diff GenomeAnalysisTK-2.7-2-g6bda569/resources/CountLoci.java @ 0:1485d70afa12 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GenomeAnalysisTK-2.7-2-g6bda569/resources/CountLoci.java	Tue Oct 15 03:09:34 2013 -0400
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+/*
+* 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.walkers.qc;
+
+import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.gatk.walkers.NanoSchedulable;
+import org.broadinstitute.sting.gatk.walkers.TreeReducible;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
+import org.broadinstitute.sting.utils.help.HelpConstants;
+
+import java.io.PrintStream;
+
+/**
+ * Walks over the input data set, calculating the total number of covered loci for diagnostic purposes.
+ *
+ * <p>
+ * This is the simplest example of a locus walker.
+ * </p>
+ *
+ * <h3>Input</h3>
+ * <p>
+ * One or more BAM files.
+ * </p>
+ *
+ * <h3>Output</h3>
+ * <p>
+ * Number of loci traversed. If an output file name is provided, then the result will be written to that file.
+ * Otherwise it will be sent to standard console output.
+ * </p>
+ *
+ * <h3>Examples</h3>
+ * <pre>
+ * java -Xmx2g -jar GenomeAnalysisTK.jar \
+ *   -T CountLoci \
+ *   -R ref.fasta \
+ *   -I input.bam \
+ *   -o output.txt \
+ *   [-L input.intervals]
+ * </pre>
+ *
+ */
+@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
+public class CountLoci extends LocusWalker<Integer, Long> implements TreeReducible<Long>, NanoSchedulable {
+    @Output
+    PrintStream out;
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        return 1;
+    }
+
+    public Long reduceInit() { return 0l; }
+
+    public Long reduce(Integer value, Long sum) {
+        return value + sum;
+    }
+
+    /**
+     * Reduces two subtrees together.  In this case, the implementation of the tree reduce
+     * is exactly the same as the implementation of the single reduce.
+     */
+    public Long treeReduce(Long lhs, Long rhs) {
+        return lhs + rhs;
+    }
+
+    public void onTraversalDone( Long c ) {
+        out.println(c);
+    }
+}