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adding checks to the RefSeq rod for line's that contain less than the required number of columns (we expect there to be 16 columns) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4041 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-08-16 13:34:32 +00:00
parent cc58a27b00
commit 9ab647b730
1 changed files with 5 additions and 0 deletions
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5
java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
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@ -2,11 +2,13 @@ package org.broadinstitute.sting.gatk.refdata.features.refseq;
import org.broad.tribble.Feature; import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader; import org.broad.tribble.readers.LineReader;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import java.io.IOException;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
@ -18,6 +20,7 @@ public class RefSeqCodec implements FeatureCodec {
@Override @Override
public Feature decodeLoc(String line) { public Feature decodeLoc(String line) {
String fields[] = line.split("\t"); String fields[] = line.split("\t");
if (fields.length < 3) throw new TribbleException("RefSeq (decodeLoc) : Unable to parse line -> " + line + ", we expected at least 3 columns, we saw " + fields.length);
String contig_name = fields[2]; String contig_name = fields[2];
return new RefSeqFeature(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])); return new RefSeqFeature(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
} }
@ -27,6 +30,8 @@ public class RefSeqCodec implements FeatureCodec {
public Feature decode(String line) { public Feature decode(String line) {
String fields[] = line.split("\t"); String fields[] = line.split("\t");
// we reference postion 15 in the split array below, make sure we have at least that many columns
if (fields.length < 16) throw new TribbleException("RefSeq (decode) : Unable to parse line -> " + line + ", we expected at least 16 columns, we saw " + fields.length);
String contig_name = fields[2]; String contig_name = fields[2];
RefSeqFeature feature = new RefSeqFeature(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])); RefSeqFeature feature = new RefSeqFeature(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));