zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

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
This commit is contained in:
aaron 2010-04-16 06:17:31 +00:00
parent 6dc1275cfb
commit 4d75b26b7a
3 changed files with 5 additions and 6 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

5
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -233,7 +233,6 @@ public class GenomeAnalysisEngine {
/** /**
* if we have a ROD specified as a 'rodToIntervalTrackName', convert its records to RODs * 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<GenomeLoc> checkRODToIntervalArgument() { private static List<GenomeLoc> checkRODToIntervalArgument() {
Map<String, ReferenceOrderedDataSource> rodNames = RMDIntervalGenerator.getRMDTrackNames(instance.rodDataSources); Map<String, ReferenceOrderedDataSource> rodNames = RMDIntervalGenerator.getRMDTrackNames(instance.rodDataSources);
// Do we have any RODs that overloaded as interval lists with the 'rodToIntervalTrackName' flag? // 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; String rodName = GenomeAnalysisEngine.instance.argCollection.RODToInterval;
// check to make sure we have a rod of that name // 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"); 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()) for (String str : rodNames.keySet())
if (str.toLowerCase().equals(rodName.toLowerCase())) { if (str.equals(rodName)) {
RMDIntervalGenerator intervalGenerator = new RMDIntervalGenerator(rodNames.get(str).getReferenceOrderedData()); RMDIntervalGenerator intervalGenerator = new RMDIntervalGenerator(rodNames.get(str).getReferenceOrderedData());
ret.addAll(intervalGenerator.toGenomeLocList()); ret.addAll(intervalGenerator.toGenomeLocList());
} }

2
java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
View File

@ -53,7 +53,7 @@ public class ReferenceOrderedDataSource implements SimpleDataSource {
* @return Name of the underlying rod. * @return Name of the underlying rod.
*/ */
public String getName() { 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();
} }
/** /**

4
java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/RODTrackBuilder.java
View File

@ -114,8 +114,8 @@ public class RODTrackBuilder implements RMDTrackBuilder {
public ReferenceOrderedData createROD(final String trackName, Class type, File fileName) { public ReferenceOrderedData createROD(final String trackName, Class type, File fileName) {
// Create the ROD // Create the ROD
ReferenceOrderedData<?> rod = new ReferenceOrderedData<ReferenceOrderedDatum>(trackName.toLowerCase(), fileName, type ); ReferenceOrderedData<?> rod = new ReferenceOrderedData<ReferenceOrderedDatum>(trackName, fileName, type );
logger.info(String.format("Created binding from %s to %s of type %s", trackName.toLowerCase(), fileName, type)); logger.info(String.format("Created binding from %s to %s of type %s", trackName, fileName, type));
return rod; return rod;
} }