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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::fs::File;
use std::error::Error;
use std::io::{self, Read, Seek, Write};
use crate::bigwig::{BigWigReader, OptionBigWig};
use crate::track_generic::GenericTrack;
use crate::track_simple::SimpleTrack;
use crate::track_statistics::BinSummaryStatistics;
/* -------------------------------------------------------------------------- */
impl SimpleTrack {
pub fn read_bigwig<R: Read + Seek>(
&mut self,
reader: &mut R,
name : &str,
f : BinSummaryStatistics,
mut bin_size: usize,
bin_overlap: usize,
init: f64,
) -> Result<(), Box<dyn Error>> {
let mut bwr = BigWigReader::new(reader)?;
let mut sequences: Vec<Vec<f64>> = Vec::new();
let genome = bwr.genome().clone();
for seqname in genome.seqnames {
let (s, b) = bwr.query_sequence(&seqname, f, bin_size, bin_overlap, init)?;
if bin_size == 0 {
bin_size = b;
}
sequences.push(s);
}
let tmp = SimpleTrack::new(name.to_string(), sequences, bwr.genome().clone(), bin_size)?;
*self = tmp;
Ok(())
}
pub fn import_bigwig(
&mut self,
filename : &str,
name : &str,
s : BinSummaryStatistics,
bin_size : usize,
bin_overlap: usize,
init : f64,
) -> Result<(), Box<dyn Error>> {
let mut f = File::open(filename)?;
Ok(self.read_bigwig(&mut f, name, s, bin_size, bin_overlap, init)
.map_err(|e| {
io::Error::new(io::ErrorKind::Other, format!("importing bigWig file from `{}` failed: {}", filename, e))
}
)?)
}
pub fn write_bigwig<W: Write + Seek>(
&self,
writer: &mut W,
params: Vec<OptionBigWig>
) -> Result<(), Box<dyn Error>> {
GenericTrack { track: self }.write_bigwig(writer, params)
}
pub fn export_bigwig(
&self,
filename: &str,
params : Vec<OptionBigWig>
) -> Result<(), Box<dyn Error>> {
let mut f = File::create(filename)?;
Ok(self.write_bigwig(&mut f, params).map_err(|e| {
io::Error::new(io::ErrorKind::Other, format!("exporting bigWig file to `{}` failed: {}", filename, e))
})?)
}
}