From bb0d87666adb9f3cdb0702534f57e32beedb1809 Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 21 May 2012 10:59:31 -0400
Subject: [PATCH] Finally just deleted equals() method in
 GATKArgumentCollection.

-- We never compare these things in the codebase anyway...
---
 .../arguments/GATKArgumentCollection.java     | 110 ------------------
 1 file changed, 110 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index 3a1408d59..5b9ca8470 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -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;
-    }
-
 }