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Naughty use of assertions means that malformed records are not caught. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4596 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-10-29 14:41:38 +00:00
parent 9a60e72364
commit 58f7b4c595
1 changed files with 5 additions and 3 deletions
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8
java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqCodec.java
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@ -38,7 +38,7 @@ public class RefSeqCodec implements FeatureCodec {
feature.setTranscript_id(fields[1]);
if ( fields[3].length()==1 && fields[3].charAt(0)=='+') feature.setStrand(1);
else if ( fields[3].length()==1 && fields[3].charAt(0)=='-') feature.setStrand(-1);
else throw new UserException.MalformedFile("Expected strand symbol (+/-), found: "+fields[3]);
else throw new UserException.MalformedFile("Expected strand symbol (+/-), found: "+fields[3] + " for line=" + line);
feature.setTranscript_interval(GenomeLocParser.parseGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5])));
@ -48,8 +48,10 @@ public class RefSeqCodec implements FeatureCodec {
String[] exon_stops = fields[10].split(",");
String[] eframes = fields[15].split(",");
assert exon_starts.length == exon_stops.length : "Data format error: numbers of exon start and stop positions differ";
assert exon_starts.length == eframes.length : "Data format error: numbers of exons and exon frameshifts differ";
if ( exon_starts.length == exon_stops.length )
throw new UserException.MalformedFile("Data format error: numbers of exon start and stop positions differ for line=" + line);
if ( exon_starts.length == eframes.length )
throw new UserException.MalformedFile("Data format error: numbers of exons and exon frameshifts differ for line=" + line);
ArrayList<GenomeLoc> exons = new ArrayList<GenomeLoc>(exon_starts.length);
ArrayList<Integer> exon_frames = new ArrayList<Integer>(eframes.length);