noodles_tabix/async/io/
reader.rs

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
use indexmap::IndexMap;
use noodles_bgzf as bgzf;
use noodles_csi::{
    self as csi,
    binning_index::index::{
        reference_sequence::{bin::Chunk, index::LinearIndex, Bin, Metadata},
        Header, ReferenceSequence,
    },
};
use tokio::io::{self, AsyncRead, AsyncReadExt};

use crate::Index;

/// An async tabix reader.
pub struct Reader<R>
where
    R: AsyncRead,
{
    inner: bgzf::AsyncReader<R>,
}

impl<R> Reader<R>
where
    R: AsyncRead + Unpin,
{
    /// Creates an async tabix reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_tabix as tabix;
    /// let data = [];
    /// let reader = tabix::r#async::io::Reader::new(&data[..]);
    /// ```
    pub fn new(inner: R) -> Self {
        Self {
            inner: bgzf::AsyncReader::new(inner),
        }
    }

    /// Returns a reference to the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_tabix as tabix;
    /// use tokio::io;
    /// let reader = tabix::r#async::io::Reader::new(io::empty());
    /// let _inner = reader.get_ref();
    /// ```
    pub fn get_ref(&self) -> &bgzf::AsyncReader<R> {
        &self.inner
    }

    /// Returns a mutable reference to the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_tabix as tabix;
    /// use tokio::io;
    /// let mut reader = tabix::r#async::io::Reader::new(io::empty());
    /// let _inner = reader.get_mut();
    /// ```
    pub fn get_mut(&mut self) -> &mut bgzf::AsyncReader<R> {
        &mut self.inner
    }

    /// Returns the underlying reader.
    ///
    /// # Examples
    ///
    /// ```
    /// use noodles_tabix as tabix;
    /// use tokio::io;
    /// let reader = tabix::r#async::io::Reader::new(io::empty());
    /// let _inner = reader.into_inner();
    /// ```
    pub fn into_inner(self) -> bgzf::AsyncReader<R> {
        self.inner
    }

    /// Reads the tabix index.
    ///
    /// The position of the stream is expected to be at the beginning.
    ///
    /// # Examples
    ///
    /// ```no_run
    /// # use std::io;
    /// #
    /// # #[tokio::main]
    /// # async fn main() -> io::Result<()> {
    /// use noodles_tabix as tabix;
    /// use tokio::fs::File;
    ///
    /// let mut reader = File::open("sample.vcf.gz.tbi")
    ///     .await
    ///     .map(tabix::r#async::io::Reader::new)?;
    ///
    /// let index = reader.read_index().await?;
    /// # Ok(())
    /// # }
    /// ```
    pub async fn read_index(&mut self) -> io::Result<Index> {
        read_index(&mut self.inner).await
    }
}

async fn read_index<R>(reader: &mut R) -> io::Result<Index>
where
    R: AsyncRead + Unpin,
{
    read_magic(reader).await?;

    let n_ref = reader.read_i32_le().await.and_then(|n| {
        usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    let header = read_header(reader).await?;
    let reference_sequences = read_reference_sequences(reader, n_ref).await?;
    let unplaced_unmapped_record_count = read_unplaced_unmapped_record_count(reader).await?;

    let mut builder = Index::builder()
        .set_header(header)
        .set_reference_sequences(reference_sequences);

    if let Some(count) = unplaced_unmapped_record_count {
        builder = builder.set_unplaced_unmapped_record_count(count);
    }

    Ok(builder.build())
}

async fn read_magic<R>(reader: &mut R) -> io::Result<()>
where
    R: AsyncRead + Unpin,
{
    use crate::MAGIC_NUMBER;

    let mut magic = [0; 4];
    reader.read_exact(&mut magic).await?;

    if magic == MAGIC_NUMBER {
        Ok(())
    } else {
        Err(io::Error::new(
            io::ErrorKind::InvalidData,
            "invalid tabix header",
        ))
    }
}

async fn read_header<R>(reader: &mut R) -> io::Result<Header>
where
    R: AsyncRead + Unpin,
{
    use std::mem;

    use csi::io::reader::index::read_header;

    const STATIC_FIELD_COUNT: usize = 6;
    const STATIC_HEADER_SIZE: usize = mem::size_of::<i32>() * STATIC_FIELD_COUNT;

    let mut buf = vec![0; STATIC_HEADER_SIZE];
    reader.read_exact(&mut buf).await?;

    let l_nm = reader.read_i32_le().await?;

    let names_len =
        usize::try_from(l_nm).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))?;
    let mut names = vec![0; names_len];
    reader.read_exact(&mut names).await?;

    buf.extend(l_nm.to_le_bytes());
    buf.extend(names);

    let mut buf_reader = &buf[..];
    read_header(&mut buf_reader).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
}

async fn read_reference_sequences<R>(
    reader: &mut R,
    reference_sequence_count: usize,
) -> io::Result<Vec<ReferenceSequence<LinearIndex>>>
where
    R: AsyncRead + Unpin,
{
    let mut reference_sequences = Vec::with_capacity(reference_sequence_count);

    for _ in 0..reference_sequence_count {
        let reference_sequence = read_reference_sequence(reader).await?;
        reference_sequences.push(reference_sequence);
    }

