| line |
true |
false |
branch |
|
36
|
6 |
1 |
if (defined $line) |
|
49
|
3 |
0 |
if ($sam_file =~ /\.sam$/) { } |
|
|
0 |
0 |
elsif ($self->{'sam_file'} =~ /\.sam.gz$/) { } |
|
|
0 |
0 |
elsif ($self->{'sam_file'} =~ /\.bam$/) { } |
|
50
|
0 |
3 |
unless open SAM, "< $sam_file" |
|
52
|
0 |
0 |
unless open SAM, "gunzip -c $sam_file |" |
|
54
|
0 |
0 |
unless open SAM, '-|', "samtools view -h $sam_file" |
|
56
|
0 |
0 |
unless open SAM, "< $sam_file" |
|
63
|
1 |
2 |
if (defined $option and $option eq 'IGNORE_HEADERS') { } |
|
65
|
1 |
3 |
unless ($line =~ /^@/) |
|
79
|
37 |
2 |
if ($sam_line) { } |
|
82
|
0 |
0 |
$! ? : |
|
|
0 |
2 |
unless close SAM |
|
99
|
0 |
1 |
unless defined $ref_seq |
|
110
|
25 |
5 |
if ($_ =~ /\@SQ.*SN:/) |
|
121
|
2 |
0 |
if (defined $self->header) { } |
|
125
|
2 |
4 |
if ($_ =~ /\@PG.*PN:crac/) |
|
140
|
2 |
0 |
if (defined $command_line) { } |
|
152
|
0 |
0 |
unless defined $option |
|
153
|
0 |
0 |
if (defined $self->commandLine) { } |
|
163
|
1 |
0 |
if (defined $self->header) { } |
|
167
|
1 |
2 |
if ($_ =~ /\@PG.*PN:crac/) |
|
184
|
30 |
1 |
if ($line =~ /^@/) { } |