it's valid, otherwise we throw an exception
*/ */
@ -470,6 +472,20 @@ public class GenomeLocParser {
} }
/**
* Verify the locus against the bounds of the contig.
* @param locus Locus to verify.
*/
private static void verifyGenomeLocBounds(GenomeLoc locus) {
verifyGenomeLoc(locus);
int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength();
if(locus.getStart() > contigSize)
throw new StingException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig()));
if(locus.getStop() > contigSize)
throw new StingException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig()));
}
/** /**
* Move this Genome loc to the next contig, with a start * Move this Genome loc to the next contig, with a start