seqan3

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FEATURE: add seqan3::default_printer

4

This PR will resolve seqan/product_backlog#63. This issue is a long-standing open to-do of mine. I hope that you can take it over and push it over the finishing line. The...

marehr

Convert vertor<dna5> to std:string

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## Platform - SeqAn version: 3.2.0 - Operating system: Ubuntu - Compiler: 11.4 ## Question With the following code, is there any way to Convert vertor to std:string as I...

nhhaidee

output_sequence1_id and output_sequence2_id are same

4

Hi there, Thanks so much for this excellent C++ library for bioinformatics. I had a question when I was using it; please have a look at the following, ## Platform...

JappyPing

alignment slice positions

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## Platform - SeqAn version: 3.3.0 ## Question Is there a documented way to extract, from a pairwise alignment result, the alignment slice positions (equivalent to the coordinates[] list of...

notestaff

several same-score pairwise alignments

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## Platform - SeqAn version: 3.3.0 - Operating system: > Linux bpb23-acc 5.4.0-136-generic #153-Ubuntu SMP Thu Nov 24 15:56:58 UTC 2022 x86_64 x86_64 x86_64 GNU/Linux - Compiler: x86_64-conda-linux-gnu-c++ (conda-forge gcc...

notestaff

Tests fail to compile

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### Does this problem persist on the current master? - [X] I have verified the issue on the current master ### Is there an existing issue for this? - [X]...

yurivict

Use OS/system packaged sdsl library

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## Platform - SeqAn version: 3.2.0 - Operating system: Archlinux - Compiler: gcc 13.1.1 ## Question Is there a way to use sdsl library packaged in distribution repository? we have...

kbipinkumar

Allow min_score alignment config for arbitrary (user defined) edit distance schemes

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I want to align sequences with a custom `uint8_t` based alphabet and edit distance. I also have a bound on the number of allowed errors in the alignment, so I...

feldroop

Multi-threading, banding, other speed-ups

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## Platform - SeqAn version: 3 - Operating system: `Linux raptor.ucsd.edu 5.4.0-149-generic #166-Ubuntu SMP Tue Apr 18 16:51:45 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux` - Compiler: gcc (Ubuntu 13.1.0-8ubuntu1~20.04.2) 13.1.0...

jaysunl

Refactor selection of Myers' bitparallel edit distance algorithm.

1

This PR fixes #3253 by: 1. adding a new dedicated scoring scheme for enabling hamming distance, which is agnostic to the alphabet type, 2. switching to use this hamming scoring...

rrahn