From cae54ec52d92ccfe0a1e2e8718985728d4b90971 Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Apr 2009 17:58:19 +0000
Subject: [PATCH] Walker for creating intervals to be used in the indel cleaner

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@508 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/IndelIntervalWalker.java     | 88 +++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java

diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java
new file mode 100644
index 000000000..700708de5
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/IndelIntervalWalker.java
@@ -0,0 +1,88 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.AlignmentBlock;
+
+import java.util.List;
+
+// A walker to determine intervals within which reads should be cleaned and realigned
+// because they contain one or more indels (which possibly caused them not to align perfectly).
+// Note that the reduce step assumes that reductions occur in order (i.e. no hierarchical reductions),
+// although this can easily be changed if necessary.
+
+@WalkerName("IndelIntervals")
+public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval, IndelIntervalWalker.Interval> {
+    @Argument(fullName="maxReadLength", shortName="maxRead", required=false, defaultValue="-1")
+    public int maxReadLength;
+    @Argument(fullName="minIndelsPerInterval", shortName="minIndels", required=false, defaultValue="1")
+    public int minIntervalIndelCount;
+
+    public void initialize() {}
+
+    public boolean filter(LocusContext context, SAMRecord read) {
+        return ( !read.getReadUnmappedFlag() &&            // mapped
+                 read.getReadLength() <= maxReadLength &&  // not too big
+                 read.getAlignmentBlocks().size() > 1);    // indel
+    }
+
+    public Interval map(LocusContext context, SAMRecord read) {
+        List<AlignmentBlock> blocks = read.getAlignmentBlocks();
+        long indelLeftEdge = read.getAlignmentStart() + blocks.get(0).getLength() - 1;
+        long indelRightEdge = read.getAlignmentEnd() - blocks.get(blocks.size()-1).getLength() + 1;
+        GenomeLoc indelLoc = new GenomeLoc(context.getLocation().getContigIndex(), indelLeftEdge, indelRightEdge);
+        return new Interval(context.getLocation(), indelLoc);
+    }
+
+    public Interval reduceInit() {
+        return null;
+    }
+
+    public Interval reduce(Interval value, Interval sum) {
+        // if there is no interval to the left, then this is the first one
+        if ( sum == null )
+            return value;
+
+        //System.out.println(sum + " ==> " + value);
+
+        // if the intervals don't overlap, print out the leftmost one and start a new one
+        if ( !sum.readLoc.overlapsP(value.readLoc) ) {
+            if ( sum.indelCount >= minIntervalIndelCount )
+                out.println(sum);
+            return value;
+        }
+        // otherwise, merge them
+        return sum.merge(value);
+    }
+
+    public void onTraversalDone(Interval result) {}
+
+    public class Interval {
+        public GenomeLoc readLoc = null;
+        public GenomeLoc indelLoc = null;
+        public int indelCount;
+
+        Interval(GenomeLoc readLoc, GenomeLoc indelLoc) {
+            this.indelLoc = indelLoc;
+            this.readLoc = readLoc;
+            indelCount = 1;
+        }
+
+        public Interval merge(Interval i) {
+            long indelLeftEdge = Math.min(this.indelLoc.getStart(), i.indelLoc.getStart());
+            long indelRightEdge = Math.max(this.indelLoc.getStop(), i.indelLoc.getStop());
+            GenomeLoc mergedIndelLoc = new GenomeLoc(this.indelLoc.getContigIndex(), indelLeftEdge, indelRightEdge);
+            Interval mergedInterval = new Interval(this.readLoc.merge(i.readLoc), mergedIndelLoc);
+            mergedInterval.indelCount = this.indelCount + i.indelCount;
+            return mergedInterval;
+        }
+
+        public String toString() {
+            return indelLoc.toString();
+        }
+    }
+}
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