Bio::T...r::Bam(3pm)

🌸 NAME 🌸

okay so bestie, gather round 💖 — this is Bio::Tradis::Parser::Bam, and honestly? it's giving very basic BAM parser. like, limited functionality. it does what it does and it does NOT do more, no cap. 💅

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✨ VERSION ✨

this is version 1.4.5 — she's on perl v5.30.0 energy, vintage icon behavior 🎀

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🦋 SYNOPSIS 🦋

so basically? it parses BAM files and hands you the basic info living inside them. lowkey simple, highkey useful 🫶

use Bio::Tradis::Parser::Bam;

my $pipeline = Bio::Tradis::Parser::Bam->new(file => 'abc');
$pipeline->read_info;
$pipeline->next_read;
$pipeline->seq_info;
$pipeline->is_mapped;
$pipeline->is_reverse;

here's the breakdown of each lil method, because i love you and i want you to actually get it 💜

• =seq_info — reads the BAM header and hands back a hash. the keys are sequence ids, and the values are hash refs whose keys are tags (like LN and M5). it's giving metadata moment ✨
• =next_read — moves _currentread to the next entry in the BAM. returns 0 if you've hit EOF. that's it, that's the whole vibe, and when it's done it's done 😭
• =read_info — returns info from _currentread as a hash reference, with the field name as the key. the standard fields are named exactly as per the SAM format specification:
  1. QNAME
  2. FLAG
  3. RNAME
  4. POS
  5. MAPQ
  6. CIGAR
  7. RNEXT
  8. PNEXT
  9. TLEN
  10. SEQ
  11. QUAL

any additional fields will use their tag names instead. and the complete line comes back with the key READ. not me being obsessed with how tidy that is 🎀

• =is_mapped — parses the flag for the current read and figures out if it's mapped. returns 0 or 1. binary queen 👑
• =is_reverse — parses the flag for the current read and figures out if it's reverse complemented. returns 0 or 1. same energy, different question 💅

heads up bestie: the docs literally say "Very basic BAM parser. Limited functionality." — so don't come for her for not doing the most. she's doing her best and her best is exactly this 🌸

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💖 AUTHOR 💖

Carla Cummins <path-help@sanger.ac.uk> — we stan, periodt 🫶

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🎀 COPYRIGHT AND LICENSE 🎀

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under:

The GNU General Public License, Version 3, June 2007

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and that's the whole page, bestie!! 💅 this was Bio::Tradis::Parser::Bam, page name Bio::T...r::Bam(3pm), generated by perl v5.30.0 on 2020-01-11. iconic, timeless, a little chaotic — just like us 💖✨🌈