From 82d6c5073b16b15940e624c53d1d77204a5cabe7 Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 4 Aug 2010 23:23:50 +0000
Subject: [PATCH] A simple read strand filter for potluri on get satisfaction

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3945 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/filters/ReadStrandFilter.java  | 47 +++++++++++++++++++
 1 file changed, 47 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java

diff --git a/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
new file mode 100644
index 000000000..174a0d94b
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/filters/ReadStrandFilter.java
@@ -0,0 +1,47 @@
+/*
+ * 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.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+
+/**
+ * Filters out reads whose strand is negative or positive
+ *
+ * @author chartl
+ * @version 0.1
+ */
+public class ReadStrandFilter implements SamRecordFilter {
+    @Argument(fullName = "filterPositive", shortName = "fp", doc="Discard reads on the forward strand",required=false)
+	boolean filterForward = false;
+    
+    public boolean filterOut(SAMRecord read) {
+        // check the length
+        return read.getReadNegativeStrandFlag() != filterForward;
+    }
+
+}