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gatk-3.8
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a better error message for the situation where a RMD track generates a negitive length interval; the user will now see a message like "Bad input: A feature produced by the reference metadata track named "bed" at position chr1:10434-10433 has a start greater than the stop; this is an invalid position " 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4958 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2011-01-07 19:06:04 +00:00
parent 4272b824d6
commit 56b87da8f9
1 changed files with 6 additions and 1 deletions
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7
java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
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@ -27,6 +27,8 @@ import org.broad.tribble.Feature;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.UserException;
/**
@ -44,7 +46,7 @@ public abstract class GATKFeature implements Feature {
this.name = name;
}
private String name;
String name;
protected void setName(String name) {
this.name = name;
@ -73,6 +75,9 @@ public abstract class GATKFeature implements Feature {
}
public GenomeLoc getLocation() {
if (position == null) position = genomeLocParser.createGenomeLoc(feature.getChr(), feature.getStart(), feature.getEnd());
if (position.getStart() > position.getStop()) {
throw new UserException.BadInput("A feature produced by the reference metadata track named \"" + this.name + "\" at position " + position + " has a start greater than the stop; this is an invalid this is an invalid position");
}
return position;
}