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

a fix for a bug Eric found: if your first call contains fewer samples than calls at other loci, your VCFHeader got setup incorrectly. 

Also moved a buch of Lists over to Sets for consistancy.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1859 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-10-16 04:57:50 +00:00
parent a69ea9b57c
commit 96972c3a5c
9 changed files with 36 additions and 23 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

6
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
View File

@ -98,10 +98,12 @@ public class UnifiedGenotyper extends LocusWalker<Pair<List<GenotypeCall>, Genot
if ( VARIANTS_FILE != null )
writer = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), VARIANTS_FILE,
"UnifiedGenotyper",
this.getToolkit().getArguments().referenceFile.getName());
this.getToolkit().getArguments().referenceFile.getName(),
samples);
else
writer = GenotypeWriterFactory.create(VAR_FORMAT, GenomeAnalysisEngine.instance.getSAMFileHeader(), out, "UnifiedGenotyper",
this.getToolkit().getArguments().referenceFile.getName());
this.getToolkit().getArguments().referenceFile.getName(),
samples);
callsMetrics = new CallMetrics();
}

2
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/VariantsToVCF.java
View File

@ -49,7 +49,7 @@ public class VariantsToVCF extends RefWalker<Integer, Integer> {
public static VCFHeader getHeader(GATKArgumentCollection args, Set<String> sampleNames) {
Map<String, String> metaData = new HashMap<String, String>();
List<String> additionalColumns = new ArrayList<String>();
Set<String> additionalColumns = new HashSet<String>();
// Don't output the data for now because it kills our unit test MD5s and is optional
// TODO - figure out what to do here

20
java/src/org/broadinstitute/sting/utils/genotype/GenotypeWriterFactory.java
View File

@ -9,6 +9,8 @@ import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeWriterAdapter;
import java.io.File;
import java.io.PrintStream;
import java.util.List;
import java.util.Set;
/**
@ -31,7 +33,12 @@ public class GenotypeWriterFactory {
* @param destination the destination file
* @return the genotype writer object
*/
public static GenotypeWriter create(GENOTYPE_FORMAT format, SAMFileHeader header, File destination, String source, String referenceName ) {
public static GenotypeWriter create(GENOTYPE_FORMAT format,
SAMFileHeader header,
File destination,
String source,
String referenceName,
Set<String> sampleNames ) {
switch (format) {
case GLF:
return new GLFWriter(header.toString(), destination);
@ -40,20 +47,25 @@ public class GenotypeWriterFactory {
case GELI_BINARY:
return new GeliAdapter(destination, header);
case VCF:
return new VCFGenotypeWriterAdapter(source, referenceName, destination);
return new VCFGenotypeWriterAdapter(source, referenceName, destination, sampleNames);
default:
throw new StingException("Genotype writer " + format.toString() + " is not implemented");
}
}
public static GenotypeWriter create(GENOTYPE_FORMAT format, SAMFileHeader header, PrintStream destination, String source, String referenceName ) {
public static GenotypeWriter create(GENOTYPE_FORMAT format,
SAMFileHeader header,
PrintStream destination,
String source,
String referenceName,
Set<String> sampleNames ) {
switch (format) {
case GELI:
return new GeliTextWriter(destination);
case GLF:
return new GLFWriter(header.toString(), destination);
case VCF:
return new VCFGenotypeWriterAdapter(source, referenceName, destination);
return new VCFGenotypeWriterAdapter(source, referenceName, destination, sampleNames);
default:
throw new StingException("Genotype writer to " + format.toString() + " to standard output is not implemented");
}

10
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFGenotypeWriterAdapter.java
View File

@ -21,23 +21,26 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
private String mSource;
private String mReferenceName;
private boolean mInitialized = false;
private final Set<String> mSampleNames = new HashSet<String>();
private final File mFile;
private final OutputStream mStream;
public VCFGenotypeWriterAdapter(String source, String referenceName, File writeTo) {
public VCFGenotypeWriterAdapter(String source, String referenceName, File writeTo, Set<String> sampleNames) {
mReferenceName = referenceName;
mSource = source;
mFile = writeTo;
if (mFile == null) throw new RuntimeException("VCF output file must not be null");
mStream = null;
mSampleNames.addAll(sampleNames);
}
public VCFGenotypeWriterAdapter(String source, String referenceName, OutputStream writeTo) {
public VCFGenotypeWriterAdapter(String source, String referenceName, OutputStream writeTo, Set<String> sampleNames) {
mReferenceName = referenceName;
mSource = source;
mFile = null;
mStream = writeTo;
if (mStream == null) throw new RuntimeException("VCF output stream must not be null");
mSampleNames.addAll(sampleNames);
}
@ -49,7 +52,6 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
*/
private void lazyInitialize(List<Genotype> genotypes, File file, OutputStream stream) {
Map<String, String> hInfo = new HashMap<String, String>();
List<String> sampleNames = getSampleNames(genotypes);
// setup the header fields
hInfo.put("format", "VCRv3.2");
@ -57,7 +59,7 @@ public class VCFGenotypeWriterAdapter implements GenotypeWriter {
hInfo.put("reference", mReferenceName);
// setup the sample names
mHeader = new VCFHeader(hInfo, sampleNames);
mHeader = new VCFHeader(hInfo, mSampleNames);
if (mFile == null)
mWriter = new VCFWriter(mHeader, stream);
else

