From 8f4bc8cb6e0ce297dda19cb0a3be46a97b2314cc Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 15 Jun 2009 16:38:08 +0000
Subject: [PATCH] Move filtering functionality into the PrintReadsWalker.  More
 to come.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1010 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/PrintReadsWalker.java  | 13 +++++
 .../gatk/walkers/ReadFilterWalker.java        | 51 -------------------
 2 files changed, 13 insertions(+), 51 deletions(-)
 delete mode 100644 java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
index 91a5d4d32..885343d9e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
@@ -40,12 +40,25 @@ import java.util.Random;
  * This walker prints out the reads from the BAM files provided to the traversal engines.
  * It also supports the command line option '-outputBamFile filname', which outputs all the
  * reads to a specified BAM file
+ * The walker now also optionally filters reads based on command line options.
  */
 public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
 
     /** an optional argument to dump the reads out to a BAM file */
     @Argument(fullName = "outputBamFile", shortName = "of", doc = "Write output to this BAM filename instead of STDOUT", required = false)
     String outputBamFile = null;
+    @Argument(fullName = "maxReadLength", shortName = "maxRead", doc="Discard reads with length greater than the specified value", required = false)
+    Integer maxLength = null;
+
+    /**
+     * The reads filter function.
+     * @param ref the reference bases that correspond to our read, if a reference was provided
+     * @param read the read itself, as a SAMRecord
+     * @return true if the read passes the filter, false if it doesn't
+     */
+    public boolean filter(char[] ref, SAMRecord read) {
+		return (maxLength == null || read.getReadLength() <= maxLength);
+	}
 
     /**
      * The reads map function.
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java
deleted file mode 100644
index fcf2293f5..000000000
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadFilterWalker.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
-
-import java.io.File;
-
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMFileWriter;
-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;
-import org.broadinstitute.sting.utils.Utils;
-
-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;
-	
-    public void initialize() {
-        SAMFileHeader header = this.getToolkit().getEngine().getSAMHeader();
-        writer = Utils.createSAMFileWriterWithCompression(header, header.getSortOrder() != SAMFileHeader.SortOrder.unsorted, output, getToolkit().getBAMCompression());
-    }
-
-	@Override
-    public boolean filter(char[] ref, SAMRecord read) {
-		return read.getReadLength() <= max_len;
-	}
-
-	@Override
-	public Integer map(char[] ref, SAMRecord read) {
-		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) {
-		writer.close();
-        out.println(nReads +" reads passed the filter and were written into output file "+output);
-	}
-
-}