chore: Update README.md, check gc

Author: St4NNi

README.md

@@ -1,5 +1,6 @@
 [![Rust](https://img.shields.io/badge/built_with-Rust-dca282.svg)](https://www.rust-lang.org/)
 [![License](https://img.shields.io/badge/License-MIT-brightgreen.svg)](https://github.com/St4NNi/jam-rs/blob/main/LICENSE)
+[![Crates.io](https://img.shields.io/crates/v/jam-rs.svg)](https://crates.io/crates/jam-rs)
 [![Codecov](https://codecov.io/github/St4NNi/jam-rs/coverage.svg?branch=main)](https://codecov.io/gh/St4NNi/jam-rs)
 [![Dependency status](https://deps.rs/repo/github/St4NNi/jam-rs/status.svg)](https://deps.rs/repo/github/St4NNi/jam-rs)
 ___
@@ -9,7 +10,7 @@ ___
 Just another minhash (jam) implementation. A high performance minhash variant to screen extremely large (metagenomic) datasets in a very short timeframe.
 Implements parts of the ScaledMinHash / FracMinHash algorithm described in [sourmash](https://joss.theoj.org/papers/10.21105/joss.00027).
 
-Unlike traditional implementations like [sourmash](https://joss.theoj.org/papers/10.21105/joss.00027) or [mash](https://doi.org/10.1186/s13059-016-0997-x) this version tries to specialise more on estimating the containment of small sequences in large sets. This is intended to be used to screen terabytes of data in just a few seconds / minutes.
+Unlike traditional implementations like [sourmash](https://joss.theoj.org/papers/10.21105/joss.00027) or [mash](https://doi.org/10.1186/s13059-016-0997-x) this version tries to focus on estimating the containment of small sequences in large sets by (optionally) introducing an intentional bias towards smaller sequences. This is intended to be used to screen terabytes of data in just a few seconds / minutes.
 
 ### Installation
 
@@ -19,17 +20,17 @@ A pre-release is published via [crates.io](https://crates.io/) to install it use
 cargo install jam-rs
 ```
 
-If you want the bleeding edge development release you can install via git:
+If you want the bleeding edge development release you can install it via git:
 
 ```bash
 cargo install --git https://github.com/St4NNi/jam-rs
 ```
 
 ### Comparison
 
-- [xxhash3](https://github.com/DoumanAsh/xxhash-rust) or [ahash-fallback](https://github.com/tkaitchuck/aHash/wiki/AHash-fallback-algorithm) (for kmer < 32) instead of [murmurhash3](https://github.com/mhallin/murmurhash3-rs)
+- Multiple algorithms: [xxhash3](https://github.com/DoumanAsh/xxhash-rust), [ahash-fallback](https://github.com/tkaitchuck/aHash/wiki/AHash-fallback-algorithm) (for kmer < 32) and legacy [murmurhash3](https://github.com/mhallin/murmurhash3-rs)
 - No jaccard similarity since this is meaningless when comparing small embeded sequences against large sets
-- (coming soon) optimisations for specificity and sensitivity (and speed) specifically for search of small sequences in assembled metagenomes
+- Additional filter and sketching options to increase for specificity and sensitivity for small sequences in collections of large assembled metagenomes
 
 ### Scaling methods
 
@@ -44,12 +45,12 @@ If `KmerCountScaling` and `MinMaxAbsoluteScaling` are used together the minimum
 
 ```console
 $ jam
-Just another minhasher, obviously blazingly fast
+Just another (genomic) minhasher (jam), obviously blazingly fast
 
 Usage: jam [OPTIONS] <COMMAND>
 
 Commands:
-  sketch  Sketches one or more files and writes the result to an output file
+  sketch  Sketch one or more files and write result to output file (or stdout)
   merge   Merge multiple input sketches into a single sketch
   dist    Estimate distance of a (small) sketch against a subset of one or more sketches as database. Requires all sketches to have the same kmer size
   help    Print this message or the help of the given subcommand(s)
@@ -67,7 +68,7 @@ The easiest way to sketch files is to use the `jam sketch` command. This accepts
 
 ```console
 $ jam sketch
-Sketch one or more files and write result to output file (or stdout)
+Sketch one or more files and write the result to an output file (or stdout)
 
 Usage: jam sketch [OPTIONS] [INPUT]...
 
@@ -76,13 +77,13 @@ Arguments:
 
 Options:
   -o, --output <OUTPUT>        Output file
-  -k, --kmer-size <KMER_SIZE>  kmer size all sketches to be compared must have the same size [default: 21]
+  -k, --kmer-size <KMER_SIZE>  kmer size, all sketches must have the same size to be compared [default: 21]
       --fscale <FSCALE>        Scale the hash space to a minimum fraction of the maximum hash value (FracMinHash)
       --kscale <KSCALE>        Scale the hash space to a minimum fraction of all k-mers (SizeMinHash)
   -t, --threads <THREADS>      Number of threads to use [default: 1]
   -f, --force                  Overwrite output files
-      --nmin <NMIN>            Minimum number of k-mers (per record) to be hashed
-      --nmax <NMAX>            Maximum number of k-mers (per record) to be hashed
+      --nmin <NMIN>            Minimum number of k-mers (per record) to be hashed, bottom cut-off
+      --nmax <NMAX>            Maximum number of k-mers (per record) to be hashed, top cut-off
       --format <FORMAT>        Change to other output formats [default: bin] [possible values: bin, sourmash]
       --algorithm <ALGORITHM>  Change the hashing algorithm [default: default] [possible values: default, ahash, xxhash, murmur3]
       --singleton              Create a separate sketch for each sequence record
@@ -95,9 +96,9 @@ Calculate the distance for one or more inputs vs. a large set of database sketch
 
