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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::fmt;
use std::error::Error;
use crate::range::Range;
use crate::granges_row::GRange;
/* -------------------------------------------------------------------------- */
#[derive(Clone, Debug)]
pub struct Read {
pub seqname : String,
pub range : Range,
pub strand : char,
pub mapq : i64,
pub duplicate : bool,
pub paired_end: bool,
}
/* -------------------------------------------------------------------------- */
impl Read {
pub fn get_grange(&self) -> GRange {
GRange{
seqname: self.seqname.clone(),
range : self.range,
strand : self.strand
}
}
pub fn extend(&self, d: usize) -> Result<Range, Box<dyn Error>> {
let mut from = self.range.from;
let mut to = self.range.to;
if !self.paired_end && d > 0 {
// Extend read in 3' direction
match self.strand {
'+' => {
to = from + d;
}
'-' => {
if d > to {
from = 0;
} else {
from = to.saturating_sub(d); // Ensure `from` doesn't go negative
}
}
_ => {
return Err(Box::new(StrandMissingError(self.strand)));
}
}
}
Ok(Range::new(from, to))
}
}
/* -------------------------------------------------------------------------- */
impl fmt::Display for Read {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(f, "READ: {}:[{}-{}):{}, MAPQ={}, DUPLICATE={}, PAIRED_END={}",
self.seqname,
self.range.from,
self.range.to,
self.strand,
self.mapq,
self.duplicate,
self.paired_end)
}
}
/* -------------------------------------------------------------------------- */
#[derive(Debug)]
pub struct StrandMissingError(char);
impl fmt::Display for StrandMissingError {
fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
write!(f, "strand information is missing for read with strand `{}`", self.0)
}
}
impl Error for StrandMissingError {}