------------------------------------------------- ------ ------ ------ ------
File                                                bran    sub    pod  total
------------------------------------------------- ------ ------ ------ ------
blib/lib/Sanger/CGP/AlleleCount.pm                   n/a  100.0    n/a  100.0
blib/lib/Sanger/CGP/AlleleCount/Genotype.pm         36.1   93.7  100.0   57.8
Total                                               36.1   94.4  100.0   59.3
------------------------------------------------- ------ ------ ------ ------


Run:          t/1_pm_compile.t
Perl version: 5.22.1
OS:           linux
Start:        Tue Mar  6 10:58:25 2018
Finish:       Tue Mar  6 10:58:25 2018

Run:          t/2_pl_compile.t
Perl version: 5.22.1
OS:           linux
Start:        Tue Mar  6 10:58:26 2018
Finish:       Tue Mar  6 10:58:26 2018

Run:          t/genotype.t
Perl version: 5.22.1
OS:           linux
Start:        Tue Mar  6 10:58:27 2018
Finish:       Tue Mar  6 10:58:27 2018

Covered Subroutines
-------------------

Subroutine Count Location                             
---------- ----- -------------------------------------
BEGIN          2 blib/lib/Sanger/CGP/AlleleCount.pm:25
BEGIN          2 blib/lib/Sanger/CGP/AlleleCount.pm:27


Branches
--------

line  err      %   true  false   branch
----- --- ------ ------ ------   ------
66    ***     50      0     12   if defined $fasta
94    ***     50      0     12   if (defined $self->{'$fasta'})
97    ***     50     12      0   if ($ENV{'ALLELE_C_SILENT'})
100   ***     50      0     12   if system $command
119   ***     50      0      6   unless open my $N_LOC, '>', $tmp_loci
120   ***     50      0      6   unless open my $SNP6, '<', $loci_file
133   ***     50      0      6   unless open my $cfh, '<', $tmp_out
134   ***     50      0      6   unless open my $ofh, '>', $out_file
136   ***     50      0      6   unless print $ofh "#CHR\tPOS\tCount_Allele_A\tCount_Allele_B\tGood_depth\n"
139          100      6      6   if $line =~ /^#/
188   ***      0      0      0   unless open my $fh, '<', $tmp_out
190   ***      0      0      0   if $line =~ /^#/
193   ***      0      0      0   if (defined $sex_chr) { }
194   ***      0      0      0   if $chr ne $sex_chr
199   ***      0      0      0   if ($depth > 5)
206   ***      0      0      0   unless open my $ofh, '>', $out_file
216   ***     50      0     12   unless -e $path
217   ***     50      0     12   unless defined $path and -e $path


Covered Subroutines
-------------------

Subroutine            Count Pod Location                                       
--------------------- ----- --- -----------------------------------------------
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:24 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:26 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:27 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:28 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:30 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:31 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:32 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:34 
BEGIN                     2     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:36 
_alleleCounter_c         12     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:213
_wrap_c_alleleCounter    12     blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:82 
configure                12   1 blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:65 
get_full_loci_profile     6   1 blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:161
get_full_snp6_profile     6   1 blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:111
new                       3   1 blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:50 

Uncovered Subroutines
---------------------

Subroutine            Count Pod Location                                       
--------------------- ----- --- -----------------------------------------------
gender_chk                0   1 blib/lib/Sanger/CGP/AlleleCount/Genotype.pm:180