    Ok(reference_sequences)
}

async fn read_reference_sequence<R>(reader: &mut R) -> io::Result<ReferenceSequence<LinearIndex>>
where
    R: AsyncRead + Unpin,
{
    let (bins, metadata) = read_bins(reader).await?;
    let intervals = read_intervals(reader).await?;
    Ok(ReferenceSequence::new(bins, intervals, metadata))
}

async fn read_bins<R>(reader: &mut R) -> io::Result<(IndexMap<usize, Bin>, Option<Metadata>)>
where
    R: AsyncRead + Unpin,
{
    use crate::index::DEPTH;

    const METADATA_ID: usize = Bin::metadata_id(DEPTH);

    let n_bin = reader.read_i32_le().await.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_le().await.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).await?;
            metadata.replace(m).is_some()
        } else {
            let chunks = read_chunks(reader).await?;
            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))
}

async fn read_chunks<R>(reader: &mut R) -> io::Result<Vec<Chunk>>
where
    R: AsyncRead + Unpin,
{
    let n_chunk = reader.read_i32_le().await.and_then(|n| {
        usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    let mut chunks = Vec::with_capacity(n_chunk);

    for _ in 0..n_chunk {
        let chunk = read_chunk(reader).await?;
        chunks.push(chunk);
    }

    Ok(chunks)
}

async fn read_chunk<R>(reader: &mut R) -> io::Result<Chunk>
where
    R: AsyncRead + Unpin,
{
    let cnk_beg = reader
        .read_u64_le()
        .await
        .map(bgzf::VirtualPosition::from)?;

    let cnk_end = reader
        .read_u64_le()
        .await
        .map(bgzf::VirtualPosition::from)?;

    Ok(Chunk::new(cnk_beg, cnk_end))
}

async fn read_intervals<R>(reader: &mut R) -> io::Result<Vec<bgzf::VirtualPosition>>
where
    R: AsyncRead + Unpin,
{
    let n_intv = reader.read_i32_le().await.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_le()
            .await
            .map(bgzf::VirtualPosition::from)?;

        intervals.push(ioff);
    }

    Ok(intervals)
}

async fn read_metadata<R>(reader: &mut R) -> io::Result<Metadata>
where
    R: AsyncRead + Unpin,
{
    const METADATA_CHUNK_COUNT: usize = 2;

    let n_chunk = reader.read_u32_le().await.and_then(|n| {
        usize::try_from(n).map_err(|e| io::Error::new(io::ErrorKind::InvalidData, e))
    })?;

    if n_chunk != METADATA_CHUNK_COUNT {
        return Err(io::Error::new(
            io::ErrorKind::InvalidData,
            format!(
                "invalid metadata pseudo-bin chunk count: expected {METADATA_CHUNK_COUNT}, got {n_chunk}"
            ),
        ));
    }

    let ref_beg = reader
        .read_u64_le()
        .await
        .map(bgzf::VirtualPosition::from)?;

    let ref_end = reader
        .read_u64_le()
        .await
        .map(bgzf::VirtualPosition::from)?;

    let n_mapped = reader.read_u64_le().await?;
    let n_unmapped = reader.read_u64_le().await?;

    Ok(Metadata::new(ref_beg, ref_end, n_mapped, n_unmapped))
}

async fn read_unplaced_unmapped_record_count<R>(reader: &mut R) -> io::Result<Option<u64>>
where
    R: AsyncRead + Unpin,
{
    match reader.read_u64_le().await {
        Ok(n_no_coor) => Ok(Some(n_no_coor)),
        Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof => Ok(None),
        Err(e) => Err(e),
    }
}

#[cfg(test)]
mod tests {
    use bstr::BString;

    use super::*;

    #[tokio::test]
    async fn test_read_magic() {
        let data = b"TBI\x01";
        let mut reader = &data[..];
        assert!(read_magic(&mut reader).await.is_ok());

        let data = [];
        let mut reader = &data[..];
        assert!(matches!(
            read_magic(&mut reader).await,
            Err(ref e) if e.kind() == io::ErrorKind::UnexpectedEof
        ));

        let data = b"MThd";
        let mut reader = &data[..];
        assert!(matches!(
            read_magic(&mut reader).await,
            Err(ref e) if e.kind() == io::ErrorKind::InvalidData
        ));
    }

    #[tokio::test]
    async fn test_read_header() -> io::Result<()> {
        let data = [
            0x00, 0x00, 0x00, 0x00, // format = Generic(GFF)
            0x01, 0x00, 0x00, 0x00, // col_seq = 1
            0x04, 0x00, 0x00, 0x00, // col_beg = 4
            0x05, 0x00, 0x00, 0x00, // col_end = 5
            0x23, 0x00, 0x00, 0x00, // meta = '#'
            0x00, 0x00, 0x00, 0x00, // skip = 0
            0x08, 0x00, 0x00, 0x00, // l_nm = 8
            b's', b'q', b'0', 0x00, // names[0] = "sq0"
            b's', b'q', b'1', 0x00, // names[1] = "sq1"
        ];

        let mut reader = &data[..];
        let actual = read_header(&mut reader).await?;

        let names = [BString::from("sq0"), BString::from("sq1")]
            .into_iter()
            .collect();
        let expected = csi::binning_index::index::header::Builder::gff()
            .set_reference_sequence_names(names)
            .build();

        assert_eq!(actual, expected);

        Ok(())
    }
}