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Old -B syntax is long gone at this point. Safe to remove the warning.

This commit is contained in:
Eric Banks 2012-04-02 22:25:16 -04:00
parent 326220c91c
commit 659b82e74d
2 changed files with 0 additions and 20 deletions
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15
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
View File

@ -103,21 +103,6 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
argumentSources.add(walker); argumentSources.add(walker);
Collection<RMDTriplet> rodBindings = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser); Collection<RMDTriplet> rodBindings = 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 has been eliminated 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("################################################################################");
System.exit(1);
}
engine.setReferenceMetaDataFiles(rodBindings); engine.setReferenceMetaDataFiles(rodBindings);
for (ReadFilter filter: filters) { for (ReadFilter filter: filters) {

5
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -107,11 +107,6 @@ public class GATKArgumentCollection {
@Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false) @Input(fullName = "reference_sequence", shortName = "R", doc = "Reference sequence file", required = false)
public File referenceFile = null; public File referenceFile = null;
@Deprecated
@Hidden
@Input(fullName = "rodBind", shortName = "B", doc = "Bindings for reference-ordered data, in the form :<name>,<type> <file>", required = false)
public ArrayList<String> RODBindings = new ArrayList<String>();
@Argument(fullName = "nonDeterministicRandomSeed", shortName = "ndrs", doc = "Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run", required = false) @Argument(fullName = "nonDeterministicRandomSeed", shortName = "ndrs", doc = "Makes the GATK behave non deterministically, that is, the random numbers generated will be different in every run", required = false)
public boolean nonDeterministicRandomSeed = false; public boolean nonDeterministicRandomSeed = false;