Struct Record

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pub struct Record<const N: usize>(/* private fields */);

Expand description

A BED record.

Implementations§

Source §

impl<const N: usize> Record<N>

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pub const fn standard_field_count(&self) -> usize

Returns the number of standard fields.

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pub fn other_fields(&self) -> OtherFields<'_, N>

Returns the other fields.

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impl Record<3>

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pub fn reference_sequence_name(&self) -> &BStr

Returns the reference sequence name.

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pub fn feature_start(&self) -> Result<Position>

Returns the feature start.

Examples found in repository ?

examples/bed_query.rs (line 39)

13fn main() -> Result<(), Box<dyn std::error::Error>> {
14    let mut args = env::args().skip(1);
15
16    let src = args.next().expect("missing src");
17    let region: Region = args.next().expect("missing region").parse()?;
18
19    let index_src = format!("{src}.tbi");
20    let index = tabix::fs::read(index_src)?;
21
22    let header = index.header().expect("missing tabix header");
23    let reference_sequence_id = header
24        .reference_sequence_names()
25        .get_index_of(region.name())
26        .expect("invalid reference sequence name");
27
28    let mut decoder = File::open(src).map(bgzf::io::Reader::new)?;
29    let chunks = index.query(reference_sequence_id, region.interval())?;
30    let query = csi::io::Query::new(&mut decoder, chunks);
31
32    let mut reader = bed::io::Reader::<3, _>::new(query);
33    let mut record = bed::Record::default();
34
35    let stdout = io::stdout().lock();
36    let mut writer = bed::io::Writer::<3, _>::new(stdout);
37
38    while reader.read_record(&mut record)? != 0 {
39        let start = record.feature_start()?;
40        let end = record.feature_end().expect("missing feature end")?;
41        let interval = (start..=end).into();
42
43        if !region.interval().intersects(interval) {
44            continue;
45        }
46
47        writer.write_record(&record)?;
48    }
49
50    Ok(())
51}

Source

pub fn feature_end(&self) -> Option<Result<Position>>

Returns the feature end.

Examples found in repository ?

examples/bed_query.rs (line 40)

13fn main() -> Result<(), Box<dyn std::error::Error>> {
14    let mut args = env::args().skip(1);
15
16    let src = args.next().expect("missing src");
17    let region: Region = args.next().expect("missing region").parse()?;
18
19    let index_src = format!("{src}.tbi");
20    let index = tabix::fs::read(index_src)?;
21
22    let header = index.header().expect("missing tabix header");
23    let reference_sequence_id = header
24        .reference_sequence_names()
25        .get_index_of(region.name())
26        .expect("invalid reference sequence name");
27
28    let mut decoder = File::open(src).map(bgzf::io::Reader::new)?;
29    let chunks = index.query(reference_sequence_id, region.interval())?;
30    let query = csi::io::Query::new(&mut decoder, chunks);
31
32    let mut reader = bed::io::Reader::<3, _>::new(query);
33    let mut record = bed::Record::default();
34
35    let stdout = io::stdout().lock();
36    let mut writer = bed::io::Writer::<3, _>::new(stdout);
37
38    while reader.read_record(&mut record)? != 0 {
39        let start = record.feature_start()?;
40        let end = record.feature_end().expect("missing feature end")?;
41        let interval = (start..=end).into();
42
43        if !region.interval().intersects(interval) {
44            continue;
45        }
46
47        writer.write_record(&record)?;
48    }
49
50    Ok(())
51}