pileuphi_lib 0.9.3

High-throughput, extensible SAM/BAM pileup generation library
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41

//! Library for generating pileups from the SAM/BAM formats, with APIs for live, streaming in-memory
//! traversal and multi-threaded emission to file
//!
//! Supports custom-built output formats via the [OrderedPileupOutput] trait.

pub(crate) mod alignment;
pub(crate) mod bamio;
pub(crate) mod baq;
pub(crate) mod basedepth_string;
pub(crate) mod cigar_resolve;
pub(crate) mod engine;
pub(crate) mod errors;
pub(crate) mod jobqueue;
pub(crate) mod output;
pub(crate) mod overlap;
pub(crate) mod params;
pub(crate) mod pileup_iterator;
pub(crate) mod pileup_string;
pub(crate) mod position_queue;
pub(crate) mod read_buf;
pub(crate) mod read_filter;
pub(crate) mod refseq;
pub(crate) mod threading;
pub(crate) mod utils;

pub use engine::PileupEngine;
pub use jobqueue::setup_exit_handler;
pub use output::write_multiple_outputs;

pub mod error {
    pub use crate::errors::{Error, ErrorKind};
}

pub mod outputs {
    pub use crate::basedepth_string::BaseDepthString;
    pub use crate::pileup_string::PileupString;
}

pub mod param {
    pub use crate::params::{InputParams, PileupParams, STDOUT_ARG_STR};
}