-
Notifications
You must be signed in to change notification settings - Fork 55
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
tabix/io/reader: Extract index reader
- Loading branch information
Showing
2 changed files
with
199 additions
and
186 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,194 @@ | ||
| use std::io::{self, Read}; | ||
|
|
||
| use byteorder::{LittleEndian, ReadBytesExt}; | ||
| use indexmap::IndexMap; | ||
| use noodles_bgzf as bgzf; | ||
| use noodles_csi::{ | ||
| self as csi, | ||
| binning_index::index::{ | ||
| reference_sequence::{index::LinearIndex, Bin, Metadata}, | ||
| ReferenceSequence, | ||
| }, | ||
| io::reader::index::read_header, | ||
| }; | ||
|
|
||
| use crate::{Index, MAGIC_NUMBER}; | ||
|
|
||
| pub(super) fn read_index<R>(reader: &mut R) -> io::Result<Index> | ||
| where | ||
| R: Read, | ||
| { | ||
| read_magic(reader)?; | ||
|
|
||
| let n_ref = reader.read_i32::<LittleEndian>().and_then(|n| { | ||
| usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e)) | ||
| })?; | ||
|
|
||
| let header = read_header(reader).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?; | ||
|
|
||
| let references = read_references(reader, n_ref)?; | ||
| let n_no_coor = read_unplaced_unmapped_record_count(reader)?; | ||
|
|
||
| let mut builder = Index::builder() | ||
| .set_header(header) | ||
| .set_reference_sequences(references); | ||
|
|
||
| if let Some(unplaced_unmapped_record_count) = n_no_coor { | ||
| builder = builder.set_unplaced_unmapped_record_count(unplaced_unmapped_record_count); | ||
| } | ||
|
|
||
| Ok(builder.build()) | ||
| } | ||
|
|
||
| fn read_magic<R>(reader: &mut R) -> io::Result<()> | ||
| where | ||
| R: Read, | ||
| { | ||
| let mut magic = [0; MAGIC_NUMBER.len()]; | ||
| reader.read_exact(&mut magic)?; | ||
|
|
||
| if magic == MAGIC_NUMBER { | ||
| Ok(()) | ||
| } else { | ||
| Err(io::Error::new( | ||
| io::ErrorKind::InvalidData, | ||
| "invalid tabix header", | ||
| )) | ||
| } | ||
| } | ||
|
|
||
| fn read_references<R>(reader: &mut R, len: usize) -> io::Result<Vec<ReferenceSequence<LinearIndex>>> | ||
| where | ||
| R: Read, | ||
| { | ||
| let mut references = Vec::with_capacity(len); | ||
|
|
||
| for _ in 0..len { | ||
| let (bins, metadata) = read_bins(reader)?; | ||
| let intervals = read_intervals(reader)?; | ||
| references.push(ReferenceSequence::new(bins, intervals, metadata)); | ||
| } | ||
|
|
||
| Ok(references) | ||
| } | ||
|
|
||
| fn read_bins<R>(reader: &mut R) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)> | ||
| where | ||
| R: Read, | ||
| { | ||
| use csi::io::reader::index::reference_sequences::{bins::read_chunks, read_metadata}; | ||
|
|
||
| use crate::index::DEPTH; | ||
|
|
||
| const METADATA_ID: usize = Bin::metadata_id(DEPTH); | ||
|
|
||
| let n_bin = reader.read_i32::<LittleEndian>().and_then(|n| { | ||
| usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e)) | ||
| })?; | ||
|
|
||
| let mut bins = IndexMap::with_capacity(n_bin); | ||
| let mut metadata = None; | ||
|
|
||
| for _ in 0..n_bin { | ||
| let id = reader.read_u32::<LittleEndian>().and_then(|n| { | ||
| usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e)) | ||
| })?; | ||
|
|
||
| let is_duplicate = if id == METADATA_ID { | ||
| let m = | ||
| read_metadata(reader).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?; | ||
|
|
||
| metadata.replace(m).is_some() | ||
| } else { | ||
| let chunks = | ||
| read_chunks(reader).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?; | ||
|
|
||
| let bin = Bin::new(chunks); | ||
|
|
||
| bins.insert(id, bin).is_some() | ||
| }; | ||
|
|
||
| if is_duplicate { | ||
| return Err(io::Error::new( | ||
| io::ErrorKind::InvalidData, | ||
| format!("duplicate bin ID: {id}"), | ||
| )); | ||
| } | ||
| } | ||
|
|
||
| Ok((bins, metadata)) | ||
| } | ||
|
|
||
| fn read_intervals<R>(reader: &mut R) -> io::Result<Vec<bgzf::VirtualPosition>> | ||
| where | ||
| R: Read, | ||
| { | ||
| let n_intv = reader.read_i32::<LittleEndian>().and_then(|n| { | ||
| usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e)) | ||
| })?; | ||
|
|
||
| let mut intervals = Vec::with_capacity(n_intv); | ||
|
|
||
| for _ in 0..n_intv { | ||
| let ioff = reader | ||
| .read_u64::<LittleEndian>() | ||
| .map(bgzf::VirtualPosition::from)?; | ||
|
|
||
| intervals.push(ioff); | ||
| } | ||
|
|
||
| Ok(intervals) | ||
| } | ||
|
|
||
| fn read_unplaced_unmapped_record_count<R>(reader: &mut R) -> io::Result<Option<u64>> | ||
| where | ||
| R: Read, | ||
| { | ||
| match reader.read_u64::<LittleEndian>() { | ||
| Ok(n) => Ok(Some(n)), | ||
| Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof => Ok(None), | ||
| Err(e) => Err(e), | ||
| } | ||
| } | ||
|
|
||
| #[cfg(test)] | ||
| mod tests { | ||
| use super::*; | ||
|
|
||
| #[test] | ||
| fn test_read_magic_with_invalid_magic_number() { | ||
| let data = []; | ||
| let mut reader = &data[..]; | ||
| assert!(matches!( | ||
| read_magic(&mut reader), | ||
| Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof | ||
| )); | ||
|
|
||
| let data = b"TBI"; | ||
| let mut reader = &data[..]; | ||
| assert!(matches!( | ||
| read_magic(&mut reader), | ||
| Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof | ||
| )); | ||
|
|
||
| let data = b"MThd"; | ||
| let mut reader = &data[..]; | ||
| assert!(matches!( | ||
| read_magic(&mut reader), | ||
| Err(ref e) if e.kind() == io::ErrorKind::InvalidData | ||
| )); | ||
| } | ||
|
|
||
| #[test] | ||
| fn test_read_unplaced_unmapped_record_count() -> io::Result<()> { | ||
| let data = []; | ||
| let mut reader = &data[..]; | ||
| assert_eq!(read_unplaced_unmapped_record_count(&mut reader)?, None); | ||
|
|
||
| let data = [0x08, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00, 0x00]; | ||
| let mut reader = &data[..]; | ||
| assert_eq!(read_unplaced_unmapped_record_count(&mut reader)?, Some(8)); | ||
|
|
||
| Ok(()) | ||
| } | ||
| } |