Branch Coverage

lib/Sanger/CGP/TraFiC/Parser.pm
Criterion Covered Total %
branch 20 70 28.5


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'}