diff --git a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java index f339b24da..dd98a59db 100755 --- a/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java +++ b/java/src/org/broadinstitute/sting/gatk/traversals/TraversalEngine.java @@ -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)); } }