Removed a rogue warn/sleep statement that had crept in during the las…

…t release (PE/Bowtie2 only)
FelixKrueger · Apr 25, 2016 · d32b68c · d32b68c
1 parent 65214d1
commit d32b68c
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Showing 2 changed files with 15 additions and 3 deletions.
diff --git a/RELEASE_NOTES.txt b/RELEASE_NOTES.txt
@@ -1,3 +1,15 @@
+RELEASE NOTES FOR Bismark v0.16.1 (25 04 2016)
+----------------------------------------------
+
+Bismark
+=======
+
+Removed unintended warn/sleep statement during PE/Bowtie 2 alignments that would slow alignments down
+dramatically. Sorry for that.
+
+
+
+
 RELEASE NOTES FOR Bismark v0.16.0 (20 04 2016)
 ----------------------------------------------
 

diff --git a/bismark b/bismark
@@ -25,7 +25,7 @@ use lib "$Bin/../lib";
 
 
 my $parent_dir = getcwd;
-my $bismark_version = 'v0.16.0';
+my $bismark_version = 'v0.16.1';
 my $command_line = join (" ",@ARGV);
 
 
@@ -4304,12 +4304,12 @@ sub check_bowtie_results_paired_ends_bowtie2{
     my $best_alignment_location;
     foreach my $alignment_location (sort {$alignments{$b}->{sum_of_alignment_scores} <=> $alignments{$a}->{sum_of_alignment_scores}} keys %alignments){
 
-	warn "$alignments{$alignment_location}->{sum_of_alignment_scores}\n"; sleep(1);
+	# warn "$alignments{$alignment_location}->{sum_of_alignment_scores}\n"; sleep(1);
 
 	unless (defined $best_sum_of_alignment_scores){
 	    $best_sum_of_alignment_scores = $alignments{$alignment_location}->{sum_of_alignment_scores};
 	    $best_alignment_location = $alignment_location;
-	    print "setting best alignment score to: $best_sum_of_alignment_scores\n";
+	    # print "setting best alignment score to: $best_sum_of_alignment_scores\n";
 	}
 	else{
 	    ### if the second best alignment has the same sum of alignment scores as the first one, the sequence pair will get booted