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

👑 Bio::DB::Bam::Pileup — the manual page, but make it cute

okay bestie, so this is Bio::D...Pileup(3pm) from the User Contributed Perl Documentation, and it's literally the manual for Bio::DB::Bam::Pileup 💅 pull up a chair, we're doing bioinformatics today.

---

✨ NAME ✨

Bio::DB::Bam::Pileup — the little object that gets handed to your pileup() callback 🎀

---

🌸 SYNOPSIS 🌸

See "The generic fetch() and pileup() methods" in Bio::DB::Sam for how
this object is passed to pileup callbacks.

that's it, that's the synopsis hun 💖 if you wanna know how this cutie actually reaches you, go read that section in Bio::DB::Sam.

---

🦋 DESCRIPTION 🦋

so here's the vibe 🌈: a Bio::DB::Bam::Pileup object — or a Bio::DB::Bam::PileupWrapper object — gets passed to the callback you give to the Bio::DB::Sam->pileup() method, one for every single column in a sequence alignment. yes, every column. she's thorough like that 😌

and the only difference between the two of them? the wrapper one (Bio::DB::Bam::PileupWrapper) returns the way more convenient Bio::DB::Bam::AlignWrapper objects when you call alignment() on it 💅✨ but bestie, nothing in this life is free — you pay for it with some performance loss 😭 keep that in mind.

🧚 Methods

• $alignment = $pileup->alignment — hands you back the Bio::DB::Bam::Alignment or Bio::DB::Bam::AlignWrapper object that represents the aligned read 🫶
• $alignment = $pileup->b — this one's just an alias for alignment(). she exists purely for compatibility with the C API, no cap 🤝
• $qpos = $pileup->qpos — returns the position of this aligned column in read coordinates, using zero-based coordinates 🔢
• $pos = $pileup->pos — same energy, but returns the position of this aligned column in read coordinates using 1-based coordinates. (yes the label is different-looking, that's literally what it says, don't come for me 🙈)
• $indel = $pileup->indel — if this column is an indel, she'll return a positive integer for an insertion relative to the reference, a negative integer for a deletion relative to the reference, or 0 if there's no indel at this column. three moods, one method 💀
• $is_del = $pileup->is_del — true if the base on the padded read is a deletion ✅
• $level = $pileup->level — if pileup() or fast_pileup() was invoked with the "keep_level" flag, then this returns a positive integer telling you the level of the read in a printed multiple alignment 📊 (no keep_level flag = no level for you, babe)
• $pileup->is_head
• $pileup->is_tail

— these two fields are defined in bam.h but their interpretation is obscure 🌫️ like, genuinely, nobody's explaining them here. mystery behavior. iconic in a cryptic way, honestly 😭

---

💜 SEE ALSO 💜

go read these next, bestie, they're all connected:

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

---

🎀 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 📜✨

---

and that's the whole page, bestie, you ate it 💅 no cap, fr fr.

perl v5.42.3 🦋 2026-08-19 🎀 — mwah, go read your pileups, ily 💖