made closing optional

filehandles optional

bismark

@@ -8,7 +8,7 @@ use Getopt::Long;
 use FindBin qw($RealBin);
 use lib "$RealBin/../lib";
 
-## This program is Copyright (C) 2010-22, Felix Krueger ([email protected])
+## This program is Copyright (C) 2010-23, Felix Krueger ([email protected])
 
 ## This program is free software: you can redistribute it and/or modify
 ## it under the terms of the GNU General Public License as published by
@@ -25,8 +25,8 @@ use lib "$RealBin/../lib";
 
 my $parent_dir = getcwd();
 
-my $bismark_version = 'v0.24.0';
-my $copyright_dates = "2010-22";
+my $bismark_version = 'v0.24.0dev';
+my $copyright_dates = "2010-23";
 
 my $start_run = time();
 my $command_line = join (" ",@ARGV);
@@ -2350,8 +2350,12 @@ sub process_single_end_fastA_file_for_methylation_call{
 	print "Processed $counting{sequences_count} sequences in total\n\n";
 
 	close OUT or warn "Failed to close filehandle OUT: $!\n";
-	close AMBIG or warn "Failed to close filehandle AMBIG: $!";
-	close UNMAPPED or warn "Failed to close filehandle UNMAPPED: $!";
+	if ($ambiguous){
+		close AMBIG or warn "Failed to close filehandle AMBIG: $!";
+	}
+	if ($unmapped){
+		close UNMAPPED or warn "Failed to close filehandle UNMAPPED: $!";
+	}
 
 	print_final_analysis_report_single_end($C_to_T_infile,$G_to_A_infile,$pid);
 
@@ -2434,8 +2438,12 @@ sub process_single_end_fastQ_file_for_methylation_call{
 	print "Processed $counting{sequences_count} sequences in total\n\n";
 
 	close OUT or warn "Failed to close filehandle OUT: $!";
-	close AMBIG or warn "Failed to close filehandle AMBIG: $!";
-	close UNMAPPED or warn "Failed to close filehandle UNMAPPED: $!";
+	if ($ambiguous){
+		close AMBIG or warn "Failed to close filehandle AMBIG: $!";
+	}
+	if ($unmapped){
+		close UNMAPPED or warn "Failed to close filehandle UNMAPPED: $!";
+	}
 
 	print_final_analysis_report_single_end($C_to_T_infile,$G_to_A_infile,$pid);
 	if ($ambig_bam){
@@ -2526,11 +2534,14 @@ sub process_fastA_files_for_paired_end_methylation_calls{
 
 	warn "Processed $counting{sequences_count} sequences in total\n\n";
 	close OUT or die $!;
-	close AMBIG_1 or warn "Failed to close filehandle AMBIG_1: $!";
-	close AMBIG_2 or warn "Failed to close filehandle AMBIG_2: $!";
-	close UNMAPPED_1 or warn "Failed to close filehandle UNMAPPED_1: $!";
-	close UNMAPPED_2 or warn "Failed to close filehandle UNMAPPED_2: $!";
-
+	if ($ambiguous){
+		close AMBIG_1 or warn "Failed to close filehandle AMBIG_1: $!";
+		close AMBIG_2 or warn "Failed to close filehandle AMBIG_2: $!";
+	}
+	if ($unmapped){
+		close UNMAPPED_1 or warn "Failed to close filehandle UNMAPPED_1: $!";
+		close UNMAPPED_2 or warn "Failed to close filehandle UNMAPPED_2: $!";
+	}
 	print_final_analysis_report_paired_ends($C_to_T_infile_1,$G_to_A_infile_1,$C_to_T_infile_2,$G_to_A_infile_2,$pid);
 
 }
@@ -2638,10 +2649,14 @@ sub process_fastQ_files_for_paired_end_methylation_calls{
 	warn "Processed $counting{sequences_count} sequences in total\n\n";
 
 	close OUT or warn "Failed to close filehandle OUT: $!\n\n";
-	close AMBIG_1 or warn "Failed to close filehandle AMBIG_1: $!";
-	close AMBIG_2 or warn "Failed to close filehandle AMBIG_2: $!";
-	close UNMAPPED_1 or warn "Failed to close filehandle UNMAPPED_1: $!";
-	close UNMAPPED_2 or warn "Failed to close filehandle UNMAPPED_2: $!";
+	if ($ambiguous){
+		close AMBIG_1 or warn "Failed to close filehandle AMBIG_1: $!";
+		close AMBIG_2 or warn "Failed to close filehandle AMBIG_2: $!";
+	}
+	if ($unmapped){
+		close UNMAPPED_1 or warn "Failed to close filehandle UNMAPPED_1: $!";
+		close UNMAPPED_2 or warn "Failed to close filehandle UNMAPPED_2: $!";
+	}
 
 	if ($ambig_bam){
 		close AMBIBAM or warn "Had trouble closing filehandle AMBIBAM: $!\n\n";
@@ -9978,6 +9993,6 @@ Bismark BAM/SAM OUTPUT (default):
 Each read of paired-end alignments is written out in a separate line in the above format.
 
 
-Last modified on 17 May 2022
+Last modified on 03 May 2023
 HOW_TO
 }