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Oops, working too quickly last time. This is the proper fix for the potential NPE in the equals() test.

This commit is contained in:
Eric Banks 2011-10-27 15:32:08 -04:00
parent 4d0e34109f
commit c2f343773e
1 changed files with 3 additions and 5 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -76,18 +76,16 @@ public class GATKArgumentCollection {
* One may use samtools-style intervals either explicitly (e.g. -L chr1 or -L chr1:100-200) or listed in a file (e.g. -L myFile.intervals).
* Additionally, one may specify a rod file to traverse over the positions for which there is a record in the file (e.g. -L file.vcf).
*/
//@ElementList(required = false)
@Input(fullName = "intervals", shortName = "L", doc = "One or more genomic intervals over which to operate. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
public List<IntervalBinding<Feature>> intervals = Collections.emptyList();
public List<IntervalBinding<Feature>> intervals = null;
/**
* Using this option one can instruct the GATK engine NOT to traverse over certain parts of the genome. This argument can be specified multiple times.
* One may use samtools-style intervals either explicitly (e.g. -XL chr1 or -XL chr1:100-200) or listed in a file (e.g. -XL myFile.intervals).
* Additionally, one may specify a rod file to skip over the positions for which there is a record in the file (e.g. -XL file.vcf).
*/
//@ElementList(required = false)
@Input(fullName = "excludeIntervals", shortName = "XL", doc = "One or more genomic intervals to exclude from processing. Can be explicitly specified on the command line or in a file (including a rod file)", required = false)
public List<IntervalBinding<Feature>> excludeIntervals = Collections.emptyList();
public List<IntervalBinding<Feature>> excludeIntervals = null;
/**
* How should the intervals specified by multiple -L or -XL arguments be combined? Using this argument one can, for example, traverse over all of the positions
@ -350,7 +348,7 @@ public class GATKArgumentCollection {
if (!other.referenceFile.equals(this.referenceFile)) {
return false;
}
if (!other.intervals.equals(this.intervals)) {
if ((other.intervals == null && this.intervals != null) || !other.intervals.equals(this.intervals)) {
return false;
}
if (!other.excludeIntervals.equals(this.excludeIntervals)) {