{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/37439006","id":37439006,"diff_hunk":"@@ -0,0 +1,439 @@\n+package org.broadinstitute.hellbender.engine.samples;\n+\n+import htsjdk.variant.variantcontext.Genotype;\n+import htsjdk.variant.variantcontext.GenotypeType;\n+import htsjdk.variant.variantcontext.VariantContext;\n+\n+import java.util.*;\n+\n+import org.broadinstitute.hellbender.engine.samples.Sample;\n+import org.broadinstitute.hellbender.utils.MathUtils;\n+\n+import java.util.*;\n+\n+/**\n+ * User: carneiro / lfran\n+ * Date: 3/9/11\n+ * Time: 12:38 PM\n+ *\n+ * Class for the identification and tracking of mendelian violation. It can be used in 2 distinct ways:\n+ * - Either using an instance of the MendelianViolation class to track mendelian violations for each of the families while\n+ * walking over the variants\n+ * - Or using the static methods to directly get information about mendelian violation in a family at a given locus\n+ *\n+ */\n+public class MendelianViolation {\n+    //List of families with violations\n+    private List<String> violationFamilies;\n+\n+    //Call information\n+    private int nocall = 0;\n+    private int familyCalled = 0;\n+    private int varFamilyCalled = 0;\n+    private int lowQual = 0;\n+\n+    private boolean allCalledOnly = true;\n+\n+    //Stores occurrences of inheritance\n+    private EnumMap<GenotypeType, EnumMap<GenotypeType,EnumMap<GenotypeType,Integer>>> inheritance;\n+\n+    private int violations_total=0;\n+\n+    private double minGenotypeQuality;\n+\n+    private boolean abortOnSampleNotFound;\n+\n+    //Number of families with genotype information for all members\n+    public int getFamilyCalledCount(){\n+        return familyCalled;\n+    }\n+\n+    //Number of families with genotype information for all members\n+    public int getVarFamilyCalledCount(){\n+        return varFamilyCalled;\n+    }\n+\n+    //Number of families missing genotypes for one or more of their members\n+    public int getFamilyNoCallCount(){\n+        return nocall;\n+    }\n+\n+    //Number of families with genotypes below the set quality threshold\n+    public int getFamilyLowQualsCount(){\n+        return lowQual;\n+    }\n+\n+    public int getViolationsCount(){\n+        return violations_total;\n+    }\n+\n+    //Count of alt alleles inherited from het parents (no violation)\n+    public int getParentHetInheritedVar() {\n+        return getParentsHetHetInheritedVar() + getParentsRefHetInheritedVar() + getParentsVarHetInheritedVar();\n+    }\n+\n+    //Count of ref alleles inherited from het parents (no violation)\n+    public int getParentHetInheritedRef() {\n+        return getParentsHetHetInheritedRef() + getParentsRefHetInheritedRef() + getParentsVarHetInheritedRef();\n+    }\n+\n+    //Count of HomRef/HomRef/HomRef trios\n+    public int getRefRefRef() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HOM_REF).get(GenotypeType.HOM_REF);\n+    }\n+\n+    //Count of HomVar/HomVar/HomVar trios\n+    public int getVarVarVar() {\n+        return inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_VAR);\n+    }\n+\n+    //Count of HomRef/HomVar/Het trios\n+    public int getRefVarHet() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HOM_VAR).get(GenotypeType.HET) +\n+                inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_REF).get(GenotypeType.HET);\n+    }\n+\n+    //Count of Het/Het/Het trios\n+    public int getHetHetHet(){\n+        return inheritance.get(GenotypeType.HET).get(GenotypeType.HET).get(GenotypeType.HET);\n+    }\n+\n+    //Count of Het/Het/HomRef trios\n+    public int getHetHetHomRef() {\n+        return inheritance.get(GenotypeType.HET).get(GenotypeType.HET).get(GenotypeType.HOM_REF);\n+    }\n+\n+    //Count of Het/Het/HomVar trios\n+    public int getHetHetHomVar() {\n+        return inheritance.get(GenotypeType.HET).get(GenotypeType.HET).get(GenotypeType.HOM_VAR);\n+    }\n+\n+    //Count of ref alleles inherited from Het/Het parents (no violation)\n+    public int getParentsHetHetInheritedRef() {\n+        return inheritance.get(GenotypeType.HET).get(GenotypeType.HET).get(GenotypeType.HET)\n+                + 2*inheritance.get(GenotypeType.HET).get(GenotypeType.HET).get(GenotypeType.HOM_REF);\n+        //return parentsHetHet_childRef;\n+    }\n+\n+    //Count of var alleles inherited from Het/Het parents (no violation)\n+    public int getParentsHetHetInheritedVar() {\n+        return inheritance.get(GenotypeType.HET).get(GenotypeType.HET).get(GenotypeType.HET)\n+                + 2 * inheritance.get(GenotypeType.HET).get(GenotypeType.HET).get(GenotypeType.HOM_VAR);\n+        //return parentsHetHet_childVar;\n+    }\n+\n+    //Count of ref alleles inherited from HomRef/Het parents (no violation)\n+    public int getParentsRefHetInheritedRef() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HET).get(GenotypeType.HOM_REF)\n+                + inheritance.get(GenotypeType.HET).get(GenotypeType.HOM_REF).get(GenotypeType.HOM_REF);\n+        //return parentsHomRefHet_childRef;\n+    }\n+\n+    //Count of var alleles inherited from HomRef/Het parents (no violation)\n+    public int getParentsRefHetInheritedVar() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HET).get(GenotypeType.HET)\n+                + inheritance.get(GenotypeType.HET).get(GenotypeType.HOM_REF).get(GenotypeType.HET);\n+        //return parentsHomRefHet_childVar;\n+    }\n+\n+    //Count of ref alleles inherited from HomVar/Het parents (no violation)\n+    public int getParentsVarHetInheritedRef() {\n+        return inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HET).get(GenotypeType.HET)\n+                + inheritance.get(GenotypeType.HET).get(GenotypeType.HOM_VAR).get(GenotypeType.HET);\n+        //return parentsHomVarHet_childRef;\n+    }\n+\n+    //Count of var alleles inherited from HomVar/Het parents (no violation)\n+    public int getParentsVarHetInheritedVar() {\n+        return inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HET).get(GenotypeType.HOM_VAR)\n+                + inheritance.get(GenotypeType.HET).get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_VAR);\n+        //return parentsHomVarHet_childVar;\n+    }\n+\n+    //Count of violations of the type HOM_REF/HOM_REF -> HOM_VAR\n+    public int getParentsRefRefChildVar() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HOM_REF).get(GenotypeType.HOM_VAR);\n+    }\n+\n+    //Count of violations of the type HOM_REF/HOM_REF -> HET\n+    public int getParentsRefRefChildHet() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HOM_REF).get(GenotypeType.HET);\n+    }\n+\n+    //Count of violations of the type HOM_REF/HET -> HOM_VAR\n+    public int getParentsRefHetChildVar() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HET).get(GenotypeType.HOM_VAR)\n+                + inheritance.get(GenotypeType.HET).get(GenotypeType.HOM_REF).get(GenotypeType.HOM_VAR);\n+    }\n+\n+    //Count of violations of the type HOM_REF/HOM_VAR -> HOM_VAR\n+    public int getParentsRefVarChildVar() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_VAR)\n+                + inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_REF).get(GenotypeType.HOM_VAR);\n+    }\n+\n+    //Count of violations of the type HOM_REF/HOM_VAR -> HOM_REF\n+    public int getParentsRefVarChildRef() {\n+        return inheritance.get(GenotypeType.HOM_REF).get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_REF)\n+                + inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_REF).get(GenotypeType.HOM_REF);\n+    }\n+\n+    //Count of violations of the type HOM_VAR/HET -> HOM_REF\n+    public int getParentsVarHetChildRef() {\n+        return inheritance.get(GenotypeType.HET).get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_REF)\n+                + inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HET).get(GenotypeType.HOM_REF);\n+    }\n+\n+    //Count of violations of the type HOM_VAR/HOM_VAR -> HOM_REF\n+    public int getParentsVarVarChildRef() {\n+        return inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_REF);\n+    }\n+\n+    //Count of violations of the type HOM_VAR/HOM_VAR -> HET\n+    public int getParentsVarVarChildHet() {\n+        return inheritance.get(GenotypeType.HOM_VAR).get(GenotypeType.HOM_VAR).get(GenotypeType.HET);\n+    }\n+\n+\n+    //Count of violations of the type HOM_VAR/? -> HOM_REF\n+    public int getParentVarChildRef() {\n+        return getParentsRefVarChildRef() + getParentsVarHetChildRef() +getParentsVarVarChildRef();\n+    }\n+\n+    //Count of violations of the type HOM_REF/? -> HOM_VAR\n+    public int getParentRefChildVar() {\n+        return getParentsRefVarChildVar() + getParentsRefHetChildVar() +getParentsRefRefChildVar();\n+    }\n+\n+    //Returns a String containing all trios where a Mendelian violation was observed.\n+    //The String is formatted \"mom1+dad1=child1,mom2+dad2=child2,...\"\n+    public String getViolationFamiliesString() {\n+        if (violationFamilies.isEmpty())\n+            return \"\";\n+\n+        final Iterator<String> it = violationFamilies.iterator();\n+        String violationFams = it.next();\n+        while (it.hasNext()) {\n+            violationFams += \",\"+it.next();\n+        }\n+        return violationFams;\n+    }\n+\n+    public List<String> getViolationFamilies(){\n+        return violationFamilies;\n+    }\n+\n+    static final int[] mvOffsets = new int[] { 1,2,5,6,8,11,15,18,20,21,24,25 };","path":"src/main/java/org/broadinstitute/hellbender/engine/samples/MendelianViolation.java","position":226,"original_position":226,"commit_id":"17e3147536227e7961917fa477438fae8601dbbe","original_commit_id":"17e3147536227e7961917fa477438fae8601dbbe","user":{"login":"lbergelson","id":4700332,"avatar_url":"https://avatars.githubusercontent.com/u/4700332?v=3","gravatar_id":"","url":"https://api.github.com/users/lbergelson","html_url":"https://github.com/lbergelson","followers_url":"https://api.github.com/users/lbergelson/followers","following_url":"https://api.github.com/users/lbergelson/following{/other_user}","gists_url":"https://api.github.com/users/lbergelson/gists{/gist_id}","starred_url":"https://api.github.com/users/lbergelson/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lbergelson/subscriptions","organizations_url":"https://api.github.com/users/lbergelson/orgs","repos_url":"https://api.github.com/users/lbergelson/repos","events_url":"https://api.github.com/users/lbergelson/events{/privacy}","received_events_url":"https://api.github.com/users/lbergelson/received_events","type":"User","site_admin":false},"body":"If you have any idea what theses numbers are a comment would be great.  I'm guessing you're equally mystified though.","created_at":"2015-08-19T16:59:40Z","updated_at":"2015-08-19T16:59:40Z","html_url":"https://github.com/broadinstitute/hellbender/pull/792#discussion_r37439006","pull_request_url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/792","_links":{"self":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/comments/37439006"},"html":{"href":"https://github.com/broadinstitute/hellbender/pull/792#discussion_r37439006"},"pull_request":{"href":"https://api.github.com/repos/broadinstitute/hellbender/pulls/792"}}},"pull_request":{"url":"https://api.github.com/repos/broadinstitute/hellbender/pulls/792","id":41921234,"html_url":"https://github.com/broadinstitute/hellbender/pull/792","diff_url":"https://github.com/broadinstitute/hellbender/pull/792.diff","patch_url":"https://github.com/broadinstitute/hellbender/pull/792.patch","issue_url":"https://api.github.com/repos/broadinstitute/hellbender/issues/792","number":792,"state":"open","locked":false,"title":"Port 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