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Use BufReader for reading BAM files with file-like objects #68

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Use BufReader for reading BAM files with file-like objects #68

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6c9ee85
Use BufReader for reading BAM files with file-like objects
pkerpedjiev Nov 30, 2024
6c28eee
Fix variable name and read error
pkerpedjiev Nov 30, 2024
c00b02c
One more variable change
pkerpedjiev Nov 30, 2024
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17 changes: 10 additions & 7 deletions oxbow/src/bam.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -17,20 +17,22 @@ use noodles::{bam, bgzf, csi, sam};

use crate::batch_builder::{write_ipc_err, BatchBuilder};

pub fn index_from_reader<R>(mut read: R) -> io::Result<csi::Index>
pub fn index_from_reader<R>(read: R) -> io::Result<csi::Index>
where
R: Read + Seek,
{
// Unlike .tbi and .csi, .bai is not bgzf-compressed
// so we read off the magic directly.
let mut buf_read = std::io::BufReader::with_capacity(1024 * 1024, read);

let mut magic = [0; 4];
read.read_exact(&mut magic)?;
read.seek(io::SeekFrom::Start(0))?;
buf_read.read_exact(&mut magic)?;
buf_read.seek(io::SeekFrom::Start(0))?;
if magic == b"BAI\x01" as &[u8] {
let mut bai_reader = bam::bai::Reader::new(read);
let mut bai_reader = bam::bai::Reader::new(buf_read);
bai_reader.read_index()
} else {
let mut csi_reader = csi::Reader::new(read);
let mut csi_reader = csi::Reader::new(buf_read);
csi_reader.read_index()
}
}
Expand Down Expand Up @@ -71,10 +73,11 @@ impl BamReader<BufReader<File>> {
}
}

impl<R: Read + Seek> BamReader<R> {
impl<R: Read + Seek> BamReader<BufReader<R>> {
/// Creates a BAM reader.
pub fn new(read: R, index: csi::Index) -> std::io::Result<Self> {
let mut reader = bam::Reader::new(read);
let buf_read = std::io::BufReader::with_capacity(1024 * 1024, read);
let mut reader = bam::Reader::new(buf_read);
let header = reader.read_header()?;
Ok(Self {
reader,
Expand Down