- rust samtools view.
- given an sam alignment file and a give range of the coordinate from the genome, will produce a colour coded alignment for the reads aligned in that region.
- Especially important for showing the reads specific to abundance, metabolites, genomic association to phenotypes.
- 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.
- explanation : The first read related to the normal phenotype, the second to the diseased one and the third one to the mutant and so on.
cargo build
Usage: rust-samtools-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
- sample view from the sample alignment, choose any number or coordinate from your aligned file.
./target/debug/rust-samtools-viewer ./sample-files/alignreads.sam 200 250
Gaurav Sablok