line |
true |
false |
branch |
81
|
0 |
0 |
unless $command
|
86
|
0 |
0 |
if $line =~ /^[\@](HD|SQ)/
|
93
|
0 |
0 |
unless -e $root_path
|
94
|
0 |
0 |
unless -d $root_path
|
95
|
0 |
0 |
unless -w $root_path
|
98
|
0 |
0 |
if (defined $chr) { }
|
99
|
0 |
0 |
if ($chr eq '*') { }
|
108
|
0 |
0 |
if (defined $bam)
|
133
|
0 |
0 |
unless system($full_command) == 0
|
143
|
0 |
0 |
unless &opendir(my $dh, $indir)
|
145
|
0 |
0 |
if $thing =~ /^[.]/
|
146
|
0 |
0 |
if $thing =~ /.*[.]o[.]sam$/
|
159
|
0 |
0 |
if (defined $exclude) { }
|
162
|
0 |
0 |
if (defined $chr)
|
170
|
0 |
0 |
defined $chr ? :
|
178
|
0 |
0 |
defined $chr ? :
|
|
0 |
0 |
defined $chr ? :
|
189
|
0 |
0 |
if substr($read1, 0, 1) eq '@'
|
190
|
0 |
0 |
unless ($read2 = <$process>)
|
203
|
0 |
0 |
unless ($read2)
|
213
|
0 |
0 |
unless defined $class
|
228
|
1 |
9 |
if $r1[$FLAG] & $READ_UNMAPPED and $r2[$FLAG] & $READ_UNMAPPED
|
230
|
1 |
0 |
if $r1[$FLAG] & $PROPER_PAIR and not $r1[$FLAG] & $READ_UNMAPPED and not $r2[$FLAG] & $READ_UNMAPPED
|
234
|
2 |
6 |
if (not $r1[$FLAG] & $READ_UNMAPPED and $r2[$FLAG] & $READ_UNMAPPED or not $r2[$FLAG] & $READ_UNMAPPED and $r1[$FLAG] & $READ_UNMAPPED) { }
|
236
|
0 |
2 |
if $r1[$FLAG] & $READ_UNMAPPED
|
239
|
0 |
6 |
if $r1[$MAPQ] == 0 and $r2[$MAPQ] == 0 or $r1[$MAPQ] == $r2[$MAPQ]
|
240
|
3 |
3 |
if $r1[$MAPQ] < $r2[$MAPQ]
|
241
|
4 |
2 |
if ($r1[$RNAME] eq $r2[$RNAME]) { }
|
250
|
0 |
8 |
unless defined $fasta
|
257
|
3 |
5 |
if $swap == 1
|
259
|
0 |
8 |
if $$r1[$MAPQ] == 0
|
260
|
0 |
8 |
unless index($$r2[$SEQ], $N_LIMIT) == -1
|
262
|
3 |
5 |
$$r1[$FLAG] & $READ_REVCOMP ? :
|
273
|
0 |
2 |
if defined $$self{'CANDIDATE_FH'}
|
274
|
0 |
2 |
if defined $$self{'ORPHAN_FH'}
|