Merge pull request #50 from broadinstitute/gg_new_ReassignOneMappingQualityFilter_GSATDG-77

New ReadFilter allows users to reassign a specific mapping quality...

public/java/src/org/broadinstitute/sting/gatk/filters/ReassignOneMappingQualityFilter.java

@@ -0,0 +1,88 @@
+/*
+* Copyright (c) 2012 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.filters;
+
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.commandline.Argument;
+
+/**
+ * A read filter (transformer) that changes a given read mapping quality to a different value.
+ *
+ *  <p>
+ *     This 'filter' will change a certain read mapping quality to a different value without affecting reads that
+ *     have other mapping qualities. This is intended primarily for users of RNA-Seq data handling programs such
+ *     as TopHat, which use MAPQ = 255 to designate uniquely aligned reads. According to convention, 255 normally
+ *     designates "unknown" quality, and most GATK tools automatically ignore such reads. By reassigning a different
+ *     mapping quality to those specific reads, users of TopHat and other tools can circumvent this problem without
+ *     affecting the rest of their dataset.
+ *  </p>
+ *
+ *  <p>
+ *     This differs from the ReassignMappingQuality filter by its selectivity -- only one mapping quality is targeted.
+ *     ReassignMappingQuality will change ALL mapping qualities to a single one, and is typically used for datasets
+ *     that have no assigned mapping qualities.
+ *  </p>
+ *
+ *
+ * <h2>Input</h2>
+ *  <p>
+ *	    BAM file(s)
+ *  </p>
+ *
+ *
+ * <h2>Output</h2>
+ *  <p>
+ *      BAM file(s) with one read mapping quality selectively reassigned as desired
+ *  </p>
+ *
+ * <h2>Examples</h2>
+ *  <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -rf ReassignOneMappingQuality
+ *      -RMQF 255
+ *      -RMQT 60
+ *  </pre>
+ *
+ * @author vdauwera
+ * @since 2/19/13
+ */
+
+public class ReassignOneMappingQualityFilter extends ReadFilter {
+
+    @Argument(fullName = "reassign_mapping_quality_from", shortName = "RMQF", doc = "Original mapping quality", required = false)
+    public int reassignMappingQualityFrom = 255;
+
+    @Argument(fullName = "reassign_mapping_quality_to", shortName = "RMQT", doc = "Desired mapping quality", required = false)
+    public int reassignMappingQualityTo = 60;
+
+    public boolean filterOut(SAMRecord rec) {
+        if (rec.getMappingQuality() == reassignMappingQualityFrom)
+        rec.setMappingQuality(reassignMappingQualityTo);
+        return false;
+    }
+}
+