Fixes...

pfeiferd · Jan 30, 2025 · ece8912 · ece8912
1 parent 613eaa6
commit ece8912
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/src/main/java/org/metagene/genestrip/fastq/AbstractLoggingFastqStreamer.java b/src/main/java/org/metagene/genestrip/fastq/AbstractLoggingFastqStreamer.java
@@ -120,7 +120,7 @@ protected void doLog() {
 				double totalHours = totalTime == -1 ? -1 : totalTime / 1000 / 60 / 60;
 				logger.trace("Progress for fastq: " + currentFastq);
 				logger.trace("Elapsed hours: " + diff / 1000 / 60 / 60);
-				if (totalHours != -1) {
+				if (totalHours != -1 && !Double.isNaN(totalHours) && !Double.isInfinite(totalHours)) {
 					logger.trace("Estimated total hours: " + totalHours);
 				}
 			}
@@ -137,7 +137,7 @@ protected void doLog() {
 				double totalHours = totalTime == -1 ? -1 : totalTime / 1000 / 60 / 60;
 				logger.trace("Total progress: ");
 				logger.trace("Elapsed hours: " + diff / 1000 / 60 / 60);
-				if (totalHours != -1) {
+				if (totalHours != -1 && !Double.isNaN(totalHours) && !Double.isInfinite(totalHours)) {
 					logger.trace("Estimated total hours: " + totalHours);
 				}
 				logger.trace("Reads processed: " + (totalReads + reads));

diff --git a/src/main/java/org/metagene/genestrip/match/ResultReporter.java b/src/main/java/org/metagene/genestrip/match/ResultReporter.java
@@ -131,7 +131,7 @@ public void printMatchResult(MatchingResult res, PrintStream out, Database wrapp
 		if (estimator != null) {
 			out.print("db coverage;normalized kmers;exp. unique kmers;unique kmers / exp.;quality prediction;");
 		}
-		out.print("normalized reads; reads >= 1 kmer; normalized reads >= 1 kmer; reads >= 1 kmer bps; avg read >= 1 kmer len; normalized reads >= 1 kmer * avg len;");
+		out.print("normalized reads; reads >= 1 kmer; normalized reads >= 1 kmer; reads >= 1 kmer bps; avg read >= 1 kmer len; normalized reads * avg len;");
 		if (res.isWithMaxKMerCounts()) {
 			out.print("max kmer counts;");
 		}
@@ -231,7 +231,7 @@ public void printMatchResult(MatchingResult res, PrintStream out, Database wrapp
 					double avg1 = ((double) stats.getReads1KmerBPs()) / stats.getReads1Kmer();
 					out.print(DF.format(avg1));
 					out.print(';');
-					out.print(DF.format(n1 * avg1));
+					out.print(DF.format(nreads * avg1));
 					out.print(';');
 					if (res.isWithMaxKMerCounts()) {
 						short[] counts = stats.getMaxKMerCounts();