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fix: RefSeq contains records with zero coding length and the refsec codec/feature used to crash on those; now such records are ignored, with warning printed (once)

This commit is contained in:
Andrey Sivachenko 2011-08-17 15:17:31 -04:00
parent 710d34633e
commit a423546cdd
1 changed files with 14 additions and 2 deletions
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16
public/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
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@ -1,5 +1,6 @@
package org.broadinstitute.sting.gatk.refdata.features.refseq;
import org.apache.commons.io.filefilter.FalseFileFilter;
import org.broad.tribble.Feature;
import org.broad.tribble.TribbleException;
import org.broad.tribble.readers.LineReader;
@ -20,7 +21,7 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
* The parser to use when resolving genome-wide locations.
*/
private GenomeLocParser genomeLocParser;
private boolean zero_coding_length_user_warned = false;
/**
* Set the parser to use when resolving genetic data.
* @param genomeLocParser The supplied parser.
@ -60,9 +61,20 @@ public class RefSeqCodec implements ReferenceDependentFeatureCodec<RefSeqFeature
else if ( fields[3].length()==1 && fields[3].charAt(0)=='-') feature.setStrand(-1);
else throw new UserException.MalformedFile("Expected strand symbol (+/-), found: "+fields[3] + " for line=" + line);
int coding_start = Integer.parseInt(fields[6])+1;
int coding_stop = Integer.parseInt(fields[7]);
if ( coding_start > coding_stop ) {
if ( ! zero_coding_length_user_warned ) {
Utils.warnUser("RefSeq file contains transcripts with zero coding length. "+
"Such transcripts will be ignored (this warning is printed only once)");
zero_coding_length_user_warned = true;
}
return null;
}
feature.setTranscript_interval(genomeLocParser.createGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])));
feature.setTranscript_coding_interval(genomeLocParser.createGenomeLoc(contig_name, Integer.parseInt(fields[6])+1, Integer.parseInt(fields[7])));
feature.setTranscript_coding_interval(genomeLocParser.createGenomeLoc(contig_name, coding_start, coding_stop));
feature.setGene_name(fields[12]);
String[] exon_starts = fields[9].split(",");
String[] exon_stops = fields[10].split(",");