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

💅 Bio::D...rapper(3pm)

okay bestie, pull up a chair, we're looking at Bio::DB::Bam::AlignWrapper — that's a User Contributed Perl Documentation page, and it's genuinely serving. 🎀

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✨ NAME ✨

Bio::DB::Bam::AlignWrapper — it's the glow-up edition: adds all the high-level methods to Bio::DB::Bam::Alignment 🦋

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🌸 SYNOPSIS 🌸

No synopsis of its own, babe. Go look at Bio::DB::Bam::Alignment. 👀

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💖 DESCRIPTION 💖

So here's the whole vibe: this thing is a wrapper around Bio::DB::Bam::Alignment, and what it does is add the high-level methods listed below. All of them are described in full detail in the section "High-level Bio::DB::Bam::Alignment methods" over in Bio::DB::Bam::Alignment. Go read that for the deep dive, fr fr.

And here's the full menu, nothing skipped, we don't gatekeep here:

 add_segment()         add a new subfeature to split alignments
 get_SeqFeatures()     fetch subfeatures from split alignments
 split_splices()       process cigar strings to produce split alignments
 expand_flags()        return true if flags should be expanded into tags
 seq_id()              return human-readable reference sequence name
 seq()                 return Bio::PrimarySeq object for reference sequence
 subseq()              return a subsequence across the indicated range
 mate_seq_id()         return human-readable mate reference sequence name
 dna()                 return the DNA of the reference sequence
 tam_line()            return the text representation of the alignment
 attributes()          synonym for get_tag_values()
 get_all_tags()        return all tag names
 get_tag_values()      return the values of the given tag
 has_tag()             return true if the given tag is defined

^^ that's the whole lineup, all 14, main character energy each and every one. 💅

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🫶 SEE ALSO 🫶

Go be nosy in these, they're iconic:

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

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👑 AUTHOR 👑

Lincoln Stein — lincoln.stein@oicr.on.ca — and also 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. Three options?? we love a choose-your-own-adventure licensing moment. ✨

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no cap, that's the entire page. every method, every license, every email. nothing left behind. 🧚

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and that's a wrap, bestie!! 🎀 this whole thing comes to you from perl v5.42.3, dated 2026-08-19, and it lives in the manual as Bio::D...rapper(3pm). mwah, take care of her. 💖💅✨