Not supported. I'm checking this in for Ryan only.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4756 348d0f76-0448-11de-a6fe-93d51630548a
2010-11-30 16:59:18 +00:00 · 2010-11-30 16:59:18 +00:00 · 21256909bb
parent e21a66d876
commit 21256909bb
1 changed files with 114 additions and 0 deletions
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/AssessMissingBroadCalls.java
@ -0,0 +1,114 @@
+/*
+ * Copyright (c) 2010.
+ *
+ * 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.oneoffprojects.walkers;
+
+import org.broad.tribble.util.variantcontext.VariantContext;
+import org.broad.tribble.vcf.*;
+import org.broadinstitute.sting.commandline.Output;
+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.walkers.Reference;
+import org.broadinstitute.sting.gatk.walkers.Requires;
+import org.broadinstitute.sting.gatk.walkers.RodWalker;
+import org.broadinstitute.sting.gatk.walkers.Window;
+import org.broadinstitute.sting.utils.vcf.VCFUtils;
+
+import java.util.*;
+
+/**
+ * Assesses calls missing from the BI set that are made by all other centers.
+ * Use -B:broad,vcf and -B:1kg,vcf
+ */
+@Reference(window=@Window(start=-50,stop=50))
+@Requires(value={})
+public class AssessMissingBroadCalls extends RodWalker<Integer, Integer> {
+
+    private static final String status_key = "BI_STATUS";
+    private static final String qual_key = "BI_QUAL";
+
+    @Output(doc="File to which variants should be written",required=true)
+    protected VCFWriter writer = null;
+
+    public void initialize() {
+        final ArrayList<String> inputNames = new ArrayList<String>();
+        inputNames.add("1kg");
+
+        // setup the header fields
+        Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
+        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+        writer.writeHeader(new VCFHeader(hInfo, new HashSet<String>()));
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        if ( tracker == null ) // RodWalkers can make funky map calls
+            return 0;
+
+        List<Object> kgRods = tracker.getReferenceMetaData("1kg");
+        // ignore places where we don't have a variant
+        if ( kgRods.size() == 0 )
+            return 0;
+
+        VariantContext vc = (VariantContext)kgRods.get(0);
+        Map<String, Object> attrs = new HashMap<String, Object>(vc.getAttributes());
+
+        List<Object> biRods = tracker.getReferenceMetaData("broad");
+        if ( biRods.size() == 0 )
+            attrs.put(status_key, "NotCalled");
+        else {
+            VariantContext BIvc = (VariantContext)biRods.get(0);
+            // skip the site if we called it
+            if ( !BIvc.isFiltered() )
+                return 0;
+
+            attrs.put(qual_key, BIvc.getPhredScaledQual());
+            
+            Set<String> filters = BIvc.getFilters();
+            StringBuilder sb = new StringBuilder();
+            for ( String filter : filters ) {
+                if ( sb.length() != 0 )
+                    sb.append("-");
+                sb.append(filter);
+            }
+            attrs.put(status_key, sb.toString());
+        }
+
+        vc = VariantContext.modifyAttributes(vc, attrs);
+        writer.add(vc, ref.getBase());
+
+        return 1;
+    }
+
+    public Integer reduceInit() {
+        return 0;
+    }
+
+    public Integer reduce(Integer counter, Integer sum) {
+        return counter + sum;
+    }
+
+    public void onTraversalDone(Integer sum) {}
+}