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ArtificialReadPileupTestProvider now creates GATKSamRecords with good header values

This commit is contained in:
Mark DePristo 2012-12-23 08:54:27 -05:00
parent 295455eee2
commit 7d250a789a
1 changed files with 7 additions and 6 deletions
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13
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
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@ -37,6 +37,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl; import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils; import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord; import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import java.util.*; import java.util.*;
@ -53,11 +54,11 @@ public class ArtificialReadPileupTestProvider {
final String artificialReadName = "synth"; final String artificialReadName = "synth";
final int artificialRefStart = 1; final int artificialRefStart = 1;
final int artificialMappingQuality = 60; final int artificialMappingQuality = 60;
Map<String, SAMReadGroupRecord> sample2RG = new HashMap<String, SAMReadGroupRecord>(); Map<String, GATKSAMReadGroupRecord> sample2RG = new HashMap<String, GATKSAMReadGroupRecord>();
List<SAMReadGroupRecord> sampleRGs; List<SAMReadGroupRecord> sampleRGs;
List<String> sampleNames = new ArrayList<String>(); List<String> sampleNames = new ArrayList<String>();
private String sampleName(int i) { return sampleNames.get(i); } private String sampleName(int i) { return sampleNames.get(i); }
private SAMReadGroupRecord sampleRG(String name) { return sample2RG.get(name); } private GATKSAMReadGroupRecord sampleRG(String name) { return sample2RG.get(name); }
public final int locStart = 105; // start position where we desire artificial variant public final int locStart = 105; // start position where we desire artificial variant
private final int readLength = 10; // desired read length in pileup private final int readLength = 10; // desired read length in pileup
public final int readOffset = 4; public final int readOffset = 4;
@ -75,7 +76,7 @@ public class ArtificialReadPileupTestProvider {
for ( int i = 0; i < numSamples; i++ ) { for ( int i = 0; i < numSamples; i++ ) {
sampleNames.add(String.format("%s%04d", SAMPLE_PREFIX, i)); sampleNames.add(String.format("%s%04d", SAMPLE_PREFIX, i));
SAMReadGroupRecord rg = createRG(sampleName(i)); GATKSAMReadGroupRecord rg = createRG(sampleName(i));
sampleRGs.add(rg); sampleRGs.add(rg);
sample2RG.put(sampleName(i), rg); sample2RG.put(sampleName(i), rg);
} }
@ -134,8 +135,8 @@ public class ArtificialReadPileupTestProvider {
return contexts; return contexts;
} }
private SAMReadGroupRecord createRG(String name) { private GATKSAMReadGroupRecord createRG(String name) {
SAMReadGroupRecord rg = new SAMReadGroupRecord(name); GATKSAMReadGroupRecord rg = new GATKSAMReadGroupRecord(name);
rg.setPlatform("ILLUMINA"); rg.setPlatform("ILLUMINA");
rg.setSample(name); rg.setSample(name);
return rg; return rg;
@ -189,7 +190,7 @@ public class ArtificialReadPileupTestProvider {
read.setMappingQuality(artificialMappingQuality); read.setMappingQuality(artificialMappingQuality);
read.setReferenceName(loc.getContig()); read.setReferenceName(loc.getContig());
read.setReadNegativeStrandFlag(false); read.setReadNegativeStrandFlag(false);
read.setAttribute("RG", sampleRG(sample).getReadGroupId()); read.setReadGroup(sampleRG(sample));
pileupElements.add(new PileupElement(read,readOffset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases,Math.abs(eventLength))); pileupElements.add(new PileupElement(read,readOffset,false,isBeforeDeletion, false, isBeforeInsertion,false,false,altBases,Math.abs(eventLength)));