 ```console
 $ jam dist
-Calculate distance of a (small) sketch against one or more sketches as database. Requires all sketches to have the same kmer size
+Estimate containment of a (small) sketch against a subset of one or more sketches as database. Requires all sketches to have the same kmer size
 
-Usage: jam dist [OPTIONS] --input <INPUT> --database <DATABASE>
+Usage: jam dist [OPTIONS] --input <INPUT>
 
 Options:
   -i, --input <INPUT>        Input sketch or raw file
@@ -106,12 +107,13 @@ Options:
   -c, --cutoff <CUTOFF>      Cut-off value for similarity [default: 0.0]
   -t, --threads <THREADS>    Number of threads to use [default: 1]
   -f, --force                Overwrite output files
+      --stats                Use the Stats params for restricting results
+      --gc-lower <GC_LOWER>  Use GC stats with an upper bound of x% (gc_lower and gc_upper must be set)
+      --gc-upper <GC_UPPER>  Use GC stats with an lower bound of y% (gc_lower and gc_upper must be set)
   -h, --help                 Print help
 ```
 
 
-
-
 #### Merge
 
 Merge multiple sketches into one large one.
@@ -138,7 +140,7 @@ This project is licensed under the MIT license. See the [LICENSE](LICENSE) file
 
 ### Disclaimer
 
-jam-rs is still in early active development and not ready for production use. Use at your own risk. Once a stable version is released additional information and installation guidelines will be added.
+jam-rs is still in active development and not ready for production use. Use at your own risk.
 
 ### Credits
 

src/cli.rs

@@ -7,8 +7,8 @@ use std::path::PathBuf;
 #[command(bin_name = "jam")]
 #[command(version = "0.1.0-beta.1")]
 #[command(
-    about = "Just another minhasher, obviously blazingly fast",
-    long_about = "A heavily optimized minhash implementation that focuses less on accuracy and more on quick scans of large datasets."
+    about = "Just another (genomic) minhasher (jam), obviously blazingly fast",
+    long_about = "An optimized minhash implementation that focuses on quick scans for small sequences in large datasets."
 )]
 pub struct Cli {
     #[command(subcommand)]
@@ -38,7 +38,7 @@ pub enum HashAlgorithms {
 
 #[derive(Debug, Subcommand, Clone)]
 pub enum Commands {
-    /// Sketch one or more files and write result to output file (or stdout)
+    /// Sketch one or more files and write the result to an output file (or stdout)
     #[command(arg_required_else_help = true)]
     Sketch {
         /// Input file(s), one directory or one file with list of files to be hashed
@@ -48,7 +48,7 @@ pub enum Commands {
         #[arg(short, long)]
         #[arg(value_parser = clap::value_parser!(std::path::PathBuf))]
         output: Option<PathBuf>,
-        /// kmer size all sketches to be compared must have the same size
+        /// kmer size, all sketches must have the same size to be compared
         #[arg(short = 'k', long = "kmer-size", default_value = "21")]
         kmer_size: u8,
         /// Scale the hash space to a minimum fraction of the maximum hash value (FracMinHash)
@@ -57,10 +57,10 @@ pub enum Commands {
         /// Scale the hash space to a minimum fraction of all k-mers (SizeMinHash)
         #[arg(long)]
         kscale: Option<u64>,
-        /// Minimum number of k-mers (per record) to be hashed
+        /// Minimum number of k-mers (per record) to be hashed, bottom cut-off
         #[arg(long)]
         nmin: Option<u64>,
-        /// Maximum number of k-mers (per record) to be hashed
+        /// Maximum number of k-mers (per record) to be hashed, top cut-off
         #[arg(long)]
         nmax: Option<u64>,
         /// Change to other output formats
@@ -84,7 +84,7 @@ pub enum Commands {
         #[arg(value_parser = clap::value_parser!(std::path::PathBuf))]
         output: PathBuf,
     },
-    /// Estimate distance of a (small) sketch against a subset of one or more sketches as database.
+    /// Estimate containment of a (small) sketch against a subset of one or more sketches as database.
     /// Requires all sketches to have the same kmer size
     #[command(arg_required_else_help = true)]
     Dist {
@@ -104,10 +104,10 @@ pub enum Commands {
         /// Use the Stats params for restricting results
         #[arg(long)]
         stats: bool,
-        /// Use GC stats with an upper bound of x% and a lower bound of y%
+        /// Use GC stats with an upper bound of x% (gc_lower and gc_upper must be set)
         #[arg(long)]
         gc_lower: Option<u8>,
-        /// Use GC stats with an upper bound of x% and a lower bound of y%
+        /// Use GC stats with an lower bound of y% (gc_lower and gc_upper must be set)
         #[arg(long)]
         gc_upper: Option<u8>,
     },

src/main.rs

@@ -64,7 +64,14 @@ fn main() {
 
             let gc_bounds = match (gc_lower, gc_upper) {
                 (Some(l), Some(u)) => Some((l, u)),
-                _ => None,
+                (None, None) => None,
+                _ => {
+                    cmd.error(
+                        ErrorKind::ArgumentConflict,
+                        "Both gc_lower and gc_upper must be set",
+                    )
+                    .exit();
+                }
             };
 
             let mut input_sketch = Vec::new();