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Restored SVN history for phasing 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4373 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-09-29 00:02:02 +00:00
parent 720aaca8a0
commit e322e71c2f
3 changed files with 9 additions and 9 deletions
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2
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 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE. * 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.Allele;
import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.Genotype;

14
java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasingWalker.java
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@ -22,7 +22,7 @@
* OTHER DEALINGS IN THE SOFTWARE. * 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.Allele;
import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.Genotype;
@ -534,8 +534,8 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
edgeToReads.addRead(e, rdName); edgeToReads.addRead(e, rdName);
sitesWithEdges.add(e.v1); sitesWithEdges.add(e.getV1());
sitesWithEdges.add(e.v2); 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, 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. 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 prevTo2and1ToCur = removedSiteSameCCAsPrev[e.getV1()].contains(e.getV2()) && removedSiteSameCCAsCur[e.getV2()].contains(e.getV1());
boolean prevTo1and2ToCur = removedSiteSameCCAsPrev[e.v2].contains(e.v1) && removedSiteSameCCAsCur[e.v1].contains(e.v2); boolean prevTo1and2ToCur = removedSiteSameCCAsPrev[e.getV2()].contains(e.getV1()) && removedSiteSameCCAsCur[e.getV1()].contains(e.getV2());
if (prevTo2and1ToCur || prevTo1and2ToCur) { if (prevTo2and1ToCur || prevTo1and2ToCur) {
for (String readName : edgeToReads.getReads(e)) { for (String readName : edgeToReads.getReads(e)) {
@ -611,9 +611,9 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
if (logger.isDebugEnabled()) { if (logger.isDebugEnabled()) {
if (prevTo2and1ToCur) 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 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/gatk/walkers/phasing/SNPallelePair.java
View File

@ -21,7 +21,7 @@
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE. * 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.Allele;
import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.Genotype;