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more cleanup, depecaited the old genotype, corrected SNPCallsFromGenotypes' imports and two other classes that depend on it. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1771 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-10-06 19:09:27 +00:00
parent 3aec76136f
commit 4554ca1b28
4 changed files with 7 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/refdata/Genotype.java
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@ -1,6 +1,5 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import java.util.List; import java.util.List;
@ -12,6 +11,7 @@ import java.util.List;
* Time: 11:02:03 AM * Time: 11:02:03 AM
* To change this template use File | Settings | File Templates. * To change this template use File | Settings | File Templates.
*/ */
@Deprecated
public interface Genotype extends Comparable<ReferenceOrderedDatum> { public interface Genotype extends Comparable<ReferenceOrderedDatum> {
// ---------------------------------------------------------------------- // ----------------------------------------------------------------------
// //

3
java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java
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@ -1,8 +1,9 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.genotype.Genotype;
import java.util.ArrayList; import java.util.ArrayList;
import java.util.List; import java.util.List;
/** /**
* loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom * loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom
* chr1:1104840 A N 0.000000 -85.341265 -85.341265 0.000000 0.000000 324.000000 162 0 0 * chr1:1104840 A N 0.000000 -85.341265 -85.341265 0.000000 0.000000 324.000000 162 0 0

2
java/src/org/broadinstitute/sting/gatk/refdata/SNPCallFromGenotypes.java
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@ -2,6 +2,8 @@ package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.genotype.Variation; import org.broadinstitute.sting.utils.genotype.Variation;
import org.broadinstitute.sting.utils.genotype.Genotype;
import java.util.List; import java.util.List;
/** /**

4
java/src/org/broadinstitute/sting/gatk/refdata/SangerSNPROD.java
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@ -1,8 +1,8 @@
package org.broadinstitute.sting.gatk.refdata; package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.genotype.Genotype;
import java.util.Arrays; import java.util.Arrays;
import java.util.List; import java.util.List;