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Merge pull request #246 from broadinstitute/dr_fix_read_shard_balancer_log_output 

Fix confusing extraneous log output from the ReadShardBalancer at traversal end
This commit is contained in:
Mark DePristo 2013-05-29 13:50:26 -07:00
parent 684c91c2e7 eb206e9f71
commit 50a12df68c
2 changed files with 9 additions and 5 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -293,9 +293,11 @@ public class GenomeAnalysisEngine {
// create the output streams // create the output streams
initializeOutputStreams(microScheduler.getOutputTracker()); initializeOutputStreams(microScheduler.getOutputTracker());
logger.info("Creating shard strategy for " + readsDataSource.getReaderIDs().size() + " BAM files"); // Initializing the shard iterator / BAM schedule might take some time, so let the user know vaguely what's going on
logger.info("Preparing for traversal" +
(readsDataSource.getReaderIDs().size() > 0 ? String.format(" over %d BAM files", readsDataSource.getReaderIDs().size()) : ""));
Iterable<Shard> shardStrategy = getShardStrategy(readsDataSource,microScheduler.getReference(),intervals); Iterable<Shard> shardStrategy = getShardStrategy(readsDataSource,microScheduler.getReference(),intervals);
logger.info("Done creating shard strategy"); logger.info("Done preparing for traversal");
// execute the microscheduler, storing the results // execute the microscheduler, storing the results
return microScheduler.execute(this.walker, shardStrategy); return microScheduler.execute(this.walker, shardStrategy);

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java
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@ -177,7 +177,9 @@ public class ReadShardBalancer extends ShardBalancer {
currentContigFilePointer = null; currentContigFilePointer = null;
List<FilePointer> nextContigFilePointers = new ArrayList<FilePointer>(); List<FilePointer> nextContigFilePointers = new ArrayList<FilePointer>();
logger.info("Loading BAM index data for next contig"); if ( filePointers.hasNext() ) {
logger.info("Loading BAM index data");
}
while ( filePointers.hasNext() ) { while ( filePointers.hasNext() ) {
@ -215,8 +217,8 @@ public class ReadShardBalancer extends ShardBalancer {
} }
if ( currentContigFilePointer != null ) { if ( currentContigFilePointer != null ) {
logger.info("Done loading BAM index data for next contig"); logger.info("Done loading BAM index data");
logger.debug(String.format("Next contig FilePointer: %s", currentContigFilePointer)); logger.debug(String.format("Next FilePointer: %s", currentContigFilePointer));
} }
} }