Ali Ghaffaari

[Alignment] Multiple Sequence Alignment (MSA) and Alignment Graph

10

## Question I have just started using seqan3. I have worked with seqan2 though. I want to ask about multiple sequence alignment and alignment graphs in seqan3. I could not...

Using reference member prevents defining assignment operator for the iterator class of int_vector_buffer. This commit fixes #436.

The iterator type of `int_vector_buffer` has a non-static reference member to the container: https://github.com/simongog/sdsl-lite/blob/c32874cb2d8524119f25f3b501526fe692df29f4/include/sdsl/int_vector_buffer.hpp#L492 This prevents creating default assignment operator. For example, compiling this snippet ```c++ sdsl::int_vector_buffer< 32 > entries;...

I am using `pkg-config` for my package checking for `sdsl-lite` version. It seems that VERSION does not reflect the actual version of the library which causes my `configure` script to...

Use TMPDIR instead of cwd for temporary files during construction

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In `cache_config` [constructor](https://github.com/simongog/sdsl-lite/blob/8f5245ff17f0a8799f4bc6c650a0db527403e4c1/include/sdsl/config.hpp#L45), the default directory for temporary files is initialised by current working directory (`./`). It would be more convenient if it uses the value of TMPDIR environment variable...

Add sdsl-lite-vgteam recipe

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This is [vgteam's](https://github.com/vgteam) fork of the Succinct Data Structure Library (SDSL). The original [SDSL 2](https://github.com/simongog/sdsl-lite) is already on [conda-forge](https://github.com/conda-forge/sdsl-lite-feedstock), but the project is no longer maintained. This is one of...

Building on Apple M1

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I am trying to build gfaviz on Apple M1 (macos 12.0.1). I came across a couple of issues. First, it complained about missing _wchar.h_ header file -- the same issue...

Suggested in #2, there should be a section in the README file explaining how to install the library and alternatively how to bundle it in the source tree without installation...

The seed hits are not stored anywhere right now. Until resolving issue #7, saving the intermediate seed hits to a file would be useful. A command-line option should be added...

The reads should be aligned to the candidate locations by extending the seed hits found during the seed finding phase. All alignments will be reported based on the seed hits.