Support querying for SAM/GTF/GFF records

[claymcleod]

Currently, noodles::sam::Reader.records(), noodles::gff::Reader.records(), and noodles::gtf::Reader.records() do not support querying of noodles::core::region::Regions like BAM and CRAM do. I'm intuiting the reason why is because they do not have the specialized indexes like BAM/CRAM do. However, it would be really nice for noodles to provide the functionality of querying a region for these files, even if it required making some generic index for the files before querying.

Required for stjude-rust-labs/ngs#18 and stjude-rust-labs/ngs#19.

[zaeleus]

noodles 0.25.0/noodles-sam 0.17.0 (2022-07-05) introduced a query iterator to query SAM (sam::Reader::query).

noodles 0.39.0/noodles-gff 0.12.0/noodles-gtf 0.10.0 (2023-05-18) now have query iterators to query GFF (gff::Reader::query) and GTF (gtf::Reader::query).

noodles 0.39.0/noodles-csi 0.18.0 (2023-05-18) also has a generic indexed record parser (IndexedRecords) and filter (FilterByRegion).

let records = Query::new(&mut decoder, chunks)
    .indexed_records(&header)
    .filter_by_region(&region);

for result in records {
    let record = result?;
    // ...
}

This pattern is wrapped by tabix::io::IndexedReader.

let reader = tabix::io::IndexedReader::new(inner, index);
for result in reader.query(&region) {
    let record = result?;
    // ...
}