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Bugfix for doNotWriteGenotypes mode 

-- Was outputing GT ./. in sites only mode.  Fixed
This commit is contained in:
Mark DePristo 2012-05-17 13:20:16 -04:00
parent 64d4238e2f
commit d52bc31a47
2 changed files with 11 additions and 10 deletions
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4
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
View File

@ -62,8 +62,6 @@ class BCF2Writer extends IndexingVariantContextWriter {
@Override @Override
public void writeHeader(final VCFHeader header) { public void writeHeader(final VCFHeader header) {
this.header = header;
// create the config offsets map // create the config offsets map
for ( final VCFContigHeaderLine contig : header.getContigLines()) for ( final VCFContigHeaderLine contig : header.getContigLines())
contigDictionary.put(contig.getID(), contig.getContigIndex()); contigDictionary.put(contig.getID(), contig.getContigIndex());
@ -78,7 +76,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
// write out the header into a byte stream, get it's length, and write everything to the file // write out the header into a byte stream, get it's length, and write everything to the file
final ByteArrayOutputStream capture = new ByteArrayOutputStream(); final ByteArrayOutputStream capture = new ByteArrayOutputStream();
final OutputStreamWriter writer = new OutputStreamWriter(capture); final OutputStreamWriter writer = new OutputStreamWriter(capture);
VCFWriter.writeHeader(header, writer, doNotWriteGenotypes, VCFWriter.getVersionLine(), "BCF2 stream"); this.header = VCFWriter.writeHeader(header, writer, doNotWriteGenotypes, VCFWriter.getVersionLine(), "BCF2 stream");
writer.append('\0'); // the header is null terminated by a byte writer.append('\0'); // the header is null terminated by a byte
writer.close(); writer.close();

17
public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
View File

@ -90,8 +90,9 @@ class VCFWriter extends IndexingVariantContextWriter {
@Override @Override
public void writeHeader(VCFHeader header) { public void writeHeader(VCFHeader header) {
mHeader = header; // note we need to update the mHeader object after this call because they header
writeHeader(mHeader, mWriter, doNotWriteGenotypes, getVersionLine(), getStreamName()); // may have genotypes trimmed out of it, if doNotWriteGenotypes is true
mHeader = writeHeader(header, mWriter, doNotWriteGenotypes, getVersionLine(), getStreamName());
// determine if we use filters, so we should FORCE pass the records // determine if we use filters, so we should FORCE pass the records
// TODO -- this might not be necessary any longer as we have unfiltered, filtered, and PASS VCs // TODO -- this might not be necessary any longer as we have unfiltered, filtered, and PASS VCs
@ -105,11 +106,11 @@ class VCFWriter extends IndexingVariantContextWriter {
return VERSION_LINE; return VERSION_LINE;
} }
public static void writeHeader(VCFHeader header, public static VCFHeader writeHeader(VCFHeader header,
final Writer writer, final Writer writer,
final boolean doNotWriteGenotypes, final boolean doNotWriteGenotypes,
final String versionLine, final String versionLine,
final String streamNameForError) { final String streamNameForError) {
header = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header; header = doNotWriteGenotypes ? new VCFHeader(header.getMetaData()) : header;
try { try {
@ -151,6 +152,8 @@ class VCFWriter extends IndexingVariantContextWriter {
catch (IOException e) { catch (IOException e) {
throw new ReviewedStingException("IOException writing the VCF header to " + streamNameForError, e); throw new ReviewedStingException("IOException writing the VCF header to " + streamNameForError, e);
} }
return header;
} }
/** /**