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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
This commit is contained in:
fromer 2010-09-03 13:32:30 +00:00
parent 60003aeaca
commit c0ce9ca8cc
3 changed files with 2 additions and 8 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypePhasingEvaluator.java
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@ -1,21 +1,15 @@
package org.broadinstitute.sting.gatk.walkers.varianteval; 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.Genotype;
import org.broad.tribble.util.variantcontext.VariantContext; import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.contexts.*; import org.broadinstitute.sting.gatk.contexts.*;
import org.broadinstitute.sting.gatk.refdata.*; import org.broadinstitute.sting.gatk.refdata.*;
import org.broadinstitute.sting.playground.gatk.walkers.Biallele; 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.Analysis;
import org.broadinstitute.sting.playground.utils.report.tags.DataPoint; import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
import org.broadinstitute.sting.playground.utils.report.utils.TableType; import org.broadinstitute.sting.playground.utils.report.utils.TableType;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
import org.apache.log4j.Logger; import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.collections.Pair;
import java.util.*; import java.util.*;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/Biallele.java → java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.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; package org.broadinstitute.sting.playground.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;

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/BialleleSNP.java → java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.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; package org.broadinstitute.sting.playground.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;