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

Keep the list of zipped suffixes in sync with Variant

This commit is contained in:
Joel Thibault 2014-03-31 13:29:13 -04:00
parent a2cd9703fa
commit a2d40c84ba
1 changed files with 3 additions and 9 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
View File

@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter; import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException; import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
import java.io.File; import java.io.File;
import java.io.OutputStream; import java.io.OutputStream;
@ -48,15 +49,8 @@ public class VCFWriterArgumentTypeDescriptor extends ArgumentTypeDescriptor {
public static final String NO_HEADER_ARG_NAME = "no_cmdline_in_header"; public static final String NO_HEADER_ARG_NAME = "no_cmdline_in_header";
public static final String SITES_ONLY_ARG_NAME = "sites_only"; public static final String SITES_ONLY_ARG_NAME = "sites_only";
public static final String FORCE_BCF = "bcf"; public static final String FORCE_BCF = "bcf";
public static final HashSet<String> SUPPORTED_ZIPPED_SUFFIXES = new HashSet<String>(); public static final HashSet<String> SUPPORTED_ZIPPED_SUFFIXES =
new HashSet<>(Arrays.asList(VariantContextWriterFactory.BLOCK_COMPRESSED_EXTENSIONS));
//
// static list of zipped suffixes supported by this system.
//
static {
SUPPORTED_ZIPPED_SUFFIXES.add(".gz");
SUPPORTED_ZIPPED_SUFFIXES.add(".gzip");
}
/** /**
* The engine into which output stubs should be fed. * The engine into which output stubs should be fed.