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For some reason, a class of Codecs (including TableCodec) require that a GenomeLocParser be passed in to do the position processing. Why can't they just return a Feature with chr, start, stop? Isn't that the right thing?

This commit is contained in:
Eric Banks 2011-10-27 23:54:28 -04:00
parent ccfd853b34
commit cafc245a43
1 changed files with 3 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/commandline/IntervalBinding.java
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@ -29,6 +29,7 @@ import org.broad.tribble.Feature;
import org.broad.tribble.FeatureCodec; import org.broad.tribble.FeatureCodec;
import org.broad.tribble.readers.AsciiLineReader; import org.broad.tribble.readers.AsciiLineReader;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine; import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager; import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -83,6 +84,8 @@ public final class IntervalBinding<T extends Feature> {
// TODO -- after ROD system cleanup, go through the ROD system so that we can handle things like gzipped files // TODO -- after ROD system cleanup, go through the ROD system so that we can handle things like gzipped files
FeatureCodec codec = new FeatureManager().getByName(featureIntervals.getTribbleType()).getCodec(); FeatureCodec codec = new FeatureManager().getByName(featureIntervals.getTribbleType()).getCodec();
if ( codec instanceof ReferenceDependentFeatureCodec )
((ReferenceDependentFeatureCodec)codec).setGenomeLocParser(toolkit.getGenomeLocParser());
try { try {
FileInputStream fis = new FileInputStream(new File(featureIntervals.getSource())); FileInputStream fis = new FileInputStream(new File(featureIntervals.getSource()));
AsciiLineReader lineReader = new AsciiLineReader(fis); AsciiLineReader lineReader = new AsciiLineReader(fis);