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Removed -B support. Now explodes with error if -B provided.

This commit is contained in:
Mark DePristo 2011-08-16 16:13:47 -04:00
parent 2d5bbecd9e
commit 6e828260a0
3 changed files with 6 additions and 21 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/CommandLineExecutable.java
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@ -96,24 +96,23 @@ public abstract class CommandLineExecutable extends CommandLineProgram {
loadArgumentsIntoObject(walker); loadArgumentsIntoObject(walker);
argumentSources.add(walker); argumentSources.add(walker);
Collection<RMDTriplet> newStyle = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser); Collection<RMDTriplet> rodBindings = ListFileUtils.unpackRODBindings(parser.getRodBindings(), parser);
// todo: remove me when the old style system is removed // todo: remove me when the old style system is removed
if ( getArgumentCollection().RODBindings.size() > 0 ) { if ( getArgumentCollection().RODBindings.size() > 0 ) {
logger.warn("################################################################################"); logger.warn("################################################################################");
logger.warn("################################################################################"); logger.warn("################################################################################");
logger.warn("Deprecated -B rod binding syntax detected. This syntax will be retired in GATK 1.2."); 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."); logger.warn("Please use arguments defined by each specific walker instead.");
for ( String oldStyleRodBinding : getArgumentCollection().RODBindings ) { for ( String oldStyleRodBinding : getArgumentCollection().RODBindings ) {
logger.warn(" -B rod binding with value " + oldStyleRodBinding + " tags: " + parser.getTags(oldStyleRodBinding).getPositionalTags()); logger.warn(" -B rod binding with value " + oldStyleRodBinding + " tags: " + parser.getTags(oldStyleRodBinding).getPositionalTags());
} }
logger.warn("################################################################################"); logger.warn("################################################################################");
logger.warn("################################################################################"); logger.warn("################################################################################");
System.exit(1);
} }
Collection<RMDTriplet> oldStyle = ListFileUtils.unpackRODBindingsOldStyle(getArgumentCollection().RODBindings, parser); engine.setReferenceMetaDataFiles(rodBindings);
oldStyle.addAll(newStyle);
engine.setReferenceMetaDataFiles(oldStyle);
for (ReadFilter filter: filters) { for (ReadFilter filter: filters) {
loadArgumentsIntoObject(filter); loadArgumentsIntoObject(filter);

10
public/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -101,6 +101,8 @@ 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
@ElementList(required = false) @ElementList(required = false)
@Input(fullName = "rodBind", shortName = "B", doc = "Bindings for reference-ordered data, in the form :<name>,<type> <file>", required = false) @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>(); public ArrayList<String> RODBindings = new ArrayList<String>();
@ -340,14 +342,6 @@ public class GATKArgumentCollection {
return false; return false;
} }
} }
if (other.RODBindings.size() != RODBindings.size()) {
return false;
}
for (int x = 0; x < RODBindings.size(); x++) {
if (!RODBindings.get(x).equals(other.RODBindings.get(x))) {
return false;
}
}
if (!other.samFiles.equals(this.samFiles)) { if (!other.samFiles.equals(this.samFiles)) {
return false; return false;
} }

8
public/java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
View File

@ -88,14 +88,6 @@ public class GATKArgumentCollectionUnitTest extends BaseTest {
collect.intervals.add("intervals".toLowerCase()); collect.intervals.add("intervals".toLowerCase());
collect.excludeIntervals = new ArrayList<String>(); collect.excludeIntervals = new ArrayList<String>();
collect.numberOfThreads = 1; collect.numberOfThreads = 1;
// make some rod bindings up
ArrayList<String> fakeBindings = new ArrayList<String>();
fakeBindings.add("Bind1");
fakeBindings.add("Bind2");
fakeBindings.add("Bind3");
collect.RODBindings = fakeBindings;
} }