zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Resolving merge conflicts

This commit is contained in:
Eric Banks 2013-01-30 10:47:59 -05:00
parent 9025567cb8 4852c7404e
commit d067c7f136
3 changed files with 3 additions and 85 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompressionStash.java
View File

@ -63,7 +63,7 @@ import java.util.TreeSet;
*/
public class CompressionStash extends TreeSet<FinishedGenomeLoc> {
public CompressionStash() {
super(new GenomeLocComparator());
super();
}
/**

5
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/ReduceReads.java
View File

@ -64,7 +64,6 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType;
import org.broadinstitute.sting.gatk.walkers.ReadFilters;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocComparator;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.clipping.ReadClipper;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@ -267,8 +266,8 @@ public class ReduceReads extends ReadWalker<LinkedList<GATKSAMRecord>, ReduceRea
public void initialize() {
super.initialize();
GenomeAnalysisEngine toolkit = getToolkit();
readNameHash = new HashMap<String, Long>(); // prepare the read name hash to keep track of what reads have had their read names compressed
intervalList = new TreeSet<GenomeLoc>(new GenomeLocComparator()); // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode
readNameHash = new HashMap<String, Long>(); // prepare the read name hash to keep track of what reads have had their read names compressed
intervalList = new TreeSet<GenomeLoc>(); // get the interval list from the engine. If no interval list was provided, the walker will work in WGS mode
if (toolkit.getIntervals() != null)
intervalList.addAll(toolkit.getIntervals());

81
public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java
View File

@ -1,81 +0,0 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.utils;
import com.google.java.contract.Ensures;
import com.google.java.contract.Requires;
import java.util.Comparator;
/**
*
* @author Mauricio Carneiro
* @since 9/28/11
*/
public class GenomeLocComparator implements Comparator<GenomeLoc> {
/**
* compares genomeLoc's contigs
*
* @param gl1 the genome loc to compare contigs
* @param gl2 the genome loc to compare contigs
* @return 0 if equal, -1 if gl2.contig is greater, 1 if gl1.contig is greater
*/
@Requires("gl2 != null")
@Ensures("result == 0 || result == 1 || result == -1")
public final int compareContigs( GenomeLoc gl1, GenomeLoc gl2 ) {
if (gl1.contigIndex == gl2.contigIndex)
return 0;
else if (gl1.contigIndex > gl2.contigIndex)
return 1;
return -1;
}
@Requires("gl2 != null")
@Ensures("result == 0 || result == 1 || result == -1")
public int compare ( GenomeLoc gl1, GenomeLoc gl2 ) {
int result = 0;
if ( gl1 == gl2 ) {
result = 0;
}
else if(GenomeLoc.isUnmapped(gl1))
result = 1;
else if(GenomeLoc.isUnmapped(gl2))
result = -1;
else {
final int cmpContig = compareContigs(gl1, gl2);
if ( cmpContig != 0 ) {
result = cmpContig;
} else {
if ( gl1.getStart() < gl2.getStart() ) result = -1;
if ( gl1.getStart() > gl2.getStart() ) result = 1;
}
}
return result;
}
}