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Retire old ROD syntax. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4564 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-10-22 23:52:11 +00:00
parent e9c6f681a4
commit 3039c0de3c
2 changed files with 22 additions and 18 deletions
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5
java/src/org/broadinstitute/sting/gatk/AbstractGenomeAnalysisEngine.java
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@ -312,15 +312,12 @@ public abstract class AbstractGenomeAnalysisEngine {
sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles); sampleDataSource = new SampleDataSource(getSAMFileHeader(), argCollection.sampleFiles);
if (argCollection.DBSNPFile != null)
bindConvenienceRods(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile);
RMDTrackBuilder manager = new RMDTrackBuilder(); RMDTrackBuilder manager = new RMDTrackBuilder();
// set the sequence dictionary of all of Tribble tracks to the sequence dictionary of our reference // set the sequence dictionary of all of Tribble tracks to the sequence dictionary of our reference
manager.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary()); manager.setSequenceDictionary(referenceDataSource.getReference().getSequenceDictionary());
List<RMDTrack> tracks = manager.getReferenceMetaDataSources(this,argCollection.RODBindings); List<RMDTrack> tracks = manager.getReferenceMetaDataSources(this,argCollection);
validateSuppliedReferenceOrderedData(tracks); validateSuppliedReferenceOrderedData(tracks);
// validate all the sequence dictionaries against the reference // validate all the sequence dictionaries against the reference

35
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RMDTrackBuilder.java
View File

@ -34,10 +34,13 @@ import org.broad.tribble.index.IndexFactory;
import org.broad.tribble.source.BasicFeatureSource; import org.broad.tribble.source.BasicFeatureSource;
import org.broad.tribble.source.CachingFeatureSource; import org.broad.tribble.source.CachingFeatureSource;
import org.broad.tribble.util.LittleEndianOutputStream; import org.broad.tribble.util.LittleEndianOutputStream;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException; import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet; import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
import org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine; import org.broadinstitute.sting.gatk.AbstractGenomeAnalysisEngine;
import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.collections.Pair; import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.classloader.PluginManager; import org.broadinstitute.sting.utils.classloader.PluginManager;
import org.broadinstitute.sting.utils.exceptions.UserException; import org.broadinstitute.sting.utils.exceptions.UserException;
@ -369,29 +372,39 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
/** /**
* find the associated reference meta data * find the associated reference meta data
* *
* @param bindings the bindings of strings from the -B command line option * @param argCollection the input arguments to the GATK.
* @param engine the GATK engine to bind the tracks to * @param engine the GATK engine to bind the tracks to
* *
* @return a list of RMDTracks, one for each -B option * @return a list of RMDTracks, one for each -B option
*/ */
public List<RMDTrack> getReferenceMetaDataSources(AbstractGenomeAnalysisEngine engine, List<String> bindings) { public List<RMDTrack> getReferenceMetaDataSources(AbstractGenomeAnalysisEngine engine, GATKArgumentCollection argCollection) {
initializeBindings(engine,bindings); initializeConvenienceBindings(engine,argCollection);
initializeFullBindings(engine,argCollection);
// try and make the tracks given their requests // try and make the tracks given their requests
return createRequestedTrackObjects(); return createRequestedTrackObjects();
} }
private void initializeConvenienceBindings(AbstractGenomeAnalysisEngine engine, GATKArgumentCollection argCollection) {
if (argCollection.DBSNPFile != null)
inputs.add(new RMDTriplet(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile));
}
/** /**
* initialize our lists of bindings * initialize our lists of bindings
* @param engine The engine, used to populate tags. * @param engine The engine, used to populate tags.
* @param bindings the input to the GATK, as a list of strings passed in through the -B options * @param argCollection input arguments to the GATK.
*/ */
private void initializeBindings(AbstractGenomeAnalysisEngine engine,List<String> bindings) { private void initializeFullBindings(AbstractGenomeAnalysisEngine engine,GATKArgumentCollection argCollection) {
// NOTE: Method acts as a static. Once the inputs have been passed once they are locked in. // NOTE: Method acts as a static. Once the inputs have been passed once they are locked in.
if (inputs.size() > 0 || bindings.size() == 0) if (argCollection.RODBindings.size() == 0)
return; return;
for (String binding: bindings) { for (String binding: argCollection.RODBindings) {
if(engine != null && engine.getTags(binding).size() == 2) { if(engine != null) {
if(engine.getTags(binding).size() != 2)
throw new UserException("Invalid syntax for -B (reference-ordered data) input flag. " +
"Please use the following syntax when providing reference-ordered " +
"data: -B:<name>,<type> <filename>.");
// Assume that if tags are present, those tags are name and type. // Assume that if tags are present, those tags are name and type.
// Name is always first, followed by type. // Name is always first, followed by type.
List<String> parameters = engine.getTags(binding); List<String> parameters = engine.getTags(binding);
@ -399,12 +412,6 @@ public class RMDTrackBuilder extends PluginManager<FeatureCodec> {
String type = parameters.get(1); String type = parameters.get(1);
inputs.add(new RMDTriplet(name,type,binding)); inputs.add(new RMDTriplet(name,type,binding));
} }
else {
// Otherwise, use old-format bindings.
String[] split = binding.split(",");
if (split.length != 3) throw new IllegalArgumentException(binding + " is not a valid reference metadata track description");
inputs.add(new RMDTriplet(split[0], split[1], split[2]));
}
} }
} }