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Removed some unused variables, fixed some javadoc. The usual. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1211 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-07-09 22:10:22 +00:00
parent 9cfd89c54f
commit ce08f5f0c3
1 changed files with 22 additions and 16 deletions
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38
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -49,9 +49,6 @@ public class GenomeAnalysisEngine {
// our traversal engine // our traversal engine
private TraversalEngine engine = null; private TraversalEngine engine = null;
// the level of debugging we're using
public boolean DEBUGGING = false;
// our argument collection // our argument collection
private final GATKArgumentCollection argCollection; private final GATKArgumentCollection argCollection;
@ -167,7 +164,6 @@ public class GenomeAnalysisEngine {
/** commands that get executed for each engine, regardless of the type */ /** commands that get executed for each engine, regardless of the type */
private void genericEngineSetup() { private void genericEngineSetup() {
Reads sourceInfo = extractSourceInfoFromArguments(argCollection);
engine.setMaximumIterations(argCollection.maximumEngineIterations); engine.setMaximumIterations(argCollection.maximumEngineIterations);
engine.initialize(); engine.initialize();
} }
@ -175,6 +171,8 @@ public class GenomeAnalysisEngine {
/** /**
* setup the interval regions, from either the interval file of the genome region string * setup the interval regions, from either the interval file of the genome region string
* *
* @param intervals the list of intervals to parse
*
* @return a list of genomeLoc representing the interval file * @return a list of genomeLoc representing the interval file
*/ */
public static List<GenomeLoc> parseIntervalRegion(final List<String> intervals) { public static List<GenomeLoc> parseIntervalRegion(final List<String> intervals) {
@ -198,13 +196,13 @@ public class GenomeAnalysisEngine {
* @return The reads object providing reads source info. * @return The reads object providing reads source info.
*/ */
private Reads extractSourceInfoFromArguments( GATKArgumentCollection argCollection ) { private Reads extractSourceInfoFromArguments(GATKArgumentCollection argCollection) {
return new Reads( argCollection.samFiles, return new Reads(argCollection.samFiles,
argCollection.strictnessLevel, argCollection.strictnessLevel,
argCollection.downsampleFraction, argCollection.downsampleFraction,
argCollection.downsampleCoverage, argCollection.downsampleCoverage,
!argCollection.unsafe, !argCollection.unsafe,
argCollection.filterZeroMappingQualityReads ); argCollection.filterZeroMappingQualityReads);
} }
private void validateInputsAgainstWalker(Walker walker, private void validateInputsAgainstWalker(Walker walker,
@ -258,16 +256,20 @@ public class GenomeAnalysisEngine {
* Convenience function that binds RODs using the old-style command line parser to the new style list for * Convenience function that binds RODs using the old-style command line parser to the new style list for
* a uniform processing. * a uniform processing.
* *
* @param name * @param name the name of the rod
* @param type * @param type its type
* @param file * @param file the file to load the rod from
*/ */
private void bindConvenienceRods(final String name, final String type, final String file) { private void bindConvenienceRods(final String name, final String type, final String file) {
argCollection.RODBindings.add(Utils.join(",", new String[]{name, type, file})); argCollection.RODBindings.add(Utils.join(",", new String[]{name, type, file}));
} }
/** Initialize the output streams as specified by the user. */ /**
* Initialize the output streams as specified by the user.
*
* @param walker the walker to initialize output streams for
*/
private void initializeOutputStreams(Walker walker) { private void initializeOutputStreams(Walker walker) {
outputTracker = (argCollection.outErrFileName != null) ? new OutputTracker(argCollection.outErrFileName, argCollection.outErrFileName) outputTracker = (argCollection.outErrFileName != null) ? new OutputTracker(argCollection.outErrFileName, argCollection.outErrFileName)
: new OutputTracker(argCollection.outFileName, argCollection.errFileName); : new OutputTracker(argCollection.outFileName, argCollection.errFileName);
@ -287,7 +289,11 @@ public class GenomeAnalysisEngine {
return this.engine; return this.engine;
} }
/** Gets the collection of GATK main application arguments for enhanced walker validation. */ /**
* Gets the collection of GATK main application arguments for enhanced walker validation.
*
* @return the GATK argument collection
*/
public GATKArgumentCollection getArguments() { public GATKArgumentCollection getArguments() {
return this.argCollection; return this.argCollection;
} }