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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "usage: $0 combined_nameSorted.sam\n\n";
my $combined_nameSorted_sam = $ARGV[0] or die $usage;
main: {
my $conglom_file = "$combined_nameSorted_sam.__conglom_tmp";
unless (-s $conglom_file) {
open (my $ofh, ">$conglom_file") or die "Error, cannot write to $conglom_file";
my @paired;
my $prev_acc = "";
open (my $fh, $combined_nameSorted_sam) or die $!;
while (<$fh>) {
chomp;
my @x = split(/\t/);
if ($x[0] ne $prev_acc) {
if (scalar(@paired) == 2) {
&process_pair($ofh, \@paired);
}
@paired = ();
}
$prev_acc = $x[0];
push (@paired, [@x]);
}
## get last ones
if (scalar(@paired) == 2) {
&process_pair($ofh, \@paired);
}
close $ofh;
}
my $cmd = "sort -k1,1 -k2,2n -k3,3 -k4,4n $conglom_file > $conglom_file.sorted";
&process_cmd($cmd) unless (-s "$conglom_file.sorted");
my $dups_removed_file = "$conglom_file.dups_removed.sam";
unless (-s $dups_removed_file) {
open (my $ofh, ">$dups_removed_file") or die $!;
open (my $fh, "$conglom_file.sorted") or die $!;
print STDERR "-writing $dups_removed_file\n";
my $prev_contig_info = "";
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $contig_info = join("\t", @x[0..3]);
my $read_A_info = $x[4];
my $read_B_info = $x[5];
if ($contig_info ne $prev_contig_info) {
$read_A_info =~ s/$;/\t/g;
$read_B_info =~ s/$;/\t/g;
print $ofh "$read_A_info\n$read_B_info\n";
}
$prev_contig_info = $contig_info;
}
close $fh;
close $ofh;
}
exit(0);
}
####
sub process_pair {
my ($ofh, $pairs_aref) = @_;
my ($read_A, $read_B) = @$pairs_aref;
if ($read_A->[2] gt $read_B->[2]) {
## swap 'em
($read_A, $read_B) = ($read_B, $read_A);
}
my $contig_A = $read_A->[2];
my $pos_A = $read_A->[3];
my $contig_B = $read_B->[2];
my $pos_B = $read_B->[3];
my $read_A_text = join("$;", @$read_A);
my $read_B_text = join("$;", @$read_B);
print $ofh join("\t", $contig_A, $pos_A, $contig_B, $pos_B, $read_A_text, $read_B_text) . "\n";
return;
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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