From 4d75b26b7a658446ed6f15de73fb991d4507de9e Mon Sep 17 00:00:00 2001 From: aaron Date: Fri, 16 Apr 2010 06:17:31 +0000 Subject: [PATCH] Removing the code that made the ROD system case insensitive. Anyone using specific ROD names in their classes should take care in naming required tracks; All lowercase is the best practice. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3184 348d0f76-0448-11de-a6fe-93d51630548a --- .../org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java | 5 ++--- .../simpleDataSources/ReferenceOrderedDataSource.java | 2 +- .../sting/gatk/refdata/tracks/builders/RODTrackBuilder.java | 4 ++-- 3 files changed, 5 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java index 3b941fa6a..955c1c8df 100755 --- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java @@ -233,7 +233,6 @@ public class GenomeAnalysisEngine { /** * if we have a ROD specified as a 'rodToIntervalTrackName', convert its records to RODs */ - // TODO: this function uses toLowerCase to work with the current ROD system, fix it if we make ROD names case-sensitive private static List checkRODToIntervalArgument() { Map rodNames = RMDIntervalGenerator.getRMDTrackNames(instance.rodDataSources); // Do we have any RODs that overloaded as interval lists with the 'rodToIntervalTrackName' flag? @@ -242,11 +241,11 @@ public class GenomeAnalysisEngine { String rodName = GenomeAnalysisEngine.instance.argCollection.RODToInterval; // check to make sure we have a rod of that name - if (!rodNames.containsKey(rodName.toLowerCase())) + if (!rodNames.containsKey(rodName)) throw new StingException("--rodToIntervalTrackName (-BTI) was pass the name '"+rodName+"', which wasn't given as a ROD name in the -B option"); for (String str : rodNames.keySet()) - if (str.toLowerCase().equals(rodName.toLowerCase())) { + if (str.equals(rodName)) { RMDIntervalGenerator intervalGenerator = new RMDIntervalGenerator(rodNames.get(str).getReferenceOrderedData()); ret.addAll(intervalGenerator.toGenomeLocList()); } diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java index 7bcf7c3d3..bfc4dc534 100755 --- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java +++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java @@ -53,7 +53,7 @@ public class ReferenceOrderedDataSource implements SimpleDataSource { * @return Name of the underlying rod. */ public String getName() { - return this.rod.getName().toLowerCase(); // TODO: Aaron fix this. this is a hack, because RODs always lowercased their names, but in for consistency for now + return this.rod.getName(); } /** diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java index 28a382582..1e270b7f3 100644 --- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java @@ -114,8 +114,8 @@ public class RODTrackBuilder implements RMDTrackBuilder { public ReferenceOrderedData createROD(final String trackName, Class type, File fileName) { // Create the ROD - ReferenceOrderedData rod = new ReferenceOrderedData(trackName.toLowerCase(), fileName, type ); - logger.info(String.format("Created binding from %s to %s of type %s", trackName.toLowerCase(), fileName, type)); + ReferenceOrderedData rod = new ReferenceOrderedData(trackName, fileName, type ); + logger.info(String.format("Created binding from %s to %s of type %s", trackName, fileName, type)); return rod; }