From 84dd72e6cb5d4cfd4a5031a75cda250142530d75 Mon Sep 17 00:00:00 2001
From: droazen <droazen@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 22 Jun 2011 22:54:15 +0000
Subject: [PATCH] Adding in some read filters, updating MathUtils.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6042 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/filters/MateSameStrandFilter.java    | 18 ++++++++++++++++
 .../gatk/filters/MaxInsertSizeFilter.java     | 21 +++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java
 create mode 100755 java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java

diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java
new file mode 100755
index 000000000..9579aac05
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java
@@ -0,0 +1,18 @@
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.samtools.SAMRecord;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 5/18/11
+ * Time: 4:25 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class MateSameStrandFilter extends ReadFilter {
+
+    public boolean filterOut(SAMRecord read) {
+        return (! read.getReadPairedFlag() ) || read.getMateUnmappedFlag() || read.getDuplicateReadFlag() ||
+                read.getReadFailsVendorQualityCheckFlag() || read.getMateNegativeStrandFlag() != read.getReadNegativeStrandFlag();
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java b/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
new file mode 100755
index 000000000..584783d34
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java
@@ -0,0 +1,21 @@
+package org.broadinstitute.sting.gatk.filters;
+
+import net.sf.picard.filter.SamRecordFilter;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: chartl
+ * Date: 5/2/11
+ * Time: 12:20 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class MaxInsertSizeFilter extends ReadFilter {
+    @Argument(fullName = "maxInsertSize", shortName = "maxInsert", doc="Discard reads with insert size greater than the specified value, defaults to 1000000", required=false)
+    private int maxInsertSize = 1000000;
+
+    public boolean filterOut(SAMRecord record) {
+        return (record.getReadPairedFlag() && (record.getInferredInsertSize() > maxInsertSize || record.getInferredInsertSize() < -1*maxInsertSize));
+    }
+}