- rust samtools regiontag-viewer
- given an sam alignment file and a give range of the coordinate from the genome, will produce a base colour encoded alignment for the reads aligned in that region.
- Especially important for showing the reads specific to diversity and phenotypes and linked mutations.
- 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.
- This feature is not present in samtools.
cargo build
λ gauravsablok rust-samtools-regiontag-viewer → λ git main* → ./rust-samtools-regiontag-viewer -h
Usage: rust-samtools-regiontag-viewer <ALIGNMENT_ARG> <GENOME_START> <GENOME_END>
Arguments:
<ALIGNMENT_ARG> please provide the path to the alignment file
<GENOME_START> please provide the genome capture region start
<GENOME_END> please provide the genome capture region end
Options:
-h, --help Print help
-V, --version Print version
./rust-samtools-regiontag-viewer ./sample-files/Col0_C1.100k.sam 3654 3804
./rust-samtools-regiontag-viewer ./sample-files/alignreads-metagenomics.sam 40 60
Gaurav Sablok