perbase_lib/
read_filter.rs

1//! A trait and default implementation of a read filter.
2use rust_htslib::bam::pileup::Alignment;
3use rust_htslib::bam::record::Record;
4
5/// Anything that implements ReadFilter can apply a filter set to read.
6pub trait ReadFilter {
7    /// filters a read, true is pass, false if fail
8    fn filter_read(&self, read: &Record, alignment: Option<&Alignment>) -> bool;
9}
10
11/// A straightforward read filter.
12pub struct DefaultReadFilter {
13    include_flags: u16,
14    exclude_flags: u16,
15    min_mapq: u8,
16}
17
18impl DefaultReadFilter {
19    /// Create an OnlyDepthReadFilter
20    pub fn new(include_flags: u16, exclude_flags: u16, min_mapq: u8) -> Self {
21        Self {
22            include_flags,
23            exclude_flags,
24            min_mapq,
25        }
26    }
27}
28
29impl ReadFilter for DefaultReadFilter {
30    /// Filter reads based SAM flags and mapping quality
31    #[inline(always)]
32    fn filter_read(&self, read: &Record, _alignment: Option<&Alignment>) -> bool {
33        let flags = read.flags();
34        (!flags) & self.include_flags == 0
35            && flags & self.exclude_flags == 0
36            && read.mapq() >= self.min_mapq
37    }
38}
perbase_lib/read_filter.rs

perbase_lib/
read_filter.rs
