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

💖 Bio::DB::HTS::AlignWrapper(3pm) 💖

okay bestie, welcome to the AlignWrapper page ✨ this is a Perl manual page (3pm, so it's a module, iykyk) and it's literally just a glow-up layer. no cap.

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📜 LICENSE

Copyright [2015-2018] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

fr fr, that's the whole legal vibe. Apache 2.0, no warranty, read it before you ship it 💅

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✨ NAME ✨

Bio::DB::HTS::AlignWrapper -- Add high-level methods to Bio::DB::HTS::Alignment

like. that's the whole point of her. she's an add-on. a little extra. main character energy applied to an alignment object 🎀

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🦋 SYNOPSIS 🦋

See Bio::DB::HTS::Alignment.

that's it. that's the synopsis. she's mysterious, she's lowkey, she's pointing you at her sister page 🙈

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💅 DESCRIPTION 💅

So here's the tea: this module is a wrapper around Bio::DB::HTS::Alignment that adds the following high-level methods. The full details live over in "High-level Bio::DB::HTS::Alignment methods" in Bio::DB::HTS::Alignment — go read that one too, bestie, it's giving required reading 📚

Every single one of the methods she brings to the table:

• add_segment() — adds a brand new subfeature, which is how you split alignments 🧚
• get_SeqFeatures() — grabs the subfeatures back out of split alignments
• split_splices() — chews through cigar strings to produce split alignments (yes, cigar strings, iconic name, no notes) 🔥
• expand_flags() — returns true if flags should be expanded into tags
• seq_id() — hands you the human-readable reference sequence name
• seq() — returns a Bio::PrimarySeq object for the reference sequence
• subseq() — returns a subsequence across the range you indicate
• mate_seq_id() — gives you the human-readable mate reference sequence name
• dna() — returns the DNA of the reference sequence 🧬
• tam_line() — returns the text representation of the alignment
• attributes() — a synonym for get_tag_values()
• get_all_tags() — returns every tag name
• get_tag_values() — returns the values of the tag you asked for
• has_tag() — returns true if the given tag is defined

not me listing all fourteen like a good student 😭 yes there are fourteen. count them. we don't skip. periodt.

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🌈 SEE ALSO 🌈

• Bio::Perl
• Bio::DB::HTS
• Bio::DB::HTS::Constants

go follow them, they're mutuals 🫶

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👑 AUTHOR 👑

Rishi Nag <rishi@ebi.ac.uk<gt>

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and that's a wrap, bestie!! this page shipped as part of perl v5.40.0, dated 2024-10-31, in the User Contributed Perl Documentation collection 💖✨ you read the whole thing, you ate, no crumbs. slay 🎀🦋💜