quick walker to find out where the reads mapped to huref were mapped in the consensus reference.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5292 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/FindReadsWithNamesWalker.java

@@ -0,0 +1,113 @@
+/*
+ * 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.walkers;
+
+import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMReadGroupRecord;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
+import org.broadinstitute.sting.utils.baq.BAQ;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.HashSet;
+import java.util.Set;
+
+/**
+ * Renders, in SAM/BAM format, all reads from the input data set in the order in which they appear
+ * in the input file.  It can dynamically merge the contents of multiple input BAM files, resulting
+ * in merged output sorted in coordinate order.  Can also optionally filter reads based on the --read-filter
+ * command line argument.
+ */
+@BAQMode(QualityMode = BAQ.QualityMode.ADD_TAG, ApplicationTime = BAQ.ApplicationTime.ON_OUTPUT)
+@Requires({DataSource.READS, DataSource.REFERENCE})
+public class FindReadsWithNamesWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
+    /** an optional argument to dump the reads out to a BAM file */
+    @Output(doc="Write output to this BAM filename instead of STDOUT")
+    SAMFileWriter out;
+    @Argument(fullName = "readNamesToKeep", shortName = "rn", doc="names to keep", required = true)
+    File readNamesFile = null;
+
+    Set<String> namesToKeep;
+
+
+    /**
+     * The initialize function.
+     */
+    public void initialize() {
+        try {
+            namesToKeep = new HashSet<String>(new XReadLines(readNamesFile).readLines());
+        } catch (FileNotFoundException e) {
+            throw new UserException.CouldNotReadInputFile(readNamesFile, e);
+        }
+    }
+
+    /**
+     * The reads filter function.
+     * @param ref the reference bases that correspond to our read, if a reference was provided
+     * @param read the read itself, as a SAMRecord
+     * @return true if the read passes the filter, false if it doesn't
+     */
+    public boolean filter(ReferenceContext ref, SAMRecord read) {
+        return namesToKeep.contains(read.getReadName());
+	}
+
+    /**
+     * The reads map function.
+     * @param ref the reference bases that correspond to our read, if a reference was provided
+     * @param read the read itself, as a SAMRecord
+     * @return the read itself
+     */
+    public SAMRecord map( ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker ) {
+        return read;
+    }
+
+    /**
+     * reduceInit is called once before any calls to the map function.  We use it here to setup the output
+     * bam file, if it was specified on the command line
+     * @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
+     */
+    public SAMFileWriter reduceInit() {
+        return out;
+    }
+
+    /**
+     * given a read and a output location, reduce by emitting the read
+     * @param read the read itself
+     * @param output the output source
+     * @return the SAMFileWriter, so that the next reduce can emit to the same source
+     */
+    public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
+        output.addAlignment(read);
+        return output;
+    }
+
+}