6
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFHeader.java
View File

@ -23,7 +23,7 @@ public class VCFHeader {
private final Map<String, String> mMetaData = new HashMap<String, String>();
// the list of auxillary tags
private final List<String> mGenotypeSampleNames = new ArrayList<String>();
private final Set<String> mGenotypeSampleNames = new HashSet<String>();
// the character string that indicates meta data
public static final String METADATA_INDICATOR = "##";
@ -56,7 +56,7 @@ public class VCFHeader {
* @param metaData the meta data associated with this header
* @param genotypeSampleNames the genotype format field, and the sample names
*/
public VCFHeader(Map<String, String> metaData, List<String> genotypeSampleNames) {
public VCFHeader(Map<String, String> metaData, Set<String> genotypeSampleNames) {
for (String key : metaData.keySet()) mMetaData.put(key, metaData.get(key));
for (String col : genotypeSampleNames) {
if (!col.equals("FORMAT"))
@ -107,7 +107,7 @@ public class VCFHeader {
*
* @return a list of the genotype column names, which may be empty if hasGenotypingData() returns false
*/
public List<String> getGenotypeSamples() {
public Set<String> getGenotypeSamples() {
return mGenotypeSampleNames;
}

2
java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java
View File

@ -126,7 +126,7 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
protected VCFHeader createHeader(List<String> headerStrings) {
Map<String, String> metaData = new HashMap<String, String>();
List<String> auxTags = new ArrayList<String>();
Set<String> auxTags = new HashSet<String>();
// iterate over all the passed in strings
for (String str : headerStrings) {
Matcher matcher = pMeta.matcher(str);

2
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFHeaderTest.java
View File

@ -19,7 +19,7 @@ public class VCFHeaderTest extends BaseTest {
private Set<VCFHeader.HEADER_FIELDS> headerFields = new LinkedHashSet<VCFHeader.HEADER_FIELDS>();
private Map<String, String> metaData = new HashMap();
private List<String> additionalColumns = new ArrayList<String>();
private Set<String> additionalColumns = new HashSet<String>();
/**
* give it fake data, and make sure we get back the right fake data

7
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFRecordTest.java
View File

@ -4,10 +4,7 @@ import org.broadinstitute.sting.BaseTest;
import org.junit.Assert;
import org.junit.Test;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.*;
/**
@ -126,7 +123,7 @@ public class VCFRecordTest extends BaseTest {
*/
public static VCFHeader createFakeHeader() {
Map<String, String> metaData = new HashMap();
List<String> additionalColumns = new ArrayList<String>();
Set<String> additionalColumns = new HashSet<String>();
metaData.put("format", "VCRv3.2"); // required
metaData.put("two", "2");
additionalColumns.add("FORMAT");

4
java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterTest.java
View File

@ -18,7 +18,7 @@ import java.util.*;
public class VCFWriterTest extends BaseTest {
private Set<VCFHeader.HEADER_FIELDS> headerFields = new LinkedHashSet<VCFHeader.HEADER_FIELDS>();
private Map<String, String> metaData = new HashMap();
private List<String> additionalColumns = new ArrayList<String>();
private Set<String> additionalColumns = new HashSet<String>();
private File fakeVCFFile = new File("FAKEVCFFILEFORTESTING.vcf");
/** test, using the writer and reader, that we can output and input a VCF file without problems */
@ -45,7 +45,7 @@ public class VCFWriterTest extends BaseTest {
* create a fake header of known quantity
* @return a fake VCF header
*/
public static VCFHeader createFakeHeader(Map<String, String> metaData, List<String> additionalColumns) {
public static VCFHeader createFakeHeader(Map<String, String> metaData, Set<String> additionalColumns) {
metaData.put("format", "VCRv3.2"); // required
metaData.put("two", "2");
additionalColumns.add("FORMAT");