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for GATK style codecs, make sure we fill in their GenomeLocParser from the RMDIndexer 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4650 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2010-11-11 18:44:15 +00:00
parent fd78ce6c86
commit 698e5cf345
1 changed files with 15 additions and 1 deletions
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16
java/src/org/broadinstitute/sting/gatk/refdata/indexer/RMDIndexer.java
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@ -10,7 +10,10 @@ import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.CommandLineProgram;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.tracks.builders.RMDTrackBuilder;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.Utils;
import java.io.File;
@ -28,7 +31,7 @@ public class RMDIndexer extends CommandLineProgram {
@Argument(shortName="t", fullName="type", doc="The reference meta data file format (e.g. vcf, bed)", required = true)
String inputFileType = null;
@Input(fullName = "referenceSequence", shortName = "R", doc = "The reference to use when indexing; this sequence will be set in the index", required = false)
@Input(fullName = "referenceSequence", shortName = "R", doc = "The reference to use when indexing; this sequence will be set in the index", required = true)
public File referenceFile = null;
@Input(shortName = "i", fullName = "indexFile", doc = "Where to write the index to (as a file), if not supplied we write to <inputFile>.idx", required = false)
@ -38,10 +41,13 @@ public class RMDIndexer extends CommandLineProgram {
IndexFactory.IndexBalanceApproach approach = IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME;
private static Logger logger = Logger.getLogger(RMDIndexer.class);
private IndexedFastaSequenceFile ref = null;
private GenomeLocParser genomeLocParser = null;
@Override
protected int execute() throws Exception {
// check parameters
// ---------------------------------------------------------------------------------
@ -68,6 +74,10 @@ public class RMDIndexer extends CommandLineProgram {
// try to index the file
// ---------------------------------------------------------------------------------
// setup the reference
ref = new IndexedFastaSequenceFile(referenceFile);
genomeLocParser = new GenomeLocParser(ref);
// get a track builder
RMDTrackBuilder builder = new RMDTrackBuilder();
@ -81,6 +91,10 @@ public class RMDIndexer extends CommandLineProgram {
// create the codec
FeatureCodec codec = builder.createByType(typeMapping.get(inputFileType));
// check if it's a reference dependent feature codec
if (codec instanceof ReferenceDependentFeatureCodec)
((ReferenceDependentFeatureCodec)codec).setGenomeLocParser(genomeLocParser);
// get some timing info
long currentTime = System.currentTimeMillis();