From 7c909bef82cc1461046ae160340228040fd7c0c5 Mon Sep 17 00:00:00 2001 From: fromer Date: Tue, 28 Sep 2010 23:21:28 +0000 Subject: [PATCH] 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 --- .../gatk/walkers/phasing/AllelePair.java | 2 +- .../walkers/phasing/ReadBackedPhasingWalker.java | 14 +++++++------- .../gatk/walkers/phasing/SNPallelePair.java | 2 +- .../varianteval/GenotypePhasingEvaluator.java | 2 +- .../walkers/phasing => utils}/DisjointSet.java | 2 +- .../phasing => utils}/DoublyLinkedList.java | 2 +- .../gatk/walkers/phasing => utils}/Graph.java | 5 ++++- .../gatk/walkers/phasing => utils}/GraphEdge.java | 2 +- 8 files changed, 17 insertions(+), 14 deletions(-) rename java/src/org/broadinstitute/sting/{playground => }/gatk/walkers/phasing/AllelePair.java (97%) rename java/src/org/broadinstitute/sting/{playground => }/gatk/walkers/phasing/ReadBackedPhasingWalker.java (99%) rename java/src/org/broadinstitute/sting/{playground => }/gatk/walkers/phasing/SNPallelePair.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/phasing => utils}/DisjointSet.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/phasing => utils}/DoublyLinkedList.java (98%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/phasing => utils}/Graph.java (97%) rename java/src/org/broadinstitute/sting/{playground/gatk/walkers/phasing => utils}/GraphEdge.java (96%) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/AllelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/AllelePair.java rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java index 4effa9767..f7e763d8c 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/AllelePair.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java similarity index 99% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBackedPhasingWalker.java rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java index 749ee83b8..33f1ebc18 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/ReadBackedPhasingWalker.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java @@ -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 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 " + 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); } } } diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/SNPallelePair.java b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/SNPallelePair.java rename to java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java index 9b2ba6e5a..55a877c57 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/SNPallelePair.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java index 227a4b2b5..1a6e66c15 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java @@ -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; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DisjointSet.java b/java/src/org/broadinstitute/sting/utils/DisjointSet.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DisjointSet.java rename to java/src/org/broadinstitute/sting/utils/DisjointSet.java index a46d423d3..9a8b96aac 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DisjointSet.java +++ b/java/src/org/broadinstitute/sting/utils/DisjointSet.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.phasing; +package org.broadinstitute.sting.utils; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DoublyLinkedList.java b/java/src/org/broadinstitute/sting/utils/DoublyLinkedList.java similarity index 98% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DoublyLinkedList.java rename to java/src/org/broadinstitute/sting/utils/DoublyLinkedList.java index 154fd6f3b..b4b2d1bd9 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/DoublyLinkedList.java +++ b/java/src/org/broadinstitute/sting/utils/DoublyLinkedList.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.phasing; +package org.broadinstitute.sting.utils; import java.util.NoSuchElementException; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Graph.java b/java/src/org/broadinstitute/sting/utils/Graph.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Graph.java rename to java/src/org/broadinstitute/sting/utils/Graph.java index dc1389be0..2d497b40f 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Graph.java +++ b/java/src/org/broadinstitute/sting/utils/Graph.java @@ -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.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/GraphEdge.java b/java/src/org/broadinstitute/sting/utils/GraphEdge.java similarity index 96% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/GraphEdge.java rename to java/src/org/broadinstitute/sting/utils/GraphEdge.java index 0170d476d..94fe17776 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/GraphEdge.java +++ b/java/src/org/broadinstitute/sting/utils/GraphEdge.java @@ -1,4 +1,4 @@ -package org.broadinstitute.sting.playground.gatk.walkers.phasing; +package org.broadinstitute.sting.utils; /* * Copyright (c) 2010, The Broad Institute