zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

removing bad file 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@534 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-04-24 21:40:04 +00:00
parent 05c6679321
commit bfce0c93ab
1 changed files with 0 additions and 90 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

90
java/src/org/broadinstitute/sting/gatk/walkers/WriteBAM.java
View File

@ -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<SAMRecord, ArrayList<SAMFileWriter>> {
@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<SAMFileWriter> reduceInit() {
SAMFileWriterFactory fact = new SAMFileWriterFactory();
ArrayList<SAMFileWriter> outputs = new ArrayList<SAMFileWriter>(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<SAMFileWriter> reduce(SAMRecord read, ArrayList<SAMFileWriter> 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<SAMFileWriter> outputs) {
for ( SAMFileWriter out : outputs ) {
out.close();
}
System.out.printf("Reads: read %d written %d%n", nReadsRead, nReadsWritten);
}
}