diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/WriteBAM.java b/java/src/org/broadinstitute/sting/gatk/walkers/WriteBAM.java deleted file mode 100644 index ba8bc3f24..000000000 --- a/java/src/org/broadinstitute/sting/gatk/walkers/WriteBAM.java +++ /dev/null @@ -1,90 +0,0 @@ -package org.broadinstitute.sting.playground.gatk.walkers; - -import org.broadinstitute.sting.gatk.LocusContext; -import org.broadinstitute.sting.gatk.walkers.ReadWalker; -import org.broadinstitute.sting.utils.cmdLine.Argument; -import org.broadinstitute.sting.utils.QualityUtils; -import net.sf.samtools.SAMRecord; -import net.sf.samtools.SAMFileWriter; -import net.sf.samtools.SAMFileWriterFactory; -import net.sf.samtools.SAMFileHeader; -import edu.mit.broad.picard.reference.ReferenceSequence; - -import java.util.ArrayList; -import java.util.Random; -import java.io.File; - -/** - * ReadErrorRateWalker assesses the error rate per read position ('cycle') by comparing the - * read to its home on the reference and noting the mismatch rate. It ignores reads with - * indels in them, treats high and low-quality references bases the same, and does not count - * ambiguous bases as mismatches. It's also thread-safe, so you can process a slew of reads - * in short order. - * - * @author Kiran Garimella - */ -public class IOCrusherWalker extends ReadWalker> { - @Argument(shortName="nWaysOut",required=false,defaultValue="1") - public int nWaysOut; - - @Argument(shortName="readScaling",required=false,defaultValue="1") - public float readScaling; - - @Argument(shortName="outputBase", required=true) - public String outputBase; - - public long nReadsRead = 0; - public long nReadsWritten = 0; - - /** - * - */ - public SAMRecord map(LocusContext context, SAMRecord read) { - nReadsRead++; - return read; - } - - /** - * - */ - public ArrayList reduceInit() { - SAMFileWriterFactory fact = new SAMFileWriterFactory(); - ArrayList outputs = new ArrayList(nWaysOut); - for ( int i = 0; i < nWaysOut; i++ ) { - SAMFileHeader header = this.getToolkit().getSamReader().getFileHeader(); - outputs.add(fact.makeBAMWriter(header, true, new File(outputBase + "." + i + ".bam"))); - } - return outputs; - } - - /** - * Summarize the error rate data. - * - */ - public ArrayList reduce(SAMRecord read, ArrayList outputs) { - for ( SAMFileWriter out : outputs ) { - if ( readScaling >= 1.0 ) { - int nCopies = (int)Math.ceil(readScaling); - for ( int i = 0; i < nCopies; i++) { - out.addAlignment(read); - nReadsWritten++; - } - } else if ( Math.random() < readScaling ) { - out.addAlignment(read); - nReadsWritten++; - } - } - - return outputs; - } - - /** - * - */ - public void onTraversalDone(ArrayList outputs) { - for ( SAMFileWriter out : outputs ) { - out.close(); - } - System.out.printf("Reads: read %d written %d%n", nReadsRead, nReadsWritten); - } -} \ No newline at end of file