From 817278be4631f96680ad4f4843eb94dfc16b69fc Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Sun, 12 Apr 2009 19:42:24 +0000
Subject: [PATCH] If a SAMRecord is on the negative strand, reverse complement
 the SQ tag.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@370 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../fourbasecaller/MatchSQTagToStrand.java    | 50 +++++++++++++++++++
 1 file changed, 50 insertions(+)
 create mode 100644 java/src/org/broadinstitute/sting/playground/fourbasecaller/MatchSQTagToStrand.java

diff --git a/java/src/org/broadinstitute/sting/playground/fourbasecaller/MatchSQTagToStrand.java b/java/src/org/broadinstitute/sting/playground/fourbasecaller/MatchSQTagToStrand.java
new file mode 100644
index 000000000..e9cd19f4d
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/playground/fourbasecaller/MatchSQTagToStrand.java
@@ -0,0 +1,50 @@
+package org.broadinstitute.sting.playground.fourbasecaller;
+
+import org.broadinstitute.sting.utils.cmdLine.CommandLineProgram;
+import org.broadinstitute.sting.utils.QualityUtils;
+
+import java.io.File;
+
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+import net.sf.samtools.SAMRecord;
+
+public class MatchSQTagToStrand extends CommandLineProgram {
+    public static MatchSQTagToStrand Instance = null;
+
+    public File SAM_IN;
+    public File SAM_OUT;
+
+    public static void main(String[] argv) {
+        Instance = new MatchSQTagToStrand();
+        start(Instance, argv);
+    }
+
+    protected void setupArgs() {
+        m_parser.addRequiredArg("sam_in",  "I", "Input SAM file",  "SAM_IN");
+        m_parser.addRequiredArg("sam_out", "O", "Output SAM file", "SAM_OUT");
+    }
+
+    protected int execute() {
+        SAMFileReader sf = new SAMFileReader(SAM_IN);
+        sf.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
+
+        SAMFileWriter sw = new SAMFileWriterFactory().makeSAMOrBAMWriter(sf.getFileHeader(), true, SAM_OUT);
+
+        for (SAMRecord sr : sf) {
+            if (sr.getReadNegativeStrandFlag()) {
+                byte[] sq = (byte[]) sr.getAttribute("SQ");
+                sq = QualityUtils.reverseComplementCompressedQualityArray(sq);
+
+                sr.setAttribute("SQ", sq);
+            }
+
+            sw.addAlignment(sr);
+        }
+
+        sw.close();
+
+        return 0;
+    }
+}