Prepared FastQ Screen for next release

Author: StevenWingett

RELEASE_NOTES.txt

@@ -1,3 +1,11 @@
+Release notes for FastQ Screen v0.15.3 (03 April 2023)
+--------------------------------------------------------
+Fixed filtering bug causing the final filtered FASTQ 
+file to have the file extension .fastq when it should be 
+.fastq.gz, since the file is actually gzipped.
+
+
+
 Release notes for FastQ Screen v0.15.2 (26 January 2022)
 --------------------------------------------------------
 Updated documentation

fastq_screen

@@ -13,12 +13,12 @@ use File::Path;
 use Data::Dumper;
 
 
-our $VERSION = "0.15.3.dev";
+our $VERSION = "0.15.3";
 
 ###########################################################################
 ###########################################################################
 ##                                                                       ##
-## Copyright 2022, Simon Andrews    (The Babraham Institute, UK)         ##
+## Copyright 2023, Simon Andrews    (The Babraham Institute, UK)         ##
 ##                 Steven Wingett   (MRC-LMB, Cambridge, UK)             ##
 ##                 Felix Krueger    (The Babraham Institute, UK)         ##
 ##                 Mark Fiers       (Plant & Food Research, NZ)          ##
@@ -163,7 +163,6 @@ if(defined $get_genomes){
 	exit(0);
 }
 
-
 # Identify input files
 my @files = get_paths(@ARGV);
 
@@ -174,7 +173,6 @@ foreach my $file (@files) {
     }
 }
 
-
 if(defined $filter){
 	die "Option --filter not in the correct format, see --help for more details.\n" unless($filter =~ /^[012345-]+$/);
 	die "Option --filter may not contain only hyphens '-'\n" if($filter =~ /^-+$/);
@@ -322,19 +320,9 @@ if ( ( ( 1 << 32 ) != 4294967296 ) and ( scalar @libraries > 15 ) ) {    #32-bit
     die "Maximum number of reference genomes exceeded, please adjust configuration and specify at most 32 libraries.\n";
 }
 
-#my @files = get_paths(@ARGV);
 
 die "No files to process\n" unless (@files);
 
-#If the --no_hits option is selected, decide whether the output should be
-#be compressed by assessing whether any of the input is compressed
-#foreach my $file (@files) {
-#    if ( $file =~ /\.gz$/ ) {
-#        $zip_data_output = 1;
-#        last;
-#    }
-#}
-
 my $index = 0;
 while ( $index <= $#files ) {
     process_file( $files[$index] );