| line |
true |
false |
branch |
|
166
|
6 |
1 |
if (defined $line) |
|
193
|
2 |
0 |
if ($sam_file =~ /\.sam$/) { } |
|
|
0 |
0 |
elsif ($$self{'sam_file'} =~ /\.sam.gz$/) { } |
|
|
0 |
0 |
elsif ($$self{'sam_file'} =~ /\.bam$/) { } |
|
194
|
0 |
2 |
unless open SAM, "< $sam_file" |
|
196
|
0 |
0 |
unless open SAM, "gunzip -c $sam_file |" |
|
198
|
0 |
0 |
unless open SAM, '-|', "samtools view -h $sam_file" |
|
206
|
1 |
1 |
if (defined $option and $option eq 'IGNORE_HEADERS') { } |
|
208
|
1 |
3 |
unless ($line =~ /^@/) |
|
222
|
10 |
1 |
if ($sam_line) { } |
|
257
|
0 |
0 |
unless defined $ref_seq |
|
261
|
0 |
0 |
if ($_ =~ /\@SQ.*SN:$ref_seq/) |
|
277
|
2 |
0 |
if (defined $self->header) { } |
|
281
|
2 |
4 |
if ($_ =~ /\@PG.*PN:crac/) |
|
301
|
2 |
0 |
if (defined $command_line) { } |
|
318
|
0 |
0 |
unless defined $option |
|
319
|
0 |
0 |
if (defined $self->commandLine) { } |
|
341
|
3 |
1 |
if ($line =~ /^@/) { } |