Merged bug fix from Stable into Unstable

public/java/test/org/broadinstitute/sting/gatk/walkers/qc/TestVariantContextWalker.java

@@ -0,0 +1,132 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.qc;
+
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.ArgumentCollection;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
+import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.VariantContextAdaptors;
+import org.broadinstitute.sting.gatk.walkers.Reference;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.Window;
+import org.broadinstitute.sting.utils.codecs.vcf.VCFWriter;
+import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+
+import java.io.PrintStream;
+import java.util.Arrays;
+import java.util.EnumSet;
+import java.util.List;
+
+/**
+ * Test routine for new VariantContext object
+ */
+@Reference(window=@Window(start=-20,stop=1))
+public class TestVariantContextWalker extends RodWalker<Integer, Integer> {
+    @Output
+    PrintStream out;
+
+    @ArgumentCollection
+    protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
+
+    @Argument(fullName="takeFirstOnly", doc="Only take the first second at a locus, as opposed to all", required=false)
+    boolean takeFirstOnly = false;
+
+    @Argument(fullName="onlyContextsOfType", doc="Only take variant contexts of this type", required=false)
+    VariantContext.Type onlyOfThisType = null;
+
+    @Argument(fullName="onlyContextsStartinAtCurrentPosition", doc="Only take variant contexts at actually start at the current position, excluding those at span to the current location but start earlier", required=false)
+    boolean onlyContextsStartinAtCurrentPosition = false;
+
+    @Argument(fullName="printPerLocus", doc="If true, we'll print the variant contexts, in addition to counts", required=false)
+    boolean printContexts = false;
+
+    @Argument(fullName="outputVCF", doc="If provided, we'll convert the first input context into a VCF", required=false)
+    VCFWriter writer = null;
+
+    private boolean wroteHeader = false;
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( ref == null )
+            return 0;
+        else {
+            EnumSet<VariantContext.Type> allowedTypes = onlyOfThisType == null ? null : EnumSet.of(onlyOfThisType);
+
+            int n = 0;
+            List<VariantContext> contexts;
+            if ( onlyContextsStartinAtCurrentPosition )
+                contexts = tracker.getValues(variantCollection.variants, context.getLocation());
+            else // ! onlyContextsStartinAtCurrentPosition
+                contexts = tracker.getValues(variantCollection.variants);
+
+            for ( VariantContext vc : contexts ) {
+                if ( allowedTypes == null || allowedTypes.contains(vc.getType()) ) {
+                    // we need to trigger decoding of the genotype string to pass integration tests
+                    vc.getGenotypes();
+
+                    if ( writer != null && n == 0 ) {
+                        if ( ! wroteHeader ) {
+                            writer.writeHeader(VariantContextAdaptors.createVCFHeader(null, vc));
+                            wroteHeader = true;
+                        }
+
+                        writer.add(vc);
+                    }
+
+                    n++;
+                    if ( printContexts ) out.printf("       %s%n", vc);
+                    if ( takeFirstOnly ) break;
+                }
+            }
+
+            if ( n > 0 && printContexts ) {
+                out.printf("%s => had %d variant context objects%n", context.getLocation(), n);
+                out.printf("---------------------------------------------%n");
+            }
+            
+            return n;
+        }
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer point, Integer sum) {
+        return point + sum;
+    }
+
+    @Override
+    public void onTraversalDone(Integer result) {
+        // Double check traversal result to make count is the same.
+        // TODO: Is this check necessary?
+        out.println("[REDUCE RESULT] Traversal result is: " + result);
+    }
+}