| line |
true |
false |
branch |
|
31
|
1 |
0 |
if (@tab > 0) |
|
47
|
0 |
0 |
if ($v1_nums[$i] >= $v2_nums[$i]) { } |
|
53
|
0 |
0 |
if (scalar @v2_nums > @v1_nums) { } |
|
64
|
50 |
0 |
defined $strand ? : |
|
88
|
0 |
1 |
if @pos_list == 0 |
|
93
|
1 |
0 |
if ($length % $Base64_BITNESS > 0) |
|
131
|
6 |
30 |
if ($index[$e] & 1 << $i) |
|
147
|
0 |
5 |
unless defined $file |
|
153
|
5 |
0 |
if (not defined $format) { } |
|
154
|
2 |
3 |
if ($file =~ /\.(fasta|fa)(\.|$)/) { } |
|
|
3 |
0 |
elsif ($file =~ /\.(fastq|fq)(\.|$)/) { } |
|
166
|
2 |
3 |
if ($format eq 'fasta') { } |
|
|
3 |
0 |
elsif ($format eq 'fastq') { } |
|
173
|
5 |
2 |
if (defined $prev_line) { } |
|
193
|
6 |
1 |
if defined $line |
|
194
|
6 |
1 |
if (defined $name) { } |
|
220
|
2 |
0 |
if (defined $entry1 and defined $entry2) { } |
|
231
|
0 |
0 |
if ($format eq 'fasta') { } |
|
|
0 |
0 |
elsif ($format eq 'fastq') { } |
|
266
|
0 |
0 |
unless defined $region |
|
269
|
0 |
0 |
if ($file =~ /\.bam$/) { } |
|
270
|
0 |
0 |
unless open $fh, '-|', "samtools view $file $region" |
|
284
|
0 |
0 |
unless defined $format |
|
290
|
0 |
0 |
unless ($fasta_seq =~ /^>\S+\n\S+/) |
|
294
|
0 |
0 |
if ($format eq 'raw') |
|
309
|
1 |
0 |
if (defined $block_starts) |
|
344
|
1 |
0 |
if ($type =~ /gff3/i) { } |
|
|
0 |
0 |
elsif ($type eq 'gtf' or $type eq 'gff2') { } |
|
356
|
4 |
0 |
if (defined $k and defined $v) |
|
377
|
1 |
0 |
defined $alt ? : |
|
379
|
1 |
0 |
defined $info ? : |
|
406
|
0 |
0 |
if (defined $key and defined $val) |
|
473
|
0 |
4 |
unless defined $file |
|
475
|
3 |
1 |
if (not defined $parsing_method and defined $type) |
|
476
|
1 |
2 |
if ($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) { } |
|
499
|
0 |
4 |
unless defined $parsing_method |
|
511
|
0 |
4 |
if (defined $skip) |
|
519
|
4 |
0 |
if (defined $header_regex) |
|
528
|
34 |
1 |
if (defined $line) { } |
|
548
|
0 |
10 |
if ($file =~ /\.gz$/) { } |
|
549
|
0 |
0 |
unless open $fh, "gunzip -c $file |" |
|
551
|
0 |
10 |
unless open $fh, "< $file" |
|
560
|
0 |
0 |
if ($file =~ /\.gz$/) { } |
|
561
|
0 |
0 |
unless open $fh, "| gzip > $file" |
|
563
|
0 |
0 |
unless open $fh, "> $file" |