applicativesystem

Finished  writing the code today and no internet and hence able to push this now. Final and binary release.

Cargo.toml

@@ -0,0 +1,8 @@
+[package]
+name = "rust-pangenome-matcher"
+version = "0.1.0"
+edition = "2021"
+
+[dependencies]
+clap = { version = "4.5.23", features = ["derive"] }
+rayon = "1.10.0"

README.md

@@ -1,2 +1,32 @@
-# rust-pangenome-matcher
-rust pangenome matcher
+# rust-pangenome-tools
+ - writing all pangenome tools in rust. 
+ - This part compares the two pangenome alignment with the same query and a different reference and anchors the query across both. 
+ - general note: Incase of Golang and RUST, please see the last commit message and if it says compiled binary then it is completed or else still in development version.
+
+ ```
+ cargo build
+ 
+ ```
+ λ gauravsablok rust-pangenome-matcher → λ git main* → ./target/debug/rust-pangenome-matcher -h
+ Usage: rust-pangenome-matcher <PAFALIGNMENT1> <PAFALIGNMENT2>
+
+ Arguments:
+  <PAFALIGNMENT1>  please provide the path to the first alignment file
+  <PAFALIGNMENT2>  please provide the path to the second alignment file
+
+ Options:
+  -h, --help     Print help
+  -V, --version  Print version
+
+ ```
+
+ ```
+ - to run the binary
+ ```
+λ gauravsablok rust-pangenome-matcher → λ git main* → ./target/debug/rust-pangenome-matcher ./sample-files/test1.paf ./sample-files/test2.paf
+The comparative reference files have been written
+The comparative query files have been written
+The pangenome matcher has produced the results: The pangenome alignments have been parsed and the comparative results have been written
+
+ ```
+ Gaurav Sablok