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We now automatically compress the output VCF if the file suffix is one of the supported types (.gz, .bz, .bz2). You can still specify -bzip if you want to use another file suffix (or pipe it to sdout for some reason). 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4096 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-24 14:39:59 +00:00
parent 7a8b6b87da
commit 7957b60768
1 changed files with 23 additions and 1 deletions
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24
java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
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@ -33,6 +33,7 @@ import java.io.File;
import java.io.OutputStream; import java.io.OutputStream;
import java.util.List; import java.util.List;
import java.util.Arrays; import java.util.Arrays;
import java.util.HashSet;
/** /**
* Injects new command-line arguments into the system providing support for the genotype writer. * Injects new command-line arguments into the system providing support for the genotype writer.
@ -44,6 +45,15 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
private static final String COMPRESSION_FULLNAME = "bzip_compression"; private static final String COMPRESSION_FULLNAME = "bzip_compression";
private static final String COMPRESSION_SHORTNAME = "bzip"; private static final String COMPRESSION_SHORTNAME = "bzip";
private static final HashSet<String> SUPPORTED_ZIPPED_SUFFIXES = new HashSet<String>();
//
// static list of zipped suffixes supported by this system.
//
static {
SUPPORTED_ZIPPED_SUFFIXES.add(".gz");
SUPPORTED_ZIPPED_SUFFIXES.add(".bz");
SUPPORTED_ZIPPED_SUFFIXES.add(".bz2");
}
/** /**
* The engine into which output stubs should be fed. * The engine into which output stubs should be fed.
@ -111,7 +121,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
File writerFile = writerFileName != null ? new File(writerFileName) : null; File writerFile = writerFileName != null ? new File(writerFileName) : null;
// Should we compress the output stream? // Should we compress the output stream?
boolean compress = argumentIsPresent(createVCFCompressionArgumentDefinition(source), matches); boolean compress = argumentIsPresent(createVCFCompressionArgumentDefinition(source), matches) || (writerFileName != null && SUPPORTED_ZIPPED_SUFFIXES.contains(getFileSuffix(writerFileName)));
// Create a stub for the given object. // Create a stub for the given object.
VCFWriterStub stub = (writerFile != null) ? new VCFWriterStub(engine, writerFile, compress) : new VCFWriterStub(engine, System.out, compress); VCFWriterStub stub = (writerFile != null) ? new VCFWriterStub(engine, writerFile, compress) : new VCFWriterStub(engine, System.out, compress);
@ -121,6 +131,18 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
return stub; return stub;
} }
/**
* Returns a lower-cased version of the suffix of the provided file.
* @param fileName the file name. Must not be null.
* @return lower-cased version of the file suffix. Will not be null.
*/
private String getFileSuffix(String fileName) {
int indexOfLastDot = fileName.lastIndexOf(".");
if ( indexOfLastDot == -1 )
return "";
return fileName.substring(indexOfLastDot);
}
/** /**
* Creates the optional compression argument for the VCF file. * Creates the optional compression argument for the VCF file.
* @param source Argument source for the VCF file. Must not be null. * @param source Argument source for the VCF file. Must not be null.