removing unused fastqtobam
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4985 348d0f76-0448-11de-a6fe-93d51630548a
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depristo
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ce3d226183
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e3956148ac
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package org.broadinstitute.sting.playground.tools;
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import net.sf.picard.cmdline.CommandLineProgram;
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import net.sf.picard.cmdline.Usage;
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import net.sf.picard.cmdline.Option;
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import net.sf.samtools.*;
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import java.io.*;
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import org.broadinstitute.sting.utils.fastq.FastqReader;
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import org.broadinstitute.sting.utils.fastq.FastqRecord;
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public class FastqToBam extends CommandLineProgram {
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@Usage(programVersion="1.0") public String USAGE = "Extracts read sequences and qualities from the input fastq file and writes them into the output file in unaligned BAM format.";
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@Option(shortName="I1", doc="Input file (fastq.gz) to extract reads from (single-end fastq or, if paired, first end of the pair fastq).", optional=false) public File IN1 = null;
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@Option(shortName="I2", doc="Input file (fastq.gz) to extract reads from (if paired, second end of the pair fastq).", optional=true) public File IN2 = null;
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@Option(shortName="O", doc="Output file (bam).", optional=false) public File OUT = null;
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@Option(shortName="RB", doc="Run barcode", optional=false) public String RUN_BARCODE;
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@Option(shortName="RG", doc="Read group name", optional=false) public String READ_GROUP_NAME;
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@Option(shortName="SM", doc="Sample name", optional=false) public String SAMPLE_NAME;
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@Option(shortName="V", doc="Verbose mode", optional=true) public Boolean VERBOSE = false;
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public static void main(final String[] argv) {
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System.exit(new FastqToBam().instanceMain(argv));
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}
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private String getReadName(String fqrHeader) {
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String[] headerPieces = fqrHeader.split("\\s+");
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return headerPieces[0];
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}
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protected int doWork() {
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FastqReader end1 = new FastqReader(IN1);
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FastqReader end2 = (IN2 == null) ? null : new FastqReader(IN2);
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SAMReadGroupRecord srg = new SAMReadGroupRecord(READ_GROUP_NAME);
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srg.setSample(SAMPLE_NAME);
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SAMFileHeader sfh = new SAMFileHeader();
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sfh.addReadGroup(srg);
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sfh.setSortOrder(SAMFileHeader.SortOrder.queryname);
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SAMFileWriter sfw = (new SAMFileWriterFactory()).makeSAMOrBAMWriter(sfh, false, OUT);
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int readsSeen = 0;
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while (end1.hasNext() && (end2 == null || end2.hasNext())) {
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FastqRecord fqr1 = end1.next();
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FastqRecord fqr2 = (end2 == null) ? null : end2.next();
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String fqr1Name = getReadName(fqr1.getReadHeader());
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//if (fqr2 != null && !fqr1Name.equalsIgnoreCase(fqr2Name)) {
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//throw new StingException(String.format("In paired mode, but end 1 read name (%s) does not match end 2 read name (%s)", fqr1.getReadName(), fqr2.getReadName()));
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//}
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SAMRecord sr1 = new SAMRecord(sfh);
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sr1.setReadName(RUN_BARCODE + ":" + fqr1Name);
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sr1.setReadString(fqr1.getReadString());
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sr1.setBaseQualityString(fqr1.getBaseQualityString());
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sr1.setReadUmappedFlag(true);
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sr1.setReadPairedFlag(false);
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sr1.setAttribute("RG", READ_GROUP_NAME);
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SAMRecord sr2 = null;
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if (fqr2 != null) {
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sr1.setReadPairedFlag(true);
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sr1.setFirstOfPairFlag(true);
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sr1.setSecondOfPairFlag(false);
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sr1.setMateUnmappedFlag(true);
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String fqr2Name = getReadName(fqr2.getReadHeader());
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sr2 = new SAMRecord(sfh);
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sr2.setReadName(RUN_BARCODE + ":" + fqr2Name);
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sr2.setReadString(fqr2.getReadString());
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sr2.setBaseQualityString(fqr2.getBaseQualityString());
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sr2.setReadUmappedFlag(true);
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sr2.setReadPairedFlag(true);
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sr2.setAttribute("RG", READ_GROUP_NAME);
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sr2.setFirstOfPairFlag(false);
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sr2.setSecondOfPairFlag(true);
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sr2.setMateUnmappedFlag(true);
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}
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sfw.addAlignment(sr1);
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if (fqr2 != null) {
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sfw.addAlignment(sr2);
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}
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readsSeen++;
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if (VERBOSE) {
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System.out.println(sr1.format());
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if (fqr2 != null) { System.out.println(sr2.format()); }
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}
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}
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sfw.close();
