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Stopgap fixes GFF, DbSNP being half-open rather than half-closed. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@980 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-06-10 21:38:57 +00:00
parent 94b0e46d12
commit 678ddd914f
2 changed files with 5 additions and 5 deletions
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6
java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java
View File

@ -132,7 +132,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
// ----------------------------------------------------------------------
public String toString() {
return String.format("%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
getLocation().getContig(), getLocation().getStart(), getLocation().getStop(),
getLocation().getContig(), getLocation().getStart(), getLocation().getStop()+1,
name, strand, refBases, observed, molType,
varType, validationStatus, avHet, avHetSE, func, locType, weight );
}
@ -152,7 +152,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
public String repl() {
return String.format("%d\t%s\t%d\t%d\t%s\t0\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
585, getLocation().getContig(), getLocation().getStart()-1, getLocation().getStop()-1,
585, getLocation().getContig(), getLocation().getStart()-1, getLocation().getStop(),
name, strand, refBases, refBases, observed, molType,
varType, validationStatus, avHet, avHetSE, func, locType, weight );
}
@ -162,7 +162,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
String contig = parts[1];
long start = Long.parseLong(parts[2]) + 1; // The final is 0 based
long stop = Long.parseLong(parts[3]) + 1; // The final is 0 based
loc = GenomeLoc.parseGenomeLoc(contig, start, stop);
loc = GenomeLoc.parseGenomeLoc(contig, start, stop-1);
name = parts[4];
refBases = parts[5];

4
java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java
View File

@ -104,7 +104,7 @@ public class rodGFF extends BasicReferenceOrderedDatum {
//
// ----------------------------------------------------------------------
public String toString() {
return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s\t%s", contig, source, feature, start, stop, score, strand, frame, getAttributeString());
return String.format("%s\t%s\t%s\t%d\t%d\t%f\t%s\t%s\t%s", contig, source, feature, start, stop+1, score, strand, frame, getAttributeString());
}
public String repl() {
@ -141,7 +141,7 @@ public class rodGFF extends BasicReferenceOrderedDatum {
final String source = parts[1];
final String feature = parts[2];
final long start = Long.parseLong(parts[3]);
final long stop = Long.parseLong(parts[4]);
final long stop = Long.parseLong(parts[4])-1;
double score = Double.NaN;
if ( ! parts[5].equals(".") )