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.IX Title "Sanger::CGP::AlleleCount::Genotype 3pm"
.TH Sanger::CGP::AlleleCount::Genotype 3pm "2022-09-30" "perl v5.34.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.IP "new" 4
.IX Item "new"
Null constructor
.IP "configure" 4
.IX Item "configure"
Set up the object for the current analysis.
.Sp
.Vb 1
\&  $genotype\->configure(\*(Aqmy.bam\*(Aq, $min_pbq, $min_mapq [, $fasta])
.Ve
.IP "_wrap_c_alleleCounter" 4
.IX Item "_wrap_c_alleleCounter"
Generic function to generate allele counts from a chr\etpos\en formatted file (1\-based)
by calling the C version.
.Sp
Calling function should provided an intermediate path for the output if data needs reformatting for
\&\s-1SNP6\s0 style loci input files.
.IP "get_full_snp6_profile" 4
.IX Item "get_full_snp6_profile"
Writes tab seperated allelic counts and depth to specified \s-1FH\s0
Uses all snps defined in file used by ngs_cn (format slightly different)
.IP "get_full_loci_profile" 4
.IX Item "get_full_loci_profile"
Writes tab seperated allelic counts and depth to specified \s-1FH\s0
Uses all loci defined in specified file
.IP "gender_chk" 4
.IX Item "gender_chk"
Writes the chromosome name for the Male sex chromosome as defined by loci file and 'Y/N'
indicating presence of any of the SNPs.  E.g.
.Sp
.Vb 1
\&  chrX  Y
.Ve
.Sp
or
.Sp
.Vb 1
\&  X  N
.Ve
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 43:" 4
.IX Item "Around line 43:"
\&'=item' outside of any '=over'
.Sp
=over without closing =back