Branch Coverage

blib/lib/Sanger/CGP/AlleleCount/Genotype.pm
Criterion Covered Total %
branch 13 36 36.1


line true false branch
66 0 12 if defined $fasta
94 0 12 if (defined $self->{'$fasta'})
97 12 0 if ($ENV{'ALLELE_C_SILENT'})
100 0 12 if system $command
119 0 6 unless open my $N_LOC, '>', $tmp_loci
120 0 6 unless open my $SNP6, '<', $loci_file
133 0 6 unless open my $cfh, '<', $tmp_out
134 0 6 unless open my $ofh, '>', $out_file
136 0 6 unless print $ofh "#CHR\tPOS\tCount_Allele_A\tCount_Allele_B\tGood_depth\n"
139 6 6 if $line =~ /^#/
188 0 0 unless open my $fh, '<', $tmp_out
190 0 0 if $line =~ /^#/
193 0 0 if (defined $sex_chr) { }
194 0 0 if $chr ne $sex_chr
199 0 0 if ($depth > 5)
206 0 0 unless open my $ofh, '>', $out_file
216 0 12 unless -e $path
217 0 12 unless defined $path and -e $path