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A nicer error (UserException now) for malformed genome locs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5465 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-03-18 02:58:29 +00:00
parent b45afe5ba8
commit 6281c1db6f
2 changed files with 10 additions and 3 deletions
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6
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
View File

@ -448,11 +448,11 @@ public class GenomeLocParser {
private void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) { private void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) {
int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength(); int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength();
if(locus.getStart() > contigSize) if(locus.getStart() > contigSize)
throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig())); throw new UserException.MalformedGenomeLoc("GenomeLoc is invalid: locus start is after the end of contig",locus);
if(locus.getStop() > contigSize) if(locus.getStop() > contigSize)
throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig())); throw new UserException.MalformedGenomeLoc("GenomeLoc is invalid: locus stop is after the end of contig",locus);
if (locus.getStart() > locus.getStop()) { if (locus.getStart() > locus.getStop()) {
throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position"); throw new UserException.MalformedGenomeLoc("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position", locus);
} }
} }

7
java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -30,6 +30,7 @@ import net.sf.samtools.SAMSequenceDictionary;
import net.sf.samtools.SAMSequenceRecord; import net.sf.samtools.SAMSequenceRecord;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils; import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
import org.broadinstitute.sting.utils.GenomeLoc;
import java.io.File; import java.io.File;
import java.util.Arrays; import java.util.Arrays;
@ -54,6 +55,12 @@ public class UserException extends ReviewedStingException {
} }
} }
public static class MalformedGenomeLoc extends UserException {
public MalformedGenomeLoc(String message, GenomeLoc loc) {
super(String.format("Badly formed genome loc: %s: %s", message, loc));
}
}
public static class BadInput extends UserException { public static class BadInput extends UserException {
public BadInput(String message) { public BadInput(String message) {
super(String.format("Bad input: %s", message)); super(String.format("Bad input: %s", message));