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Added "unbiased" downsampling parameter to PrintReads 

* also cleaned up and updated part of the unit tests for print reads. Needs a more thorough cleaning.
This commit is contained in:
Mauricio Carneiro 2012-01-12 15:07:11 -05:00
parent 2c3176eb80
commit 28aa353501
2 changed files with 39 additions and 30 deletions
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35
public/java/src/org/broadinstitute/sting/gatk/walkers/PrintReadsWalker.java
View File

@ -30,11 +30,13 @@ import net.sf.samtools.SAMReadGroupRecord;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.baq.BAQ;
import java.io.File;
import java.util.Collection;
import java.util.Random;
import java.util.Set;
import java.util.TreeSet;
@ -70,12 +72,21 @@ import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
* -I input2.bam \
* --read_filter MappingQualityZero
*
* // Prints the first 2000 reads in the BAM file
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T PrintReads \
* -o output.bam \
* -I input.bam \
* -n 2000
*
* // Downsamples BAM file to 25%
* java -Xmx2g -jar GenomeAnalysisTK.jar \
* -R ref.fasta \
* -T PrintReads \
* -o output.bam \
* -I input.bam \
* -ds 0.25
* </pre>
*
*/
@ -95,9 +106,18 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
@Argument(fullName = "platform", shortName = "platform", doc="Exclude all reads with this platform from the output", required = false)
String platform = null;
/**
* Only prints the first n reads of the file
*/
@Argument(fullName = "number", shortName = "n", doc="Print the first n reads from the file, discarding the rest", required = false)
int nReadsToPrint = -1;
/**
* Downsamples the bam file by the given ratio, printing only approximately the given percentage of reads. The downsampling is balanced (over the entire coverage)
*/
@Argument(fullName = "downsample_coverage", shortName = "ds", doc="Downsample BAM to desired coverage", required = false)
public double downsampleRatio = 1.0;
/**
* Only reads from samples listed in the provided file(s) will be included in the output.
*/
@ -112,6 +132,8 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
private TreeSet<String> samplesToChoose = new TreeSet<String>();
private boolean SAMPLES_SPECIFIED = false;
Random random;
/**
* The initialize function.
@ -132,13 +154,15 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
if(!samplesToChoose.isEmpty()) {
SAMPLES_SPECIFIED = true;
}
random = GenomeAnalysisEngine.getRandomGenerator();
}
/**
* The reads filter function.
*
* @param ref the reference bases that correspond to our read, if a reference was provided
* @param ref the reference bases that correspond to our read, if a reference was provided
* @param read the read itself, as a SAMRecord
* @return true if the read passes the filter, false if it doesn't
*/
@ -188,12 +212,13 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
* @return the read itself
*/
public SAMRecord map( ReferenceContext ref, GATKSAMRecord read, ReadMetaDataTracker metaDataTracker ) {
return read;
return (random.nextDouble() < downsampleRatio) ? read : null;
}
/**
* reduceInit is called once before any calls to the map function. We use it here to setup the output
* bam file, if it was specified on the command line
*
* @return SAMFileWriter, set to the BAM output file if the command line option was set, null otherwise
*/
public SAMFileWriter reduceInit() {
@ -202,12 +227,14 @@ public class PrintReadsWalker extends ReadWalker<SAMRecord, SAMFileWriter> {
/**
* given a read and a output location, reduce by emitting the read
* @param read the read itself
*
* @param read the read itself
* @param output the output source
* @return the SAMFileWriter, so that the next reduce can emit to the same source
*/
public SAMFileWriter reduce( SAMRecord read, SAMFileWriter output ) {
output.addAlignment(read);
if (read != null)
output.addAlignment(read);
return output;
}

34
public/java/test/org/broadinstitute/sting/gatk/walkers/PrintReadsWalkerUnitTest.java
View File

@ -60,19 +60,23 @@ public class PrintReadsWalkerUnitTest extends BaseTest {
private ReferenceContext bases = null;
//private ReferenceContext ref = new ReferenceContext()
PrintReadsWalker walker;
ArtificialSAMFileWriter writer;
@BeforeMethod
public void before() {
trav = new ArtificialReadsTraversal();
readTotal = ( ( trav.endingChr - trav.startingChr ) + 1 ) * trav.readsPerChr + trav.unMappedReads;
walker = new PrintReadsWalker();
writer = new ArtificialSAMFileWriter();
walker.out = writer;
walker.initialize();
}
/** test that we get out the same number of reads we put in */
@Test
public void testReadCount() {
PrintReadsWalker walker = new PrintReadsWalker();
ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
walker.out = writer;
trav.traverse(walker, null, writer);
assertEquals(writer.getRecords().size(), readTotal);
}
@ -80,10 +84,6 @@ public class PrintReadsWalkerUnitTest extends BaseTest {
/** test that we're ok with a null read */
@Test
public void testNullRead() {
PrintReadsWalker walker = new PrintReadsWalker();
ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
walker.out = writer;
SAMRecord rec = walker.map(bases, null, null);
assertTrue(rec == null);
}
@ -91,10 +91,6 @@ public class PrintReadsWalkerUnitTest extends BaseTest {
/** tes that we get the read we put into the map function */
@Test
public void testReturnRead() {
PrintReadsWalker walker = new PrintReadsWalker();
ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
walker.out = writer;
SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
GATKSAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
SAMRecord ret = walker.map(bases, rec, null);
@ -102,20 +98,6 @@ public class PrintReadsWalkerUnitTest extends BaseTest {
assertTrue(ret.getReadName().equals(rec.getReadName()));
}
/** test that the read makes it to the output source */
@Test
public void testReducingRead() {
PrintReadsWalker walker = new PrintReadsWalker();
ArtificialSAMFileWriter writer = new ArtificialSAMFileWriter();
walker.out = writer;
SAMFileHeader head = ArtificialSAMUtils.createArtificialSamHeader(3,1,1000);
SAMRecord rec = ArtificialSAMUtils.createArtificialRead(head, "FakeRead", 1, 1, 50);
SAMRecord ret = walker.map(bases, null,null);
walker.reduce(ret,writer);
assertTrue(writer.getRecords().size() == 1);
}
}