A comparison tool for Sequence Alignment/Map files written in Rust.
if you want to build samcomp from source, you need Rust. You can then use cargo to build everything:
bash
cargo install samcomp
```bash
Usage: samcomp [options]
Options: -h, --help print this help menu -o NAME generate gain, loss and diff files and output them with the prefix NAME -d FLOAT a location in the tested file is considered to be similar to the one in the target file if the distance between both locations is less than FLOAT fraction of the read length [1.0] -q UINT1,UINT2,... output the results using UINT1,UINT2,... (such as UINT1 > UINT2 > ...) as the quality thresholds [60,10,1,0] -m STR Comparison mode [all] - all: match the primary and the secondary alignments of the test file with the primary and the secondary of the target file respectively - prim_tgt: match the primary and the secondary alignments of the test file with the primar aligments of the target file - prim: match the primary alignments of the test file with the primary aligments of the target file ```