Adding some functions I keep reinventing, especially for testing purposes.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@772 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/utils/sam/ArtificialSamUtils.java

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+package org.broadinstitute.sting.utils.sam;
+
+import net.sf.samtools.*;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * User: aaron
+ * Date: May 21, 2009
+ * Time: 2:57:48 PM
+ *
+ * The Broad Institute
+ * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * This software and its documentation are copyright 2009 by the
+ * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ *
+ */
+
+
+/**
+ * @author aaron
+ * @version 1.0
+ * @date May 21, 2009
+ * <p/>
+ * Class samUtils
+ * <p/>
+ * A collection of utilities for making sam and bam files.  Mostly these are for creating sam and bam files for testing purposes.
+ */
+public class ArtificialSamUtils {
+    /**
+     * create an artificial sam file
+     * @param filename the filename to write to
+     * @param numberOfChromosomes the number of chromosomes
+     * @param startingChromosome where to start counting
+     * @param chromosomeSize how large each chromosome is
+     * @param readsPerChomosome how many reads to make in each chromosome.  They'll be aligned from position 1 to x (which is the number of reads)
+     */
+    public static void createArtificialBamFile(String filename, int numberOfChromosomes, int startingChromosome, int chromosomeSize, int readsPerChomosome) {
+        SAMFileHeader header = createArtificialSamHeader(numberOfChromosomes, startingChromosome, chromosomeSize);
+        File outFile = new File(filename);
+
+        SAMFileWriter out = new SAMFileWriterFactory().makeBAMWriter(header, false, outFile);
+
+        for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) {
+            for (int readNumber = 0; readNumber < readsPerChomosome; readNumber++) {
+                out.addAlignment(createArtificialRead(header, "Read_" + readNumber, x - startingChromosome, readNumber, 100));
+            }
+        }
+
+        out.close();
+    }
+
+    /**
+     * create an artificial sam file
+     * @param filename the filename to write to
+     * @param numberOfChromosomes the number of chromosomes
+     * @param startingChromosome where to start counting
+     * @param chromosomeSize how large each chromosome is
+     * @param readsPerChomosome how many reads to make in each chromosome.  They'll be aligned from position 1 to x (which is the number of reads)
+     */
+    public static void createArtificialSamFile(String filename, int numberOfChromosomes, int startingChromosome, int chromosomeSize, int readsPerChomosome) {
+        SAMFileHeader header = createArtificialSamHeader(numberOfChromosomes, startingChromosome, chromosomeSize);
+        File outFile = new File(filename);
+
+        SAMFileWriter out = new SAMFileWriterFactory().makeSAMWriter(header, false, outFile);
+
+        for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) {
+            for (int readNumber = 0; readNumber < readsPerChomosome; readNumber++) {
+                out.addAlignment(createArtificialRead(header, "Read_" + readNumber, x - startingChromosome, readNumber, 100));
+            }
+        }
+
+        out.close();
+    }
+
+    /**
+     * Creates an artificial sam header, matching the parameters, chromosomes which will be labeled chr1, chr2, etc
+     * @param numberOfChromosomes the number of chromosomes to create
+     * @param startingChromosome the starting number for the chromosome (most likely set to 1)
+     * @param chromosomeSize the length of each chromosome
+     * @return
+     */
+    public static SAMFileHeader createArtificialSamHeader(int numberOfChromosomes, int startingChromosome, int chromosomeSize) {
+        SAMFileHeader header = new SAMFileHeader();
+        SAMSequenceDictionary dict = new SAMSequenceDictionary();
+        // make up some sequence records
+        for (int x = startingChromosome; x < startingChromosome + numberOfChromosomes; x++) {
+            SAMSequenceRecord rec = new SAMSequenceRecord("chr" + (x), chromosomeSize /* size */);
+            rec.setSequenceLength(1000);
+            dict.addSequence(rec);
+        }
+        header.setSequenceDictionary(dict);
+        return header;
+    }
+
+    /**
+     * Create an artificial read based on the parameters.  The cigar string will be *M, where * is the length of the read
+     * @param header the SAM header to associate the read with
+     * @param name the name of the read
+     * @param refIndex the reference index, i.e. what chromosome to associate it with
+     * @param alignmentStart where to start the alignment
+     * @param length the length of the read
+     * @return the artificial read
+     */
+    public static SAMRecord createArtificialRead(SAMFileHeader header, String name, int refIndex, int alignmentStart, int length) {
+        SAMRecord record = new SAMRecord(header);
+        record.setReadName(name);
+        record.setReferenceIndex(refIndex);
+        record.setAlignmentStart(alignmentStart + 1);
+        List<CigarElement> elements = new ArrayList<CigarElement>();
+        elements.add(new CigarElement( length, CigarOperator.characterToEnum('M')));
+        record.setCigar(new Cigar(elements));
+        record.setProperPairFlag(false);
+        return record;
+    }
+
+}