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Moved phasing classes out of playground! The code is still under production, though... 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4369 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-09-28 23:21:28 +00:00
parent 8d8980e8eb
commit 7c909bef82
8 changed files with 17 additions and 14 deletions
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2
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/AllelePair.java → java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
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@ -21,7 +21,7 @@
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.phasing;
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;

14
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBackedPhasingWalker.java → java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.phasing;
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;
@ -534,8 +534,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
edgeToReads.addRead(e, rdName);
sitesWithEdges.add(e.v1);
sitesWithEdges.add(e.v2);
sitesWithEdges.add(e.getV1());
sitesWithEdges.add(e.getV2());
}
}
}
@ -602,8 +602,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
Note that the path from prev ---> v1 will NOT contain v2, since we removed all of v2's edges,
and the path from v2 ---> cur will NOT contain v1.
*/
boolean prevTo2and1ToCur = removedSiteSameCCAsPrev[e.v1].contains(e.v2) && removedSiteSameCCAsCur[e.v2].contains(e.v1);
boolean prevTo1and2ToCur = removedSiteSameCCAsPrev[e.v2].contains(e.v1) && removedSiteSameCCAsCur[e.v1].contains(e.v2);
boolean prevTo2and1ToCur = removedSiteSameCCAsPrev[e.getV1()].contains(e.getV2()) && removedSiteSameCCAsCur[e.getV2()].contains(e.getV1());
boolean prevTo1and2ToCur = removedSiteSameCCAsPrev[e.getV2()].contains(e.getV1()) && removedSiteSameCCAsCur[e.getV1()].contains(e.getV2());
if (prevTo2and1ToCur || prevTo1and2ToCur) {
for (String readName : edgeToReads.getReads(e)) {
@ -611,9 +611,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
if (logger.isDebugEnabled()) {
if (prevTo2and1ToCur)
logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.v2 + " -> " + e.v1 + " ---> " + cur);
logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.getV2() + " -> " + e.getV1() + " ---> " + cur);
else
logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.v1 + " -> " + e.v2 + " ---> " + cur);
logger.debug("Keep read " + readName + " due to path: " + prev + " ---> " + e.getV1() + " -> " + e.getV2() + " ---> " + cur);
}
}
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/SNPallelePair.java → java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
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@ -21,7 +21,7 @@
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.playground.gatk.walkers.phasing;
package org.broadinstitute.sting.gatk.walkers.phasing;
import org.broad.tribble.util.variantcontext.Allele;
import org.broad.tribble.util.variantcontext.Genotype;

2
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
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@ -4,7 +4,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.playground.gatk.walkers.phasing.*;
import org.broadinstitute.sting.gatk.walkers.phasing.*;
import org.broadinstitute.sting.utils.report.tags.Analysis;
import org.broadinstitute.sting.utils.report.tags.DataPoint;
import org.broadinstitute.sting.utils.report.utils.TableType;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DisjointSet.java → java/src/org/broadinstitute/sting/utils/DisjointSet.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.phasing;
package org.broadinstitute.sting.utils;
import java.util.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DoublyLinkedList.java → java/src/org/broadinstitute/sting/utils/DoublyLinkedList.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.phasing;
package org.broadinstitute.sting.utils;
import java.util.NoSuchElementException;

5
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Graph.java → java/src/org/broadinstitute/sting/utils/Graph.java
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@ -1,4 +1,7 @@
package org.broadinstitute.sting.playground.gatk.walkers.phasing;
package org.broadinstitute.sting.utils;
import org.broadinstitute.sting.utils.DisjointSet;
import org.broadinstitute.sting.utils.GraphEdge;
import java.util.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/GraphEdge.java → java/src/org/broadinstitute/sting/utils/GraphEdge.java
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@ -1,4 +1,4 @@
package org.broadinstitute.sting.playground.gatk.walkers.phasing;
package org.broadinstitute.sting.utils;
/*
* Copyright (c) 2010, The Broad Institute