- rust bedtools single merge pangenome, merge across a single bed file.
- it uses a two tuple based approach which avoid quadratic cost.
- 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
Usage: rust-bedtools-pangenome-single-merge <BED1> <FASTA>
Arguments:
<BED1> please provide the path to the first alignment file
<FASTA> please provide the path to the reference fasta file
Options:
-h, --help Print help
-V, --version Print version
- to run the binary
./rust-bedtools-pangenome-single-merge ./sample-files/exon-sample.bed ./sample-files/sample.fasta
- bedtools, it doesnt report the merged sequences, rust-bedtools report the merged sequences.
➜ rust-bedtools-pangenome-single-merge git:(main) ✗ cat merged_cordinates.txt
chr1 10 30 CTGACCATGACTGACTGACT
chr1 50 60 CTGACATGAC
chr1 70 80 GACTGACTGA
chr1 70 90 GACTGACTGACTGACTGACT
chr1 90 98 GACATGAC
chr1 92 100 CATGACTG
Gaurav Sablok