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Minor function renaming

This commit is contained in:
Mark DePristo 2011-10-03 14:41:13 -07:00
parent dd71884b0c
commit 2e3dc52088
3 changed files with 23 additions and 6 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -44,6 +44,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator; import org.broadinstitute.sting.gatk.refdata.utils.RMDIntervalGenerator;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.samples.SampleDBBuilder;
import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.utils.*; import org.broadinstitute.sting.utils.*;
import org.broadinstitute.sting.utils.baq.BAQ; import org.broadinstitute.sting.utils.baq.BAQ;
@ -686,10 +687,22 @@ public class GenomeAnalysisEngine {
for (ReadFilter filter : filters) for (ReadFilter filter : filters)
filter.initialize(this); filter.initialize(this);
sampleDB = new SampleDB(getSAMFileHeader(), argCollection.sampleFiles);
// set the sequence dictionary of all of Tribble tracks to the sequence dictionary of our reference // set the sequence dictionary of all of Tribble tracks to the sequence dictionary of our reference
rodDataSources = getReferenceOrderedDataSources(referenceMetaDataFiles,referenceDataSource.getReference().getSequenceDictionary(),genomeLocParser,argCollection.unsafe); rodDataSources = getReferenceOrderedDataSources(referenceMetaDataFiles,referenceDataSource.getReference().getSequenceDictionary(),genomeLocParser,argCollection.unsafe);
// set up sample db
initializeSampleDB();
}
/**
* Entry-point function to initialize the samples database from input data and pedigree arguments
*/
private void initializeSampleDB() {
SampleDBBuilder sampleDBBuilder = new SampleDBBuilder(this, argCollection.pedigreeValidationType);
sampleDBBuilder.addSamplesFromSAMHeader(getSAMFileHeader());
sampleDBBuilder.addSamplesFromSampleNames(SampleUtils.getUniqueSamplesFromRods(this));
sampleDBBuilder.addSamplesFromPedigreeArgument(argCollection.pedigreeData);
sampleDB = sampleDBBuilder.getFinalSampleDB();
} }
/** /**

11
public/java/src/org/broadinstitute/sting/gatk/samples/SampleDBBuilder.java
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@ -56,8 +56,12 @@ public class SampleDBBuilder {
/** /**
* Hallucinates sample objects for all the samples in the SAM file and stores them * Hallucinates sample objects for all the samples in the SAM file and stores them
*/ */
public SampleDBBuilder addSamples(SAMFileHeader header) { public SampleDBBuilder addSamplesFromSAMHeader(final SAMFileHeader header) {
for (String sampleName : SampleUtils.getSAMFileSamples(header)) { return addSamplesFromSampleNames(SampleUtils.getSAMFileSamples(header));
}
public SampleDBBuilder addSamplesFromSampleNames(final Collection<String> sampleNames) {
for (final String sampleName : sampleNames) {
if (sampleDB.getSample(sampleName) == null) { if (sampleDB.getSample(sampleName) == null) {
final Sample newSample = new Sample(sampleName, sampleDB); final Sample newSample = new Sample(sampleName, sampleDB);
addSample(newSample); addSample(newSample);
@ -66,7 +70,7 @@ public class SampleDBBuilder {
return this; return this;
} }
public SampleDBBuilder addSamples(final List<String> pedigreeArguments) { public SampleDBBuilder addSamplesFromPedigreeArgument(final List<String> pedigreeArguments) {
for (final String ped : pedigreeArguments) { for (final String ped : pedigreeArguments) {
final File pedFile = new File(ped); final File pedFile = new File(ped);
if ( pedFile.exists() ) if ( pedFile.exists() )
@ -105,6 +109,7 @@ public class SampleDBBuilder {
* @param sample to be added * @param sample to be added
*/ */
protected SampleDBBuilder addSample(Sample sample) { protected SampleDBBuilder addSample(Sample sample) {
// todo -- merge with existing record if we have one
sampleDB.addSample(sample); sampleDB.addSample(sample);
return this; return this;
} }

1
public/java/test/org/broadinstitute/sting/gatk/samples/PedReaderUnitTest.java
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@ -299,7 +299,6 @@ public class PedReaderUnitTest extends BaseTest {
super(PedReaderTestTagParsing.class); super(PedReaderTestTagParsing.class);
this.tags = tags; this.tags = tags;
this.expected = missingDesc; this.expected = missingDesc;
} }
} }