Bio::D...nstants(3pm)

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version 1.43 · 7 versions
, in ubuntu stonking

💖 Bio::DB::Sam::Constants — the group chat, but make it SAM/BAM 💖

okay so bestie, welcome to Bio::DB::Sam::Constants(3pm), coming at you from the User Contributed Perl Documentation section of the manual. This is the little stash of constants you use with SAM/BAM, and honestly? It's giving "small module, big main character energy." 🌸

✨ NAME ✨

Bio::DB::Sam::Constants — literally just constants for use with SAM/BAM. That's the whole job. She's a simple queen. 💅

🎀 SYNOPSIS 🎀

use Bio::DB::Sam::Constants;
my $pad_flag = BAM_CPAD;

See? Pull the module in, grab a constant, go live your life. No cap. 🦋

🌈 DESCRIPTION 🌈

This module exports a bunch of constants for use with the SAM/BAM module. For what they actually mean — the interpretation, the lore, the whole backstory — go read the SAM documentation, because that's where the real answers live. 📚

🧬 Cigar operations 🧬

Here's the full lineup of cigar-operation constants. Every single one, no skipping, we don't gatekeep here:

  • BAM_CIGAR_SHIFT
  • BAM_CIGAR_MASK
  • BAM_CMATCH
  • BAM_CINS
  • BAM_CDEL
  • BAM_CREF_SKIP
  • BAM_CSOFT_CLIP
  • BAM_CHARD_CLIP
  • BAM_CPAD

Slay. That's the set. ✨

🚩 FLAGS 🚩

A hashref that maps flag values to human-readable names. So when you've got a cryptic little number and you want to know what it feels, you look it up here. For example:

FLAGS->{0x0008} == 'M_UNMAPPED'

Look at her. Number in, name out. Iconic behaviour tbh. 👑

🔄 RFLAGS 🔄

The reverse of FLAGS — so instead of number ➡️ name, it's name ➡️ number. The page presents it like this, bestie, and we are copying it exactly as written:

FLAGS->{M_UNMAPPED} == 0x0008

(yes, it literally says FLAGS in that snippet in the source. Not me editing anything, I am a faithful narrator. 🙈)

👀 SEE ALSO 👀

Go check out her friends, they're all icons too:

  • Bio::Perl
  • Bio::DB::Sam
  • Bio::DB::Bam::Alignment

💜 AUTHOR 💜

Lincoln Stein <lincoln.stein@oicr.on.ca>. <lincoln.stein@bmail.com>

Copyright (c) 2009-2015 Ontario Institute for Cancer Research.

This package and its accompanying libraries are free software; you can redistribute it and/or modify it under the terms of the Artistic License 2.0, the Apache 2.0 License, or the GNU General Public License (version 1 or higher). Refer to LICENSE for the full license text. 🫶

Fr fr, that's the actual license situation — three options, pick your fighter, and read LICENSE if you want the whole thing spelled out.

And that's the page!! This was Bio::D...nstants(3pm) from perl v5.42.3, dated 2026-08-19. Thank you for coming to my TED talk, mwah, love you, bye!! 💖✨🎀🦋🌸💅👑

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