Repackaged datasource-specific command-line tools into their own package. Added a tag renamer tool.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3854 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java

@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.gatk.datasources;
+package org.broadinstitute.sting.gatk.datasources.utilities;
 
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
@@ -32,8 +32,6 @@ import org.broadinstitute.sting.utils.StingException;
 import java.io.File;
 import java.io.PrintStream;
 
-import net.sf.samtools.*;
-
 /**
  *
  *

java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMTagRenamer.java

@@ -0,0 +1,94 @@
+/*
+ * 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.datasources.utilities;
+
+import org.broadinstitute.sting.commandline.CommandLineProgram;
+import org.broadinstitute.sting.commandline.Argument;
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMFileWriterFactory;
+
+import java.io.File;
+
+/**
+ * A simple utility written directly in Picard that will rename tags
+ * from one name to another.
+ *
+ * @author hanna
+ * @version 0.1
+ */
+
+public class BAMTagRenamer extends CommandLineProgram {
+    @Argument(fullName="input",shortName="I",doc="Input file to process",required=true)
+    private File input = null;
+
+    @Argument(fullName="output",shortName="O",doc="Output file to create",required=true)
+    private File output = null;
+
+    @Argument(fullName="bam_compression",shortName="compress",doc="Compression level to use when writing the BAM file.",required=false)
+    private int compressionLevel = 5;
+
+    @Argument(fullName="original_tag_name",shortName="otn",doc="Tag name to be replaced.",required=true)
+    private String sourceTagName = null;
+
+    @Argument(fullName="replacement_tag_name",shortName="rtn",doc="Tag name to be used as a replacement.",required=true)
+    private String targetTagName = null;
+
+    public int execute() {
+        long readsWritten = 0;
+        long readsAltered = 0;
+
+        SAMFileReader reader = new SAMFileReader(input);
+        SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(reader.getFileHeader(),true,output,compressionLevel);
+
+        for(SAMRecord read: reader) {
+            Object value = read.getAttribute(sourceTagName);
+            if(value != null) {
+                read.setAttribute(sourceTagName,null);
+                read.setAttribute(targetTagName,value);
+                readsAltered++;
+            }
+            writer.addAlignment(read);
+            readsWritten++;
+            if(readsWritten % 1000000 == 0)
+                System.out.printf("%d reads written.  %d tag names updated from %s to %s.%n",readsWritten,readsAltered,sourceTagName,targetTagName);
+        }
+
+        writer.close();
+        System.out.printf("%d reads written.  %d tag names updated from %s to %s.%n",readsWritten,readsAltered,sourceTagName,targetTagName);        
+
+        return 0;
+    }
+
+    /**
+     * Required main method implementation.
+     */
+    public static void main(String[] argv) {
+        BAMTagRenamer instance = new BAMTagRenamer();
+        start(instance, argv);
+        System.exit(CommandLineProgram.result);
+    }
+}