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Merge pull request #224 from broadinstitute/yf_emit_insert_length_with_pileup 

added a @hidden option to PileupWalker that causes it to emit insert sizes
This commit is contained in:
MauricioCarneiro 2013-05-16 11:30:19 -07:00
parent 9234a0efcd 3e2a0b15ed
commit 92072e1815
2 changed files with 62 additions and 21 deletions
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23
public/java/src/org/broadinstitute/sting/gatk/walkers/qc/Pileup.java
View File

@ -26,10 +26,7 @@
package org.broadinstitute.sting.gatk.walkers.qc;
import org.broad.tribble.Feature;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.commandline.Output;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@ -96,6 +93,10 @@ public class Pileup extends LocusWalker<String, Integer> implements TreeReducibl
@Input(fullName="metadata",shortName="metadata",doc="Add these ROD bindings to the output Pileup", required=false)
public List<RodBinding<Feature>> rods = Collections.emptyList();
@Hidden
@Argument(fullName="outputInsertLength",shortName = "outputInsertLength",doc="Add a column which contains the length of the insert each base comes from.",required=false)
public boolean outputInsertLength=false;
@Override
public String map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
final String rods = getReferenceOrderedData( tracker );
@ -104,6 +105,8 @@ public class Pileup extends LocusWalker<String, Integer> implements TreeReducibl
final StringBuilder s = new StringBuilder();
s.append(String.format("%s %s", basePileup.getPileupString((char)ref.getBase()), rods));
if ( outputInsertLength )
s.append(" ").append(insertLengthOutput(basePileup));
if ( SHOW_VERBOSE )
s.append(" ").append(createVerboseOutput(basePileup));
s.append("\n");
@ -143,6 +146,18 @@ public class Pileup extends LocusWalker<String, Integer> implements TreeReducibl
return rodString;
}
private static String insertLengthOutput(final ReadBackedPileup pileup) {
Integer[] insertSizes=new Integer[pileup.depthOfCoverage()];
int i=0;
for ( PileupElement p : pileup ) {
insertSizes[i]=p.getRead().getInferredInsertSize();
++i;
}
return Utils.join(",",insertSizes);
}
private static String createVerboseOutput(final ReadBackedPileup pileup) {
final StringBuilder sb = new StringBuilder();

60
public/java/test/org/broadinstitute/sting/gatk/walkers/qc/PileupWalkerIntegrationTest.java
View File

@ -26,13 +26,14 @@
package org.broadinstitute.sting.gatk.walkers.qc;
import org.broadinstitute.sting.WalkerTest;
import org.testng.annotations.DataProvider;
import org.testng.annotations.Test;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
public class PileupWalkerIntegrationTest extends WalkerTest {
String gatkSpeedupArgs="-T Pileup -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam "
+ "-R " + hg19Reference + " -o %s ";
@Test
public void testGnarleyFHSPileup() {
@ -73,25 +74,50 @@ public class PileupWalkerIntegrationTest extends WalkerTest {
//testing speedup to GATKBAMIndex
@Test
public void testPileupOnLargeBamChr20(){
WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:1-76,050", 1, Arrays.asList("8702701350de11a6d28204acefdc4775"));
executeTest("Testing single on big BAM at start of chromosome 20", spec);
@DataProvider(name="GATKBAMIndexTest")
public Object[][] makeMyDataProvider() {
List<Object[]> tests = new ArrayList<Object[]>();
tests.add(new Object[]{"-L 20:1-76,050","8702701350de11a6d28204acefdc4775"});
tests.add(new Object[]{"-L 20:10,000,000-10,001,100","818cf5a8229efe6f89fc1cd8145ccbe3"});
tests.add(new Object[]{"-L 20:62,954,114-63,025,520","22471ea4a12e5139aef62bf8ff2a5b63"});
tests.add(new Object[]{"-L 20:1-76,050 -L 20:20,000,000-20,000,100 -L 20:40,000,000-40,000,100 -L 20:30,000,000-30,000,100 -L 20:50,000,000-50,000,100 -L 20:62,954,114-63,025,520 ","08d899ed7c5a76ef3947bf67338acda1"});
return tests.toArray(new Object[][]{});
}
@Test
public void testPileupOnLargeBamMid20(){
WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:10,000,000-10,001,100", 1, Arrays.asList("818cf5a8229efe6f89fc1cd8145ccbe3"));
executeTest("Testing single on big BAM somewhere in chromosome 20", spec);
@Test(dataProvider = "GATKBAMIndexTest")
public void testGATKBAMIndexSpeedup(final String intervals, final String md5){
final String gatkArgs="-T Pileup -I " + validationDataLocation + "NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam "
+ "-R " + hg19Reference + " -o %s ";
WalkerTestSpec spec = new WalkerTestSpec(gatkArgs + intervals, 1, Arrays.asList(md5));
executeTest("Testing with intervals="+intervals, spec);
}
/***********************/
// testing hidden option -outputInsertLength
private final static String SingleReadAligningOffChromosome1withInsertLengthMD5 = "279e2ec8832e540f47a6e2bdf4cef5ea";
@Test
public void testPileupOnLargeBamEnd20(){
WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:62,954,114-63,025,520", 1, Arrays.asList("22471ea4a12e5139aef62bf8ff2a5b63"));
executeTest("Testing single at end of chromosome 20", spec);
public void testSingleReadAligningOffChromosome1withInsertLength() {
String gatk_args = "-T Pileup "
+ " -I " + privateTestDir + "readOffb37contig1.bam"
+ " -R " + b37KGReference
+ " -outputInsertLength"
+ " -o %s";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(SingleReadAligningOffChromosome1withInsertLengthMD5));
executeTest("Testing single read spanning off chromosome 1 (with insert length)", spec);
}
@Test
public void testPileupOnLargeBam20Many(){
WalkerTestSpec spec = new WalkerTestSpec(gatkSpeedupArgs + "-L 20:1-76,050 -L 20:20,000,000-20,000,100 -L 20:40,000,000-40,000,100 -L 20:30,000,000-30,000,100 -L 20:50,000,000-50,000,100 -L 20:62,954,114-63,025,520 ",
1, Arrays.asList("08d899ed7c5a76ef3947bf67338acda1"));
executeTest("Testing single on big BAM many places", spec);
public void testGnarleyFHSPileupwithInsertLength() {
String gatk_args = "-T Pileup -I " + validationDataLocation + "FHS_Pileup_Test.bam "
+ "-R " + hg18Reference
+ " -outputInsertLength"
+ " -L chr15:46,347,148 -o %s";
String expected_md5 = "53ced173768f3d4d90b8a8206e72eae5";
WalkerTestSpec spec = new WalkerTestSpec(gatk_args, 1, Arrays.asList(expected_md5));
executeTest("Testing the standard (no-indel) pileup on three merged FHS pools with 27 deletions in 969 bases (with insert length)", spec);
}
}