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// Copyright (C) 2024 Philipp Benner
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the “Software”), to deal
// in the Software without restriction, including without limitation the rights
// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
// copies of the Software, and to permit persons to whom the Software is
// furnished to do so, subject to the following conditions:
//
// The above copyright notice and this permission notice shall be included in
// all copies or substantial portions of the Software.
//
// THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
// SOFTWARE.
use std::io;
use core::pin::Pin;
use futures::{Stream, StreamExt};
use async_stream::stream;
use crate::read;
use crate::infologger::Logger;
/* -------------------------------------------------------------------------- */
type ReadStreamType<'a> = Pin<Box<dyn Stream<Item = io::Result<read::Read>> + 'a>>;
/* -------------------------------------------------------------------------- */
pub enum ReadStream {}
/* -------------------------------------------------------------------------- */
impl ReadStream {
pub fn paired_as_single_end<'a>(
mut stream_in: ReadStreamType<'a>,
_logger : Option<&'a Logger>,
switch : bool,
) -> ReadStreamType<'a> {
// If PairedAsSingleEnd is false, return the input stream directly
if !switch {
return stream_in;
}
let output_stream = Box::pin(stream! {
while let Some(item) = stream_in.next().await {
match item {
Ok(mut r) => {
r.paired_end = false;
yield Ok(r)
},
Err(e) => yield Err(e),
};
}
});
Box::pin(output_stream)
}
/* -------------------------------------------------------------------------- */
// Function to filter paired reads
pub fn filter_paired_end<'a>(
mut stream_in: ReadStreamType<'a>,
logger : Option<&'a Logger>,
switch : bool,
) -> ReadStreamType<'a> {
if !switch {
return stream_in;
}
let output_stream = async_stream::stream! {
let mut n = 0;
let mut m = 0;
while let Some(item) = stream_in.next().await {
match item {
Ok(r) => {
if r.paired_end {
yield Ok(r);
m += 1;
}
n += 1;
},
Err(e) => yield Err(e),
}
}
if let Some(log) = logger {
log!(log, "Filtered out {} unpaired reads ({:.2}%)", n - m, 100.0 * (n - m) as f64 / n as f64);
}
};
Box::pin(output_stream)
}
/* -------------------------------------------------------------------------- */
// Function to filter single-end reads
pub fn filter_single_end<'a>(
mut stream_in: ReadStreamType<'a>,
logger : Option<&'a Logger>,
switch : bool,
) -> ReadStreamType<'a> {
if !switch {
return stream_in;
}
let output_stream = async_stream::stream! {
let mut n = 0;
let mut m = 0;
while let Some(item) = stream_in.next().await {
match item {
Ok(r) => {
if !r.paired_end {
yield Ok(r);
m += 1;
}
n += 1;
},
Err(e) => yield Err(e),
}
}
if let Some(log) = logger {
log!(log, "Filtered out {} paired reads ({:.2}%)", n - m, 100.0 * (n - m) as f64 / n as f64);
}
};
Box::pin(output_stream)
}
/* -------------------------------------------------------------------------- */
// Function to filter duplicates
pub fn filter_duplicates<'a>(
mut stream_in: ReadStreamType<'a>,
logger : Option<&'a Logger>,
switch : bool,
) -> ReadStreamType<'a> {
if !switch {
return stream_in;
}
let output_stream = async_stream::stream! {
let mut n = 0;
let mut m = 0;
while let Some(item) = stream_in.next().await {
match item {
Ok(r) => {
if !r.duplicate {
yield Ok(r);
m += 1;
}
n += 1;
},
Err(e) => yield Err(e),
}
}
if let Some(log) = logger {
log!(log, "Filtered out {} duplicates ({:.2}%)", n - m, 100.0 * (n - m) as f64 / n as f64);
}
};
Box::pin(output_stream)
}
/* -------------------------------------------------------------------------- */
// Function to filter based on strand
pub fn filter_strand<'a>(
mut stream_in: ReadStreamType<'a>,
logger : Option<&'a Logger>,
strand : char,
) -> ReadStreamType<'a> {
if strand == '*' {
return stream_in;
}
let output_stream = async_stream::stream! {
let mut n = 0;
let mut m = 0;
while let Some(item) = stream_in.next().await {
match item {
Ok(r) => {
if r.strand == strand {
yield Ok(r);
m += 1;
}
n += 1;
},
Err(e) => yield Err(e),
}
}
if let Some(log) = logger {
log!(log, "Filtered out {} reads not on strand {} ({:.2}%)", n - m, strand, 100.0 * (n - m) as f64 / n as f64);
}
};
Box::pin(output_stream)
}
/* -------------------------------------------------------------------------- */
// Function to filter based on mapping quality
pub fn filter_mapq<'a>(
mut stream_in: ReadStreamType<'a>,
logger : Option<&'a Logger>,
mapq : i64,
) -> ReadStreamType<'a> {
if mapq <= 0 {
return stream_in;
}
let output_stream = async_stream::stream! {
let mut n = 0;
let mut m = 0;
while let Some(item) = stream_in.next().await {
match item {
Ok(r) => {
if r.mapq >= mapq {
yield Ok(r);
m += 1;
}
n += 1;
},
Err(e) => yield Err(e),
}
}
if let Some(log) = logger {
log!(log, "Filtered out {} reads with mapping quality lower than {} ({:.2}%)", n - m, mapq, 100.0 * (n - m) as f64 / n as f64);
}
};
Box::pin(output_stream)
}
/* -------------------------------------------------------------------------- */
// Function to filter based on read length
pub fn filter_read_length<'a>(
mut stream_in: ReadStreamType<'a>,
logger : Option<&'a Logger>,
read_lengths : &'a [usize; 2],
) -> ReadStreamType<'a> {
if read_lengths[0] == 0 && read_lengths[1] == 0 {
return stream_in;
}
let output_stream = async_stream::stream! {
let mut n = 0;
let mut m = 0;
while let Some(item) = stream_in.next().await {
match item {
Ok(r) => {
let len = r.range.to - r.range.from;
if len >= read_lengths[0] &&
(len <= read_lengths[1] || read_lengths[1] == 0) {
yield Ok(r);
m += 1;
}
n += 1;
},
Err(e) => yield Err(e),
}
}
if let Some(log) = logger {
log!(log, "Filtered out {} reads with non-admissible length ({:.2}%)", n - m, 100.0 * (n - m) as f64 / n as f64);
}
};
Box::pin(output_stream)
}
/* -------------------------------------------------------------------------- */
// Function to shift reads based on strand
pub fn shift_reads<'a>(
mut stream_in: ReadStreamType<'a>,
logger : Option<&'a Logger>,
shift : &'a [usize; 2]
) -> ReadStreamType<'a> {
if shift[0] == 0 && shift[1] == 0 {
return stream_in;
}
let output_stream = async_stream::stream! {
while let Some(item) = stream_in.next().await {
match item {
Ok(mut r) => {
if r.strand == '+' {
r.range.from += shift[0];
r.range.to += shift[0];
} else if r.strand == '-' {
r.range.from += shift[1];
r.range.to += shift[1];
}
r.range.to -= r.range.from;
r.range.from = 0;
yield Ok(r);
},
Err(e) => yield Err(e),
}
}
if let Some(log) = logger {
log!(log, "Shifted reads (forward strand: {}, reverse strand: {})", shift[0], shift[1]);
}
};
Box::pin(output_stream)
}
}