Rust rewrite

Author: bede

README.md

@@ -2,16 +2,17 @@
 
 # Seqsum
 
-Robust checksums for nucleotide sequences. Accepts input from either standard input or `fast[a|q][.gz|.zst|.xz|.bz2]` files. Generates individual checksums for each sequence, plus an aggregate checksum for a collection. Warnings are shown for duplicate sequences and within-collection checksum collisions at the selected bit depth. Sequences are uppercased before hashing with [rapidhash](https://github.com/Nicoshev/rapidhash) (`v3`) and may be normalised (with `-n`) to use only `ACGTN-`. Read IDs and FASTQ base quality scores do not inform the checksum. Output is tab-delimited text to stdout.
+> [!WARNING]  
+> Seqsum was rewritten in Rust in 0.3.0. The original Python version of seqsum and how to use is archived in the [`python`](https://github.com/bede/seqsum/tree/python) branch. It remains available on PyPI.
 
-By default, seqsum outputs individual checksums and, when there is more than one sequence, an aggregate checksum. This can be modified with `--individual` (`-i`) or `--aggregate` (`-a`).
+Robust checksums for nucleotide sequences. Accepts input from either standard input or `fast[a|q][.gz|.zst]` files. Generates *individual* checksums for each sequence, plus an *aggregate* checksum for a collection. Warnings are shown for duplicate sequences and within-collection checksum collisions at the selected bit depth. Sequences are uppercased before hashing with [RapidHash](https://github.com/Nicoshev/rapidhash) (v3) and may be normalised (with `-n`) to use only `ACGTN-`. Read IDs and FASTQ base quality scores do not inform the checksum. Output is tab-delimited text to stdout.
 
-Uses [`paraseq`](https://github.com/mbhall88/paraseq) for efficient FASTA/FASTQ parsing.
+By default, seqsum outputs individual checksums and, when there is more than one sequence, an aggregate checksum. This can be modified with `--individual` (`-i`) or `--aggregate` (`-a`).
 
 ## Install
 
 ```bash
-cargo install --path .
+cargo install seqsum
 ```
 
 ## Development
@@ -20,8 +21,6 @@ cargo install --path .
 git clone https://github.com/bede/seqsum.git
 cd seqsum
 cargo test
-cargo fmt --all --check
-cargo clippy --all-targets -- -D warnings
 ```
 
 ## Command line usage
@@ -52,3 +51,4 @@ $ cat tests/data/MN908947.fasta | seqsum -
 ```bash
 $ seqsum -h
 ```
+