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#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
my $usage = <<_EOUSAGE_;
##############################################################################################################
#
# Required:
#
# --sam <string> sam-formatted file
#
# Optional:
#
# --max_insert_size <int> maximum insert size (default: 500) : used for pair coverage and jaccard
# --min_insert_size <int> minimum insert size (default: 100) : used for jaccard
#
# --jaccard_win_length|-W <int> default: 100 (requires --jaccard)
#
# --pseudocounts <int> default: 1
# -e write extended format, including 'single' and 'both' raw counts
#
##############################################################################################################
_EOUSAGE_
;
my $help_flag;
# required
my $sam_file;
# optional
my $max_insert_size = 500;
my $min_insert_size = 100;
my $jaccard_win_length = 100;
my $pseudocounts = 1;
my $extended_flag = 0;
&GetOptions ( 'h' => \$help_flag,
# required
'sam=s' => \$sam_file,
# optional
'max_insert_size=i' => \$max_insert_size,
'min_insert_size=i' => \$min_insert_size,
'jaccard_win_length|W=i' => \$jaccard_win_length,
'pseudocounts=i' => \$pseudocounts,
'e' => \$extended_flag,
);
if ($help_flag) {
die $usage;
}
unless ($sam_file) {
die $usage;
}
if (@ARGV) {
die $usage;
}
my $util_dir = "/usr/lib/trinityrnaseq/util/support_scripts";
main: {
## generate the paired coverage info:
my $cmd = "$util_dir/SAM_to_frag_coords.pl --sam $sam_file "
. "--max_insert_size $max_insert_size "
. "--min_insert_size $min_insert_size "; ## writes file: $sam_file.frag_coords
&process_cmd($cmd) unless (-s "$sam_file.frag_coords");
## compute jaccard coeff info for pair-support
$cmd = "$util_dir/ordered_fragment_coords_to_jaccard.pl --lend_sorted_frags $sam_file.frag_coords -W $jaccard_win_length "
. " --pseudocounts $pseudocounts ";
if ($extended_flag) {
$cmd .= " -e ";
}
&process_cmd($cmd);
exit(0);
}
####
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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