Merge pull request #555 from alexcpan/master

Fix for "C methylated in Unknown context..." in PE alignment and bismark2report alignment report processing
FelixKrueger · Jan 5, 2023 · 1675a9c · 1675a9c
2 parents 430df15 + c5451a2
commit 1675a9c
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/bismark b/bismark
@@ -2271,13 +2271,13 @@ sub print_final_analysis_report_paired_ends{
 	}
 
 	### printing methylated C percentage (Unknown C context) if applicable
-	if ($percent_meC_unknown){	
-		warn "C methylated in unknown context (CN or CHN):\t${percent_meC_unknown}%\n";
-		print REPORT "C methylated in unknown context (CN or CHN):\t${percent_meC_unknown}%\n";
+	if ($percent_meC_unknown){
+		warn "C methylated in Unknown context (CN or CHN):\t${percent_meC_unknown}%\n";
+		print REPORT "C methylated in Unknown context (CN or CHN):\t${percent_meC_unknown}%\n";
 	}
 	else{
-		warn "Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0\n";
-		print REPORT "Can't determine percentage of methylated Cs in unknown context (CN or CHN) if value was 0\n";
+		warn "Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0\n";
+		print REPORT "Can't determine percentage of methylated Cs in Unknown context (CN or CHN) if value was 0\n";
 	}
 
 	print REPORT "\n\n";

diff --git a/bismark2report b/bismark2report
@@ -327,7 +327,7 @@ sub read_alignment_report{
       $perc_CHH =~ s/%//;
       print "percentage CHH >> $perc_CHH <<\n" if ($verbose);
     }
-    elsif($_ =~ /^C methylated in Unknown context:/ ){
+    elsif($_ =~ /^C methylated in Unknown context \(CN or CHN\):/ ){
       (undef,$perc_unknown) = split /\t/;
       $perc_unknown =~ s/%//;
       print "percentage Unknown >> $perc_unknown <<\n" if ($verbose);