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Warnings for old ROD system use. 

Removed unused class GATKRODFeature
This commit is contained in:
Mark DePristo 2011-07-27 12:39:12 -04:00
parent 097828a466
commit 60db6cc836
2 changed files with 17 additions and 40 deletions
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17
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
View File

@ -25,6 +25,7 @@
package org.broadinstitute.sting.gatk; package org.broadinstitute.sting.gatk;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.commandline.*; import org.broadinstitute.sting.commandline.*;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection; import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.broadinstitute.sting.gatk.filters.ReadFilter; import org.broadinstitute.sting.gatk.filters.ReadFilter;
@ -66,6 +67,8 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
*/ */
private final Collection<Object> argumentSources = new ArrayList<Object>(); private final Collection<Object> argumentSources = new ArrayList<Object>();
protected static Logger logger = Logger.getLogger(CommandLineExecutable.class);
/** /**
* this is the function that the inheriting class can expect to have called * this is the function that the inheriting class can expect to have called
* when the command line system has initialized. * when the command line system has initialized.
@ -98,6 +101,20 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
argumentSources.add(walker); argumentSources.add(walker);
Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser); Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
// todo: remove me when the old style system is removed
if ( getArgumentCollection().RODBindings.size() > 0 ) {
logger.warn("################################################################################");
logger.warn("################################################################################");
logger.warn("Deprecated -B rod binding syntax detected. This syntax will be retired in GATK 1.2.");
logger.warn("Please use arguments defined by each specific walker instead.");
for ( String oldStyleRodBinding : getArgumentCollection().RODBindings ) {
logger.warn(" -B rod binding with value " + oldStyleRodBinding + " tags: " + parser.getTags(oldStyleRodBinding).getPositionalTags());
}
logger.warn("################################################################################");
logger.warn("################################################################################");
}
Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindings(getArgumentCollection().RODBindings, getArgumentCollection().DBSNPFile, parser); Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindings(getArgumentCollection().RODBindings, getArgumentCollection().DBSNPFile, parser);
oldStyle.addAll(newStyle); oldStyle.addAll(newStyle);
engine.setReferenceMetaDataFiles(oldStyle); engine.setReferenceMetaDataFiles(oldStyle);

40
public/java/src/org/broadinstitute/sting/gatk/refdata/utils/GATKFeature.java
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@ -102,44 +102,4 @@ public abstract class GATKFeature implements Feature, HasGenomeLocation {
return feature; return feature;
} }
} }
/**
* wrapping a old style rod into the new GATK feature style
*/
public static class RODGATKFeature extends GATKFeature {
// our data
private ReferenceOrderedDatum datum;
public RODGATKFeature(ReferenceOrderedDatum datum) {
super(datum.getName());
this.datum = datum;
}
@Override
public GenomeLoc getLocation() {
return datum.getLocation();
}
@Override
public Object getUnderlyingObject() {
return datum;
}
@Override
public String getChr() {
return datum.getLocation().getContig();
}
@Override
public int getStart() {
return (int)datum.getLocation().getStart();
}
@Override
public int getEnd() {
return (int)datum.getLocation().getStop();
}
}
} }