From 13fd182b7c46bc6cdb5ecb60cfb0ea1c66b57435 Mon Sep 17 00:00:00 2001
From: kiran <kiran@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 10 May 2010 15:17:05 +0000
Subject: [PATCH] For dealing with slightly malformatted BAMs - mark every
 alignment as primary, or in the case of some BAM files from UWash, supply the
 sample information for each read group.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3340 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../tools/MarkAllAlignmentsAsPrimary.java     | 39 ++++++++++++++++
 .../tools/RepairSeattleBAM.java               | 44 +++++++++++++++++++
 2 files changed, 83 insertions(+)
 create mode 100755 java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java
 create mode 100755 java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java

diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java b/java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java
new file mode 100755
index 000000000..6e7c37174
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/tools/MarkAllAlignmentsAsPrimary.java
@@ -0,0 +1,39 @@
+package org.broadinstitute.sting.oneoffprojects.tools;
+
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.cmdline.Option;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileWriterFactory;
+
+import java.io.*;
+
+public class MarkAllAlignmentsAsPrimary extends CommandLineProgram {
+    @Usage(programVersion="1.0") public String USAGE = "Mark all alignments as primary.";
+    @Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
+            optional=true) public File IN = null;
+    @Option(shortName="O",doc="Output file (bam or sam).",
+            optional=true) public File OUT = null;
+
+    public static void main(final String[] argv) {
+        System.exit(new MarkAllAlignmentsAsPrimary().instanceMain(argv));
+    }
+
+    protected int doWork() {
+        SAMFileReader inReader = new SAMFileReader(IN);
+        SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
+
+        for (SAMRecord read : inReader ) {
+            read.setNotPrimaryAlignmentFlag(false);
+
+            outWriter.addAlignment(read);
+        }
+
+        inReader.close();
+        outWriter.close();
+
+        return 0;
+    }
+}
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java b/java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java
new file mode 100755
index 000000000..f0ee5b534
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/tools/RepairSeattleBAM.java
@@ -0,0 +1,44 @@
+package org.broadinstitute.sting.oneoffprojects.tools;
+
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.cmdline.Option;
+import net.sf.samtools.*;
+
+import java.io.*;
+
+public class RepairSeattleBAM extends CommandLineProgram {
+    @Usage(programVersion="1.0") public String USAGE = "Fix read group info";
+    @Option(shortName="I", doc="Input file (bam or sam) to extract reads from. If not specified, reads from stdin.",
+            optional=true) public File IN = null;
+    @Option(shortName="O",doc="Output file (bam or sam).",
+            optional=true) public File OUT = null;
+    @Option(shortName="S",doc="Sample.",
+            optional=true) public String SAMPLE = null;
+
+    public static void main(final String[] argv) {
+        System.exit(new RepairSeattleBAM().instanceMain(argv));
+    }
+
+    protected int doWork() {
+        SAMFileReader inReader = new SAMFileReader(IN);
+
+        for (SAMReadGroupRecord rg : inReader.getFileHeader().getReadGroups()) {
+            rg.setSample(SAMPLE);
+        }
+
+        SAMFileWriter outWriter = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(inReader.getFileHeader(), true, OUT);
+
+        for (SAMRecord read : inReader ) {
+            //read.getReadGroup().setSample(SAMPLE);
+            read.setAttribute("SM", SAMPLE);
+
+            outWriter.addAlignment(read);
+        }
+
+        inReader.close();
+        outWriter.close();
+
+        return 0;
+    }
+}
\ No newline at end of file