| line |
true |
false |
branch |
|
30
|
1 |
0 |
if (@tab > 0) |
|
46
|
0 |
0 |
if ($v1_nums[$i] >= $v2_nums[$i]) { } |
|
52
|
0 |
0 |
if (scalar @v2_nums > @v1_nums) { } |
|
81
|
0 |
5 |
unless defined $file |
|
87
|
5 |
0 |
if (not defined $format) { } |
|
88
|
2 |
3 |
if ($file =~ /\.(fasta|fa)(\.|$)/) { } |
|
|
3 |
0 |
elsif ($file =~ /\.(fastq|fq)(\.|$)/) { } |
|
100
|
2 |
3 |
if ($format eq 'fasta') { } |
|
|
3 |
0 |
elsif ($format eq 'fastq') { } |
|
107
|
5 |
2 |
if (defined $prev_line) { } |
|
127
|
6 |
1 |
if defined $line |
|
128
|
6 |
1 |
if (defined $name) { } |
|
154
|
2 |
0 |
if (defined $entry1 and defined $entry2) { } |
|
165
|
0 |
0 |
if ($format eq 'fasta') { } |
|
|
0 |
0 |
elsif ($format eq 'fastq') { } |
|
200
|
0 |
0 |
unless defined $region |
|
203
|
0 |
0 |
if ($file =~ /\.bam$/) { } |
|
204
|
0 |
0 |
unless open $fh, '-|', "samtools view $file $region" |
|
218
|
0 |
0 |
unless defined $format |
|
224
|
0 |
0 |
unless ($fasta_seq =~ /^>\S+\n\S+/) |
|
228
|
0 |
0 |
if ($format eq 'raw') |
|
243
|
1 |
0 |
if (defined $block_starts) |
|
278
|
1 |
0 |
if ($type =~ /gff3/i) { } |
|
|
0 |
0 |
elsif ($type eq 'gtf' or $type eq 'gff2') { } |
|
341
|
0 |
0 |
if (defined $key and defined $val) |
|
397
|
0 |
5 |
unless defined $file |
|
399
|
3 |
2 |
if (not defined $parsing_method and defined $type) |
|
400
|
1 |
2 |
if ($type =~ /gff3/i or $type eq 'gtf' or $type eq 'gff2') { } |
|
|
1 |
1 |
elsif ($type =~ /bed/i) { } |
|
|
1 |
0 |
elsif ($type =~ /vcf/i) { } |
|
|
0 |
0 |
elsif ($type =~ /chimCT/i) { } |
|
|
0 |
0 |
elsif ($type =~ /SAM/i or $type =~ /BAM/i) { } |
|
423
|
0 |
5 |
unless defined $parsing_method |
|
435
|
0 |
5 |
if (defined $skip) |
|
443
|
5 |
0 |
if (defined $header_regex) |
|
452
|
37 |
2 |
if (defined $line) { } |
|
471
|
0 |
11 |
if ($file =~ /\.gz$/) { } |
|
472
|
0 |
0 |
unless open $fh, "gunzip -c $file |" |
|
474
|
0 |
11 |
unless open $fh, "< $file" |
|
483
|
0 |
0 |
if ($file =~ /\.gz$/) { } |
|
484
|
0 |
0 |
unless open $fh, "| gzip > $file" |
|
486
|
0 |
0 |
unless open $fh, "> $file" |