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a little clean-up 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2007 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron 2009-11-10 06:18:34 +00:00
parent 2ed423ed56
commit f9819d5f13
1 changed files with 9 additions and 30 deletions
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39
java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java
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@ -68,38 +68,17 @@ public abstract class TraversalEngine {
if (mustPrint || nRecords == 1 || nRecords % N_RECORDS_TO_PRINT == 0 || maxElapsedIntervalForPrinting(curTime)) {
this.lastProgressPrintTime = curTime;
final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
String typeString = "loci";
switch (type) {
case LOCUS:
logger.info(String.format("[PROGRESS] Traversed to %s, processing %,d loci in %.2f secs (%.2f secs per 1M loci)",
loc,
nRecords,
elapsed,
secsPer1MReads));break;
case READ:
logger.info(String.format("[PROGRESS] Traversed %,d reads in %.2f secs %s(%.2f secs per 1M reads)",
nRecords,
elapsed,
(loc != null) ? String.format("at location %s ",loc) : "",
secsPer1MReads));break;
case DUPLICATE:
logger.info(String.format("[PROGRESS] Traversed %,d dups in %.2f secs %s(%.2f secs per 1M dups)",
nRecords,
elapsed,
(loc != null) ? String.format("at location %s ",loc) : "",
secsPer1MReads));break;
case LOCUS_WINDOW:
logger.info(String.format("[PROGRESS] Traversed %,d intervals in %.2f secs over interval %s (%.2f secs per 1M intervals)",
nRecords,
elapsed,
loc,
secsPer1MReads));break;
default:
logger.info(String.format("[PROGRESS] Traversed %,d records in %.2f secs (%.2f secs per 1M intervals)%s",
nRecords,
elapsed,
secsPer1MReads,
(loc != null) ? String.format(", last location seen was %s",loc) : ""));
case LOCUS: typeString = "loci"; break;
case READ: typeString = "reads"; break;
case DUPLICATE: typeString = "dups"; break;
case LOCUS_WINDOW: typeString = "interval"; break;
}
if (loc != null)
logger.info(String.format("[PROGRESS] Traversed to %s, processing %,d %s in %.2f secs (%.2f secs per 1M %s)", loc, nRecords, typeString, elapsed, secsPer1MReads, typeString));
else
logger.info(String.format("[PROGRESS] Traversed %,d %s in %.2f secs (%.2f secs per 1M %s)", nRecords, typeString, elapsed, secsPer1MReads, typeString));
}
}