A filtering tool for Sequence Alignment/Map files written in Rust.
if you want to build samfilt from source, you need Rust. You can then use cargo to build everything:
bash
cargo install samfilt
```
Usage: samfilt [options]
Options: -h, --help print this help menu --supplementary sel|del reads with supplementary alignments --greaterlen UINT reads with a greater length than UINT [0] --smallerlen UINT reads with a smaller length than UINT [4294967295] --qnameinput FILE alignment records with QNAME being equal to one of the lines in FILE --qnameoutput FILE output the QNAME field of all the records in the filtered SAM file (one per line) -o FILE output to FILE [stdout] ```