From c0ce9ca8cc0b4916f3ebe9db15cb676af46f988c Mon Sep 17 00:00:00 2001 From: fromer Date: Fri, 3 Sep 2010 13:32:30 +0000 Subject: [PATCH] Added phasing sub-directory to keep walkers directory clean git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4207 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/varianteval/GenotypePhasingEvaluator.java | 6 ------ .../playground/gatk/walkers/{ => phasing}/Biallele.java | 2 +- .../playground/gatk/walkers/{ => phasing}/BialleleSNP.java | 2 +- 3 files changed, 2 insertions(+), 8 deletions(-) rename java/src/org/broadinstitute/sting/playground/gatk/walkers/{ => phasing}/Biallele.java (97%) rename java/src/org/broadinstitute/sting/playground/gatk/walkers/{ => phasing}/BialleleSNP.java (97%) 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 14300a3a9..a396dc0f5 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java @@ -1,21 +1,15 @@ package org.broadinstitute.sting.gatk.walkers.varianteval; -import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype; import org.broad.tribble.util.variantcontext.VariantContext; -import org.broadinstitute.sting.commandline.Argument; import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.playground.gatk.walkers.Biallele; -import org.broadinstitute.sting.playground.gatk.walkers.BialleleSNP; -import org.broadinstitute.sting.playground.gatk.walkers.ReadBackedPhasingWalker; import org.broadinstitute.sting.playground.utils.report.tags.Analysis; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.utils.TableType; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.StingException; import org.apache.log4j.Logger; -import org.broadinstitute.sting.utils.collections.Pair; import java.util.*; diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Biallele.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/Biallele.java rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java index 2d5b6a504..19cacaebb 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/Biallele.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.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; +package org.broadinstitute.sting.playground.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/BialleleSNP.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java similarity index 97% rename from java/src/org/broadinstitute/sting/playground/gatk/walkers/BialleleSNP.java rename to java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java index 9460c6d23..94e859525 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/BialleleSNP.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.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; +package org.broadinstitute.sting.playground.gatk.walkers.phasing; import org.broad.tribble.util.variantcontext.Allele; import org.broad.tribble.util.variantcontext.Genotype;