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add ex-zd to docs
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hasindu2008 committed Sep 26, 2024
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4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -142,10 +142,10 @@ A slow5 library for RUST programming language developed by [@bsaintjo](https://g

### Current limitations & future work

slow5lib is a reference implementation for SLOW5 format. Depending on the interest from the community, the following limitations could be overcome and more performance optimis ations can be performed. Open a GitHub issue if you are interested. Contributions are welcome.
slow5lib is a reference implementation for SLOW5 format. Depending on the interest from the community, the following limitations could be overcome and more performance optimisations can be performed. Open a GitHub issue if you are interested. Contributions are welcome.

- No native windows support: slow5lib works well on Windows through WSL, in fact, this is my primary development environment. I am not aware of anyone using native Windows for nanopore bioinformatics. However, if needed, [methods used for minimap2](https://github.com/lh3/minimap2/issues/19) can be adopted.
- svb-zd compression does not big-endian systems: As of version 1.2.0, slow5lib supports big-endian systems (e.g., IBM Z), except for svb-zd compression that uses [StreamVByte](https://github.com/lemire/streamvbyte) that does not support big-endian.
- svb-zd and ex-zd compression does not support big-endian systems: As of version 1.2.0, slow5lib supports big-endian systems (e.g., IBM Z), except for svb-zd and ex-zd compression that uses [StreamVByte](https://github.com/lemire/streamvbyte) that does not support big-endian.
Note: Not to be confused with big.LITTLE architecture which is something else on which all features of slow5lib already works.
- When running with >64 threads, malloc() calls could reduce the thread efficiency. If that is the case, frequent mallocs could be replaced with kalloc in [klib](https://github.com/attractivechaos/klib). Alternatively, preloading tcmalloc or jemalloc would do.
- Aggressive compiler optimisations (e.g., -O3) and architecture-specific compiler optimisations (e.g., -march=native) are not used in the makefile. These flags will improve performance at the cost of limited portability. These could be provided in a separate make target.
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2 changes: 1 addition & 1 deletion docs/pyslow5_api/pyslow5.md
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Expand Up @@ -139,7 +139,7 @@ Compression Options:
`sig_press`:
- "none"
- "svb-zd" [default]
- "ex-zd" [best compression]
- "ex-zd" [best compression, available from v1.3.0]

Example:

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1 change: 1 addition & 0 deletions docs/slow5_api/slow5_set_press.md
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Expand Up @@ -21,6 +21,7 @@ slow5_set_press - sets the compression method for a BLOW5 file opened for writin
*sig_press* can be one of the following:
* `SLOW5_COMPRESS_NONE` No compression
* `SLOW5_COMPRESS_SVB_ZD` Stream variable byte - zig-zag delta (default)
* `SLOW5_COMPRESS_EX_ZD` Exception coding - zig-zag delta (available from slow5lib v1.3.0)

## RETURN VALUE

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