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Finally just deleted equals() method in GATKArgumentCollection. 

-- We never compare these things in the codebase anyway...
This commit is contained in:
Mark DePristo 2012-05-21 10:59:31 -04:00
parent 6f469305ab
commit bb0d87666a
1 changed files with 0 additions and 110 deletions
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110
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
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@ -324,115 +324,5 @@ public class GATKArgumentCollection {
@Argument(fullName="allow_intervals_with_unindexed_bam",doc="Allow interval processing with an unsupported BAM. NO INTEGRATION TESTS are available. Use at your own risk.",required=false)
@Hidden
public boolean allowIntervalsWithUnindexedBAM = false;
// --------------------------------------------------------------------------------------------------------------
//
// methods
//
// --------------------------------------------------------------------------------------------------------------
/**
* test equality between two arg collections. This function defines the statement:
* "not fun to write"
*
* @param other the other collection
*
* @return true if they're equal
*/
public boolean equals(GATKArgumentCollection other) {
if (other == null) return false;
if (other.samFiles.size() != samFiles.size()) {
return false;
}
for (int x = 0; x < samFiles.size(); x++) {
if (!samFiles.get(x).equals(other.samFiles.get(x))) {
return false;
}
}
if (other.walkerArgs.size() != walkerArgs.size()) {
return false;
}
for (String s : walkerArgs.keySet()) {
if (!other.walkerArgs.containsKey(s)) {
return false;
}
}
if (!other.samFiles.equals(this.samFiles)) {
return false;
}
if(other.readBufferSize == null || this.readBufferSize == null) {
// If either is null, return false if they're both null, otherwise keep going...
if(other.readBufferSize != null || this.readBufferSize != null)
return false;
}
else {
if(!other.readBufferSize.equals(this.readBufferSize))
return false;
}
if (!(other.readBufferSize == null && this.readBufferSize == null) && (other.readBufferSize == null || this.readBufferSize == null)) {
return false;
}
if (!other.strictnessLevel.equals(this.strictnessLevel)) {
return false;
}
if (!other.referenceFile.equals(this.referenceFile)) {
return false;
}
if ((other.intervals == null && this.intervals != null) || !other.intervals.equals(this.intervals)) {
return false;
}
if (!other.excludeIntervals.equals(this.excludeIntervals)) {
return false;
}
if (!other.unsafe.equals(this.unsafe)) {
return false;
}
if ((other.downsampleFraction == null && this.downsampleFraction != null) ||
(other.downsampleFraction != null && !other.downsampleFraction.equals(this.downsampleFraction))) {
return false;
}
if ((other.downsampleCoverage == null && this.downsampleCoverage != null) ||
(other.downsampleCoverage != null && !other.downsampleCoverage.equals(this.downsampleCoverage))) {
return false;
}
if (!other.numberOfThreads.equals(this.numberOfThreads)) {
return false;
}
if ((this.numberOfCPUThreads == null && other.numberOfCPUThreads != null) ||
this.numberOfCPUThreads.equals(other.numberOfCPUThreads) ) {
return false;
}
if ((this.numberOfIOThreads == null && other.numberOfIOThreads != null) ||
this.numberOfIOThreads.equals(other.numberOfIOThreads) ) {
return false;
}
if ((other.numberOfBAMFileHandles == null && this.numberOfBAMFileHandles != null) ||
(other.numberOfBAMFileHandles != null && !other.numberOfBAMFileHandles.equals(this.numberOfBAMFileHandles))) {
return false;
}
if (other.intervalMerging != this.intervalMerging) {
return false;
}
if (other.phoneHomeType != this.phoneHomeType) {
return false;
}
if (intervalSetRule != other.intervalSetRule)
return false;
if ( BAQMode != other.BAQMode ) return false;
if ( BAQGOP != other.BAQGOP ) return false;
if ((other.performanceLog == null && this.performanceLog != null) ||
(other.performanceLog != null && !other.performanceLog.equals(this.performanceLog)))
return false;
if (allowIntervalsWithUnindexedBAM != other.allowIntervalsWithUnindexedBAM)
return false;
return true;
}
}