Sanger...notype(3pm)

🌸 ok so… Sanger...notype 💅

Bestie. Sit down. Grab a boba. This is a User Contributed Perl Documentation page — that's the 3pm energy, meaning it's a Perl module manual, not a command you run in your shell. No cap.

It's giving Sanger, it's giving genotype, and honestly? The methods are kinda iconic. Let's get into it. 🦋

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✨ new — the Null constructor 🎀

That's it. That's the whole thing. It's a null constructor, bestie. It does not elaborate, it does not explain itself, and we respect that. main character energy, honestly. 💜

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✨ configure — set it up for the current analysis 🌈

Like, actually set up the object so it knows what analysis we're doing. You call it like this:

$genotype->configure('my.bam', $min_pbq, $min_mapq [, $fasta])

So: your BAM file, a $min_pbq, a $min_mapq, and optionally a $fasta. That's the whole vibe. 🫶

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✨ _wrap_c_alleleCounter — the C-version plug 🔥

Ok so this one is a generic function that generates allele counts from a chr\tpos\n formatted file — and yes, that's 1-based, don't come for me — by calling the C version. Slay.

The calling function should provide an intermediate path for the output if the data needs reformatting for SNP6 style loci input files. So like, if your data needs a glow-up before it can hang with SNP6 style loci input files, that intermediate path is where it happens. ✨

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✨ get_full_snp6_profile — the SNP6 dump 💖

Writes tab seperated allelic counts and depth to the specified FH. (Yes, "seperated." We're keeping it. It's canon. 🙈)

It uses all snps defined in the file used by ngs_cn — and heads up, that format is slightly different. Noted. 💅

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✨ get_full_loci_profile — the loci dump 🧚

Writes tab seperated allelic counts and depth to the specified FH, and uses all loci defined in the specified file. Same energy as the SNP6 one, different source file. Periodt. 👑

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✨ gender_chk — the chromosome reveal ⭐

Writes the chromosome name for the Male sex chromosome as defined by the loci file, plus 'Y/N' indicating presence of any of the SNPs. E.g.

chrX  Y

or

X  N

Like… a whole vibe check for your SNPs. 🌸

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💀 POD ERRORS

Ok bestie, don't panic, but the doc itself had some coding errors, and they are explained below. This is not on us, it's just what it says:

Around line 43:

• '=item' outside of any '=over'
• =over without closing =back

So the POD formatting got a little feral. It happens to the best of us. 😭

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That's the whole page, bb. This little masterpiece is running on perl v5.40.0 and it was dated 2024-12-10. Bye bestie, go count some alleles 💖✨🎀