1 unstable release
0.1.0 | Jul 13, 2022 |
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#729 in Science
120KB
283 lines
samfilt
A filtering tool for Sequence Alignment/Map files written in Rust.
Installation
From source
if you want to build samfilt from source, you need Rust. You can then use cargo
to build everything:
cargo install samfilt
Usage
Usage: samfilt [options] <SAM file>
Options:
-h, --help print this help menu
--supplementary sel|del
reads with supplementary alignments
--greater_len UINT
reads with a greater length than UINT [0]
--smaller_len UINT
reads with a smaller length than UINT [4294967295]
--qname_input FILE
alignment records with QNAME being equal to one of the
lines in FILE
--qname_output FILE
output the QNAME field of all the records in the
filtered SAM file (one per line)
-o FILE output to FILE [stdout]
Dependencies
~1.5MB
~20K SLoC