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Revert some bad merge changes

This commit is contained in:
Guillermo del Angel 2012-04-18 16:35:09 -04:00
parent 31c394d588
commit 82efd4457e
2 changed files with 6 additions and 6 deletions
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2
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -124,7 +124,7 @@ public class PairHMMIndelErrorModel {
} }
static private void getContextHomopolymerLength(final byte[] refBytes, final int[] hrunArray) { static private void getContextHomopolymerLength(final byte[] refBytes, final int[] hrunArray) {
// compute forward hrun length, example: // compute forward hrun length, example:
// AGGTGACCCCCCTGAGAG // AGGTGACCCCCCTGAGAG
// 001000012345000000 // 001000012345000000

10
public/java/src/org/broadinstitute/sting/utils/PairHMM.java
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@ -41,14 +41,14 @@ public class PairHMM {
private static final byte DEFAULT_GCP = (byte) 10; private static final byte DEFAULT_GCP = (byte) 10;
private static final double BANDING_TOLERANCE = 22.0; private static final double BANDING_TOLERANCE = 22.0;
private static final int BANDING_CLUSTER_WINDOW = 12; private static final int BANDING_CLUSTER_WINDOW = 12;
private final boolean doBanded; private final boolean noBanded;
public PairHMM() { public PairHMM() {
doBanded = false; noBanded = false;
} }
public PairHMM( final boolean doBanded ) { public PairHMM( final boolean noBanded ) {
this.doBanded = doBanded; this.noBanded = noBanded;
} }
@ -100,7 +100,7 @@ public class PairHMM {
readQuals[iii] = ( readQuals[iii] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : (readQuals[iii] > MAX_CACHED_QUAL ? MAX_CACHED_QUAL : readQuals[iii]) ); readQuals[iii] = ( readQuals[iii] < QualityUtils.MIN_USABLE_Q_SCORE ? QualityUtils.MIN_USABLE_Q_SCORE : (readQuals[iii] > MAX_CACHED_QUAL ? MAX_CACHED_QUAL : readQuals[iii]) );
} }
if( doBanded ) { if( false ) {
final ArrayList<Integer> workQueue = new ArrayList<Integer>(); // holds a queue of starting work location (indices along the diagonal). Will be sorted each step final ArrayList<Integer> workQueue = new ArrayList<Integer>(); // holds a queue of starting work location (indices along the diagonal). Will be sorted each step
final ArrayList<Integer> workToBeAdded = new ArrayList<Integer>(); final ArrayList<Integer> workToBeAdded = new ArrayList<Integer>();
final ArrayList<Double> calculatedValues = new ArrayList<Double>(); final ArrayList<Double> calculatedValues = new ArrayList<Double>();