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System.out.println(String.format("%s %s : processed %d reads\n", READ_GROUP_NAME, SAMPLE_NAME, readsSeen));
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return 0;
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}
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}
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@ -1,72 +0,0 @@
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package org.broadinstitute.sting.utils.fastq;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.util.Iterator;
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import java.util.zip.GZIPInputStream;
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import java.io.*;
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public class FastqReader implements Iterator<FastqRecord>, Iterable<FastqRecord>, Closeable {
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private File fastqFile;
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private BufferedReader in;
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private FastqRecord nextRecord;
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public FastqReader(File file) {
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fastqFile = file;
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try {
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if (fastqFile.getName().endsWith(".gz")) {
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in = new BufferedReader(new InputStreamReader(new GZIPInputStream(new FileInputStream(fastqFile))));
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} else {
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in = new BufferedReader(new InputStreamReader(new FileInputStream(fastqFile)));
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}
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nextRecord = readNextRecord();
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} catch (IOException e) {
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throw new UserException.CouldNotReadInputFile(file, String.format("Error opening '%s'", fastqFile.getAbsolutePath()));
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}
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}
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private FastqRecord readNextRecord() {
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try {
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String seqHeader = in.readLine();
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String seqLine = in.readLine();
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String qualHeader = in.readLine();
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String qualLine = in.readLine();
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return new FastqRecord(seqHeader, seqLine, qualHeader, qualLine);
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} catch (IOException e) {
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throw new UserException.CouldNotReadInputFile(fastqFile, e);
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}
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}
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public boolean hasNext() { return nextRecord != null; }
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public FastqRecord next() {
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FastqRecord rec = nextRecord;
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try {
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if (in.ready()) {
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nextRecord = readNextRecord();
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} else {
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nextRecord = null;
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}
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} catch (IOException e) {
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throw new UserException.CouldNotReadInputFile(fastqFile, e);
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}
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return rec;
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}
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public void remove() { throw new UnsupportedOperationException("Unsupported operation"); }
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public Iterator<FastqRecord> iterator() { return this; }
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public void close() {
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try {
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in.close();
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} catch (IOException e) {
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throw new UserException.CouldNotReadInputFile(fastqFile, e);
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}
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}
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}
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@ -1,40 +0,0 @@
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package org.broadinstitute.sting.utils.fastq;
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public class FastqRecord {
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private String seqHeader;
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private String seqLine;
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private String qualHeader;
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private String qualLine;
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public FastqRecord(String seqHeader, String seqLine, String qualHeader, String qualLine) {
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setReadHeader(seqHeader);
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setReadString(seqLine);
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setBaseQualityHeader(qualHeader);
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setBaseQualityString(qualLine);
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}
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public void setReadHeader(String seqHeader) {
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this.seqHeader = seqHeader.replaceFirst("@", "");
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}
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public void setReadString(String seqLine) { this.seqLine = seqLine; }
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public void setBaseQualityHeader(String qualHeader) {
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this.qualHeader = qualHeader.replaceFirst("\\+", "");
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}
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public void setBaseQualityString(String qualLine) { this.qualLine = qualLine; }
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public String getReadHeader() { return seqHeader; }
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public String getReadString() { return seqLine; }
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public String getBaseQualityHeader() { return qualHeader; }
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public String getBaseQualityString() { return qualLine; }
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public String format() {
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return String.format("@%s\n%s\n+%s\n%s", seqHeader, seqLine, qualHeader, qualLine);
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}
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public String toString() {
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return String.format("%s : %s %s", seqHeader, seqLine, qualLine);
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}
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}
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