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Moving logging status of VCF indexing to DEBUG instead of INFO, otherwise it's painful when reading in lots of files

This commit is contained in:
Eric Banks 2014-02-04 00:24:44 -05:00
parent 91bdf069d3
commit 9cac24d1e6
2 changed files with 4 additions and 4 deletions
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2
public/gatk-framework/src/main/java/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
View File

@ -374,7 +374,7 @@ public abstract class ArgumentTypeDescriptor {
FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file); FeatureManager.FeatureDescriptor featureDescriptor = manager.getByFiletype(file);
if ( featureDescriptor != null ) { if ( featureDescriptor != null ) {
tribbleType = featureDescriptor.getName(); tribbleType = featureDescriptor.getName();
logger.info("Dynamically determined type of " + file + " to be " + tribbleType); logger.debug("Dynamically determined type of " + file + " to be " + tribbleType);
} }
} }

6
public/gatk-framework/src/main/java/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
View File

@ -169,7 +169,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
*/ */
private Pair<AbstractFeatureReader, SAMSequenceDictionary> createTabixIndexedFeatureSource(FeatureManager.FeatureDescriptor descriptor, String name, File inputFile) { private Pair<AbstractFeatureReader, SAMSequenceDictionary> createTabixIndexedFeatureSource(FeatureManager.FeatureDescriptor descriptor, String name, File inputFile) {
// we might not know the index type, try loading with the default reader constructor // we might not know the index type, try loading with the default reader constructor
logger.info("Attempting to blindly load " + inputFile + " as a tabix indexed file"); logger.debug("Attempting to load " + inputFile + " as a tabix indexed file without validating it");
try { try {
return new Pair<AbstractFeatureReader, SAMSequenceDictionary>(AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name)),null); return new Pair<AbstractFeatureReader, SAMSequenceDictionary>(AbstractFeatureReader.getFeatureReader(inputFile.getAbsolutePath(), createCodec(descriptor, name)),null);
} catch (TribbleException e) { } catch (TribbleException e) {
@ -318,7 +318,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
* @return an Index, or null if we're unable to load * @return an Index, or null if we're unable to load
*/ */
protected Index loadFromDisk( final File inputFile, final File indexFile ) { protected Index loadFromDisk( final File inputFile, final File indexFile ) {
logger.info("Loading Tribble index from disk for file " + inputFile); logger.debug("Loading Tribble index from disk for file " + inputFile);
Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath()); Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath());
// check if the file is up-to date (filestamp and version check) // check if the file is up-to date (filestamp and version check)
@ -384,7 +384,7 @@ public class RMDTrackBuilder { // extends PluginManager<FeatureCodec> {
*/ */
protected Index createIndexInMemory(File inputFile, FeatureCodec codec) { protected Index createIndexInMemory(File inputFile, FeatureCodec codec) {
// this can take a while, let them know what we're doing // this can take a while, let them know what we're doing
logger.info("Creating Tribble index in memory for file " + inputFile); logger.debug("Creating Tribble index in memory for file " + inputFile);
Index idx = IndexFactory.createDynamicIndex(inputFile, codec, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME); Index idx = IndexFactory.createDynamicIndex(inputFile, codec, IndexFactory.IndexBalanceApproach.FOR_SEEK_TIME);
validateAndUpdateIndexSequenceDictionary(inputFile, idx, dict); validateAndUpdateIndexSequenceDictionary(inputFile, idx, dict);
return idx; return idx;