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

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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

24
java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -33,6 +33,7 @@ import java.io.File;
import java.io.OutputStream;
import java.util.List;
import java.util.Arrays;
import java.util.HashSet;
/**
* 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_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.
@ -111,7 +121,7 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
File writerFile = writerFileName != null ? new File(writerFileName) : null;
// 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.
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;
}
/**
* 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.
* @param source Argument source for the VCF file. Must not be null.