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Remove some of the restrictions on getStart() and getStop(); getStart() and getStop() 

now do the minimum validation rather than the more rigorous only-within-the-contig-bounds 
header validation.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3027 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-03-17 19:39:30 +00:00
parent 4965d6b26a
commit d9398dc347
1 changed files with 4 additions and 13 deletions
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17
java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
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@ -605,6 +605,8 @@ public class GenomeLocParser {
/** /**
* create a new genome loc from an existing loc, with a new start position * create a new genome loc from an existing loc, with a new start position
* Note that this function will NOT explicitly check the ending offset, in case someone wants to
* set the start of a new GenomeLoc pertaining to a read that goes off the end of the contig.
* *
* @param loc the old location * @param loc the old location
* @param start a new start position * @param start a new start position
@ -613,18 +615,13 @@ public class GenomeLocParser {
*/ */
public static GenomeLoc setStart(GenomeLoc loc, long start) { public static GenomeLoc setStart(GenomeLoc loc, long start) {
checkSetup(); checkSetup();
if (loc.getContigIndex() < 0 || loc.getContigIndex() >= contigInfo.getSequences().size()) {
throw new StingException("Genome loc passed in to setStart has a contig index outside the range of our current sequence dictionary");
}
int length = GenomeLocParser.contigInfo.getSequences().get(loc.getContigIndex()).getSequenceLength();
if (start > length) {
throw new StingException("start value of " + start + " is greater than the contig length, and is not -1. (length = " + length + ").");
}
return exceptionOnInvalidGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop())); return exceptionOnInvalidGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop()));
} }
/** /**
* create a new genome loc from an existing loc, with a new stop position * create a new genome loc from an existing loc, with a new stop position
* Note that this function will NOT explicitly check the ending offset, in case someone wants to
* set the stop of a new GenomeLoc pertaining to a read that goes off the end of the contig.
* *
* @param loc the old location * @param loc the old location
* @param stop a new stop position * @param stop a new stop position
@ -633,12 +630,6 @@ public class GenomeLocParser {
*/ */
public static GenomeLoc setStop(GenomeLoc loc, long stop) { public static GenomeLoc setStop(GenomeLoc loc, long stop) {
checkSetup(); checkSetup();
if (loc.getContigIndex() < 0 || loc.getContigIndex() >= contigInfo.getSequences().size()) {
throw new StingException("Genome loc passed in to setStart has a contig index outside the range of our current sequence dictionary");
}
if ((stop != -1) && (stop > GenomeLocParser.contigInfo.getSequences().get(loc.getContigIndex()).getSequenceLength())) {
throw new StingException("stop value of " + stop + " is greater than the contig length, and is not -1.");
}
return exceptionOnInvalidGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start, stop)); return exceptionOnInvalidGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start, stop));
} }