Add logging to v0.3.0

.cargo/config.toml

@@ -0,0 +1,2 @@
+[build]
+rustflags = ["-C", "target-cpu=native"]

.gitignore

@@ -0,0 +1,14 @@
+# Generated by Cargo
+# will have compiled files and executables
+debug/
+target/
+
+# These are backup files generated by rustfmt
+**/*.rs.bk
+
+# MSVC Windows builds of rustc generate these, which store debugging information
+*.pdb
+
+# Generated by cargo mutants
+# Contains mutation testing data
+**/mutants.out*/

Cargo.toml

@@ -1,20 +1,22 @@
-rustflags = ["-Ctarget-cpu=native"]
+
 [package]
 name = "isONclust3"
 version = "0.3.0"
 edition = "2021"
 repository = "https://github.com/aljpetri/isONclust3"
-license="MIT"
+license = "MIT"
 description = "Rust implementation of a novel de novo clustering algorithm. isONclust3 is a tool for clustering either PacBio Iso-Seq reads, or Oxford Nanopore reads into clusters, where each cluster represents all reads that came from a gene family. Output is a tsv file with each read assigned to a cluster-ID and a folder 'fastq' containing one fastq file per cluster generated. Detailed information is available in the isONclust3 paper."
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 
 [dependencies]
 bio = "1"
 bio-seq = "0.10.0"
-clap = { version = "4.4.3", features = ["derive","cargo"] }
+clap = { version = "4.4.3", features = ["derive", "cargo"] }
 clap-cargo = "0.12.0"
 rayon = "1.7"
 memory-stats = "1.0.0"
 rustc-hash = "1.1.0"
 minimizer-iter = "1.2.1"
 nohash-hasher = "0.2.0"
+log = "0.4.27"
+simple_logger = "5.0.0"

README.md

@@ -33,12 +33,12 @@ cargo build --release
 The executable is then located in folder `target/release`.
 
 ### Testing the installation <a name="installation"></a>
-Run `target/release/isONclust3 --fastq Example_data/test_data.fastq --mode ont --outfolder Example_out --seeding minimizer --post-cluster`. 
+Run `target/release/isONclust3 --fastq example_data/test_data.fastq --mode ont --outfolder example_out --seeding minimizer --post-cluster`.
 
-This generates an output directory in the repository folder. The fastq_files folder inside clustering should now contain 94 fastq files(each representing one cluster). 
+This generates an output directory in the repository folder. The fastq_files folder inside clustering should now contain 94 fastq files(each representing one cluster).
 
 # Running isONclust3 <a name="Running"></a>
-IsONclust3 can be used on either Pacbio data or ONT data. 
+IsONclust3 can be used on either Pacbio data or ONT data.
 
 ```
 isONclust3 --fastq {input.fastq} --mode ont  --outfolder {outfolder}         # Oxford Nanopore reads