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Fix confusing log output from the engine 

-ReadShardBalancer was printing out an extra "Loading BAM index data for next contig"
 message at traversal end, which was confusing users and making the GATK look stupid.
 Suppress the extraneous message, and reword the log messages to be less confusing.

-Improve log message output when initializing the shard iterator in GenomeAnalysisEngine.
 Don't mention BAMs when the are none, and say "Preparing for traversal" rather than
 mentioning the meaningless-for-users concept of "shard strategy"

-These log messages are needed because the operations they surround might take a
 while under some circumstances, and the user should know that the GATK is actively
 doing something rather than being hung.
This commit is contained in:
David Roazen 2013-05-29 14:43:57 -04:00
parent 684c91c2e7
commit eb206e9f71
2 changed files with 9 additions and 5 deletions
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6
public/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
View File

@ -293,9 +293,11 @@ public class GenomeAnalysisEngine {
// create the output streams
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);
logger.info("Done creating shard strategy");
logger.info("Done preparing for traversal");
// execute the microscheduler, storing the results
return microScheduler.execute(this.walker, shardStrategy);

8
public/java/src/org/broadinstitute/sting/gatk/datasources/reads/ReadShardBalancer.java
View File

@ -177,7 +177,9 @@ public class ReadShardBalancer extends ShardBalancer {
currentContigFilePointer = null;
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() ) {
@ -215,8 +217,8 @@ public class ReadShardBalancer extends ShardBalancer {
}
if ( currentContigFilePointer != null ) {
logger.info("Done loading BAM index data for next contig");
logger.debug(String.format("Next contig FilePointer: %s", currentContigFilePointer));
logger.info("Done loading BAM index data");
logger.debug(String.format("Next FilePointer: %s", currentContigFilePointer));
}
}