1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
|
#!/usr/bin/env perl
use strict;
use warnings;
use Carp;
use Getopt::Long qw(:config posix_default no_ignore_case bundling pass_through);
use lib ("/usr/lib/trinityrnaseq/PerlLib");
use SAM_entry;
my $help_flag;
my $usage = <<__EOUSAGE__;
###########################################
#
# Required:
#
# --bam <string> bam file
#
# Optional:
#
# --max_cov <int> default: 200
#
###########################################
__EOUSAGE__
;
my $bam_file;
my $max_cov = 200;
&GetOptions ( 'h' => \$help_flag,
'bam=s' => \$bam_file,
'max_cov=i' => \$max_cov
);
if ($help_flag) {
die $usage;
}
unless ($bam_file) {
die $usage;
}
my $MAX_COV_DIST = 1e6;
main: {
my $curr_coord = 0;
my @cov_array;
my %retain;
my $prev_scaffold_name = "";
open(my $fh, "samtools view -h $bam_file | ") or die "Error, cannot view bam file: $bam_file";
while(<$fh>) {
if (/^\@/) {
# header line
print $_;
next;
}
my $sam_line = $_;
my $sam_entry = new SAM_entry($sam_line);
my $scaffold_name = $sam_entry->get_scaffold_name();
if ($scaffold_name ne $prev_scaffold_name) {
print STDERR "-processing $scaffold_name\n";
## reinit
$curr_coord = 0;
@cov_array = ();
%retain = ();
}
my $mate_token;
my $mate_scaffold_pos;
if ($sam_entry->is_paired() &&
$sam_entry->is_proper_pair() &&
(! $sam_entry->is_mate_unmapped()) ) {
$mate_scaffold_pos = $sam_entry->get_mate_scaffold_position();
my $read_name = $sam_entry->get_core_read_name();
$mate_token = join("$;", $read_name, $mate_scaffold_pos);
}
my $aligned_pos = $sam_entry->get_aligned_position();
if ($curr_coord < $aligned_pos) {
# shift it all over.
my $delta = $aligned_pos - $curr_coord;
if ($#cov_array > $delta) {
@cov_array = @cov_array[$delta .. $#cov_array];
}
else {
@cov_array = ();
}
$curr_coord = $aligned_pos;
}
# fill the cov array:
my @align_coords = $sam_entry->get_alignment_coords();
my $genome_align_coords = $align_coords[0];
foreach my $coordset (@$genome_align_coords) {
&add_coverage(\@cov_array, $curr_coord, $coordset);
}
my $pt_cov = $cov_array[0];
#print STDERR "$curr_coord\t$pt_cov\n";
if ($mate_token) {
if ($retain{$mate_token}) {
# force accept
delete $retain{$mate_token};
print $sam_line;
next;
}
else {
# was the mate already seen and not retained?
if ($mate_scaffold_pos < $aligned_pos) {
next;
}
}
}
if ($pt_cov <= $max_cov) {
# selected.
print $sam_line;
if ($mate_token) {
# be sure to retain the mate too:
$retain{$mate_token} = 1;
}
}
$prev_scaffold_name = $scaffold_name;
}
}
exit(0);
####
sub add_coverage {
my ($cov_array_aref, $start_coord, $coordset) = @_;
my ($lend, $rend) = @$coordset;
$lend -= $start_coord;
$rend -= $start_coord;
if ($rend > $MAX_COV_DIST) {
print STDERR "-exceeding max cov dist: start = $start_coord, lend=$lend, rend=$rend. Skipping...\n";
return;
}
for (my $i = $lend; $i <= $rend; $i++) {
$cov_array_aref->[$i]++;
}
}
|
