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

Return a TabixIndexCreator for appropriate file types 

[Fixes #68291082]
This commit is contained in:
Joel Thibault 2014-03-28 12:00:39 -04:00
parent ab5634cbac
commit 70fe7f72f1
2 changed files with 29 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java
View File

@ -213,7 +213,7 @@ public class CatVariants extends CommandLineProgram {
FileOutputStream outputStream = new FileOutputStream(outputFile);
EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile);
final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile, ref.getSequenceDictionary());
final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);
boolean firstFile = true;

28
public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
View File

@ -25,6 +25,8 @@
package org.broadinstitute.sting.utils.variant;
import net.sf.samtools.SAMSequenceDictionary;
import org.apache.log4j.Logger;
import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec;
import org.broad.tribble.FeatureCodecHeader;
@ -33,12 +35,15 @@ import org.broad.tribble.index.IndexCreator;
import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.index.interval.IntervalIndexCreator;
import org.broad.tribble.index.linear.LinearIndexCreator;
import org.broad.tribble.index.tabix.TabixFormat;
import org.broad.tribble.index.tabix.TabixIndexCreator;
import org.broad.tribble.readers.LineIterator;
import org.broad.tribble.readers.PositionalBufferedStream;
import org.broadinstitute.sting.commandline.RodBinding;
import org.broadinstitute.sting.gatk.CommandLineGATK;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
import org.broadinstitute.sting.gatk.io.stubs.VCFWriterArgumentTypeDescriptor;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.variant.variantcontext.VariantContext;
import org.broadinstitute.variant.vcf.*;
@ -59,6 +64,7 @@ public class GATKVCFUtils {
*/
private GATKVCFUtils() { }
public static final Logger logger = Logger.getLogger(GATKVCFUtils.class);
public final static String GATK_COMMAND_LINE_KEY = "GATKCommandLine";
public final static GATKVCFIndexType DEFAULT_INDEX_TYPE = GATKVCFIndexType.DYNAMIC_SEEK; // by default, optimize for seek time. All indices prior to Nov 2013 used this type.
@ -192,6 +198,28 @@ public class GATKVCFUtils {
* @return
*/
public static IndexCreator getIndexCreator(GATKVCFIndexType type, int parameter, File outFile) {
return getIndexCreator(type, parameter, outFile, null);
}
/**
* Create and return an IndexCreator
* @param type
* @param parameter
* @param outFile
* @param sequenceDictionary
* @return
*/
public static IndexCreator getIndexCreator(GATKVCFIndexType type, int parameter, File outFile, SAMSequenceDictionary sequenceDictionary) {
if (VCFWriterArgumentTypeDescriptor.isCompressed(outFile.toString())) {
if (type != GATKVCFUtils.DEFAULT_INDEX_TYPE || parameter != GATKVCFUtils.DEFAULT_INDEX_PARAMETER)
logger.warn("Creating Tabix index for " + outFile + ", ignoring user-specified index type and parameter");
if (sequenceDictionary == null)
return new TabixIndexCreator(TabixFormat.VCF);
else
return new TabixIndexCreator(sequenceDictionary, TabixFormat.VCF);
}
IndexCreator idxCreator;
switch (type) {
case DYNAMIC_SEEK: idxCreator = new DynamicIndexCreator(outFile, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); break;