| line |
true |
false |
branch |
|
37
|
6 |
1 |
if (defined $line) |
|
50
|
3 |
0 |
if ($sam_file =~ /\.sam$/) { } |
|
|
0 |
0 |
elsif ($self->{'sam_file'} =~ /\.sam.gz$/) { } |
|
|
0 |
0 |
elsif ($self->{'sam_file'} =~ /\.bam$/) { } |
|
51
|
0 |
3 |
unless open SAM, "< $sam_file" |
|
53
|
0 |
0 |
unless open SAM, "gunzip -c $sam_file |" |
|
55
|
0 |
0 |
unless open SAM, '-|', "samtools view -h $sam_file" |
|
57
|
0 |
0 |
unless open SAM, "< $sam_file" |
|
64
|
1 |
2 |
if (defined $option and $option eq 'IGNORE_HEADERS') { } |
|
66
|
1 |
3 |
unless ($line =~ /^@/) |
|
80
|
37 |
2 |
if ($sam_line) { } |
|
83
|
0 |
0 |
$! ? : |
|
|
0 |
2 |
unless close SAM |
|
100
|
0 |
1 |
unless defined $ref_seq |
|
111
|
25 |
5 |
if ($_ =~ /\@SQ.*SN:/) |
|
122
|
2 |
0 |
if (defined $self->header) { } |
|
126
|
2 |
4 |
if ($_ =~ /\@PG.*PN:crac/) |
|
141
|
2 |
0 |
if (defined $command_line) { } |
|
153
|
0 |
0 |
unless defined $option |
|
154
|
0 |
0 |
if (defined $self->commandLine) { } |
|
164
|
1 |
0 |
if (defined $self->header) { } |
|
168
|
1 |
2 |
if ($_ =~ /\@PG.*PN:crac/) |
|
185
|
30 |
1 |
if ($line =~ /^@/) { } |