comparison bin/align.pm @ 46:a03408665904 draft

Uploaded

45:ffc66227835f

	my $fout = $col_prefix.'all_mappers.fastq'; 
	my $funi = $col_prefix.'unique_mappers.fastq';
	my $frej = $col_prefix.'unmapped.fastq';
	
  my $repartition = $prefix.'distribution.txt';
	my $png_rep = $prefix.'distribution.png';
	my ( %duplicates, %genome_hits) ;

	#alignement to the first reference
	my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \%duplicates, \%genome_hits, $report );
	my $ref_fai = $return[4];

		}

		histogram($size_mappedHashR, $png_rep, $total);


		my $dup = $prefix.'dup_mapnum.txt';
		my $dup_u = $prefix .'dup_unique.txt';
		my $dup_r = $prefix .'dup_nonmapp.txt';
		open(my $tab,">".$dup) || die "cannot open output txt file\n";
		open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n";
		open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n";
		print $tab "sequence\tcount\tmapnum\n";
		print $tab_u "sequence\tcount\n";

46:a03408665904

	my $fout = $col_prefix.'all_mappers.fastq'; 
	my $funi = $col_prefix.'unique_mappers.fastq';
	my $frej = $col_prefix.'unmapped.fastq';
	
  my $repartition = $out_prefix.'distribution.txt';
	my $png_rep = $out_prefix.'distribution.png';
	my ( %duplicates, %genome_hits) ;

	#alignement to the first reference
	my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \%duplicates, \%genome_hits, $report );
	my $ref_fai = $return[4];

		}

		histogram($size_mappedHashR, $png_rep, $total);


		my $dup = $out_prefix.'dup_mapnum.txt';
		my $dup_u = $out_prefix .'dup_unique.txt';
		my $dup_r = $out_prefix .'dup_nonmapp.txt';
		open(my $tab,">".$dup) || die "cannot open output txt file\n";
		open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n";
		open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n";
		print $tab "sequence\tcount\tmapnum\n";
		print $tab_u "sequence\tcount\n";