a first, simplest version of a walker that filters out reads based on user-specified criteria and writes remaining reads into a new bam file

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@467 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java

@@ -0,0 +1,48 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import java.io.File;
+
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMRecord;
+
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+
+public class ReadFilterWalker extends ReadWalker<Integer,Integer> {
+	@Argument(fullName="output_file", shortName="O",doc="SAM or BAM file to write filtered reads into (will be overwritten if exists)",required=true ) public String output;
+	@Argument(fullName="max_read_length",doc="Discard reads with length greater than the specified value",required=false) public Integer max_len;
+
+
+	private SAMFileWriter writer = null;
+	
+	@Override
+    public boolean filter(LocusContext context, SAMRecord read) {
+		if ( read.getReadLength() > max_len ) return false;
+		return true;
+	}
+
+	@Override
+	public Integer map(LocusContext context, SAMRecord read) {
+		if ( writer == null )	writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(read.getHeader(), true, new File(output));
+		writer.addAlignment(read);
+		return 1;
+	}
+
+	@Override
+	public Integer reduce(Integer value, Integer sum) {
+		return sum+value;
+	}
+
+	@Override
+	public Integer reduceInit() {
+		return 0;
+	}
+	
+	public void onTraversalDone(Integer nReads) {
+		super.onTraversalDone(nReads);
+		 out.println(nReads +" reads passed the filter and were written into output file "+output);
+	}
+
+}