Port SelectVariants tool and dependent infrastructure.

src/main/java/org/broadinstitute/hellbender/cmdline/StandardArgumentDefinitions.java

@@ -11,12 +11,16 @@ public final class StandardArgumentDefinitions {
     public static final String REFERENCE_LONG_NAME = "reference";
     public static final String VARIANT_LONG_NAME = "variant";
     public static final String FEATURE_LONG_NAME = "feature";
+    public static final String LENIENT_LONG_NAME = "lenient";
+    public static final String INTERVAL_LONG_NAME = "interval";
 
     public static final String INPUT_SHORT_NAME = "I";
     public static final String OUTPUT_SHORT_NAME = "O";
     public static final String REFERENCE_SHORT_NAME = "R";
     public static final String VARIANT_SHORT_NAME = "V";
     public static final String FEATURE_SHORT_NAME = "F";
+    public static final String LENIENT_SHORT_NAME = "LE";
+    public static final String INTERVAL_SHORT_NAME = "IN";
     public static final String SAMPLE_ALIAS_SHORT_NAME = "ALIAS";
     public static final String LIBRARY_NAME_SHORT_NAME = "LIB";
     public static final String EXPECTED_INSERT_SIZE_SHORT_NAME = "INSERT";

src/main/java/org/broadinstitute/hellbender/engine/filters/ExcludeIDsVariantFilter.java

@@ -0,0 +1,27 @@
+package org.broadinstitute.hellbender.engine.filters;
+
+import htsjdk.variant.variantcontext.VariantContext;
+import org.broadinstitute.hellbender.utils.Utils;
+
+import java.util.Set;
+import java.util.HashSet;
+
+/**
+ * Exclude variants with any of these IDs.
+ * Matching is done by case-sensitive exact match.
+ */
+public final class ExcludeIDsVariantFilter implements VariantFilter {
+    private static final long serialVersionUID = 1L;
+
+    private final HashSet<String> excludeIDs = new HashSet<>();
+
+    public ExcludeIDsVariantFilter(Set<String> discardIDs) {
+        Utils.nonNull(discardIDs);
+        excludeIDs.addAll(discardIDs);
+    }
+
+    @Override
+    public boolean test(final VariantContext vc) {
+        return !excludeIDs.contains(vc.getID());
+    }
+}

src/main/java/org/broadinstitute/hellbender/engine/filters/IncludeIDsVariantFilter.java

@@ -0,0 +1,27 @@
+package org.broadinstitute.hellbender.engine.filters;
+
+import htsjdk.variant.variantcontext.VariantContext;
+import org.broadinstitute.hellbender.utils.Utils;
+
+import java.util.Set;
+import java.util.HashSet;
+
+/**
+ * Keep only variants with any of these IDs.
+ * Matching is done by case-sensitive exact match.
+ */
+public final class IncludeIDsVariantFilter implements VariantFilter {
+    private final static long serialVersionUID = 1L;
+
+    private final HashSet<String> includeIDs = new HashSet<>();
+
+    public IncludeIDsVariantFilter(Set<String> keepIDs) {
+        Utils.nonNull(keepIDs);
+        includeIDs.addAll(keepIDs);
+    }
+
+    @Override
+    public boolean test(final VariantContext vc) {
+        return includeIDs.contains(vc.getID());
+    }
+}

src/main/java/org/broadinstitute/hellbender/engine/filters/IntervalVariantFilter.java

@@ -0,0 +1,30 @@
+package org.broadinstitute.hellbender.engine.filters;
+
+import htsjdk.samtools.util.Locatable;
+import htsjdk.variant.variantcontext.VariantContext;
+import org.broadinstitute.hellbender.utils.GenomeLoc;
+import org.broadinstitute.hellbender.utils.IntervalUtils;
+import org.broadinstitute.hellbender.utils.Utils;
+import org.broadinstitute.hellbender.utils.variant.GATKVariantContextUtils;
+
+import java.util.List;
+
+/**
+ * Keep only variants that overlap any of the supplied genomic intervals.
+ */
+public final class IntervalVariantFilter implements VariantFilter {
+    private static final long serialVersionUID = 1L;
+
+    private final List<GenomeLoc> genomeLocs;
+
+    public IntervalVariantFilter(List<GenomeLoc> intervals) {
+        Utils.nonNull(intervals);
+        genomeLocs = intervals;
+    }
+
+    @Override
+    public boolean test( final VariantContext vc ) {
+        final Locatable targetLoc = GATKVariantContextUtils.getLocation(vc);
+        return genomeLocs.stream().anyMatch(loc -> IntervalUtils.overlaps(loc, targetLoc));
+    }
+}

src/main/java/org/broadinstitute/hellbender/engine/filters/VariantTypesVariantFilter.java

@@ -0,0 +1,26 @@
+package org.broadinstitute.hellbender.engine.filters;
+
+import htsjdk.variant.variantcontext.VariantContext;
+import org.broadinstitute.hellbender.utils.Utils;
+
+import java.util.Set;
+
+/**
+ * Keep only variants with any of these variant types.
+ */
+public final class VariantTypesVariantFilter implements VariantFilter {
+    private static final long serialVersionUID = 1L;
+
+    private final Set<VariantContext.Type> sampleTypes;
+
+    public VariantTypesVariantFilter(Set<VariantContext.Type> includeTypes) {
+        Utils.nonNull(includeTypes);
+        sampleTypes = includeTypes;
+    }
+
+    @Override
+    public boolean test(final VariantContext vc) {
+        final VariantContext.Type vcSampleType = vc.getType();
+        return sampleTypes.contains(vcSampleType);
+    }
+}

src/main/java/org/broadinstitute/hellbender/engine/samples/Affection.java

@@ -0,0 +1,22 @@
+package org.broadinstitute.hellbender.engine.samples;
+
+/**
+ * Categorical sample trait for association and analysis
+ *
+ * Samples can have unknown status, be affected or unaffected by the
+ * categorical trait, or they can be marked as actually having an
+ * other trait value (stored in an associated value in the Sample class)
+ *
+ * @author Mark DePristo
+ * @since Sept. 2011
+ */
+public enum Affection {
+    /** Status is unknown */
+    UNKNOWN,
+    /** Suffers from the disease */
+    AFFECTED,
+    /** Unaffected by the disease */
+    UNAFFECTED,
+    /** An "other" trait: value of the trait is stored elsewhere and is an arbitrary string */
+    OTHER
+}

src/main/java/org/broadinstitute/hellbender/engine/samples/Gender.java

@@ -0,0 +1,10 @@
+package org.broadinstitute.hellbender.engine.samples;
+
+/**
+ * ENUM of possible human genders: male, female, or unknown
+ */
+public enum Gender {
+    MALE,
+    FEMALE,
+    UNKNOWN
+}