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In my experiment, "zlib-ng" enabled noodles-bam reader was about 36% faster, even faster than rust-htslib. zlib-ng Normal const TEST_BAM2: &str = "NA12878.mapped.ILLUMINA.bwa.CEU.low_coverage.20121211.bam";
const BAM2_CHR1_LEN: usize = 12903629;
const SAMPLE_SIZE: usize = 100;
const MAX_ITER: usize = 200000;
const CHROM: &str = "13";
let mut reader = bam::io::indexed_reader::Builder::default()
.build_from_path(TEST_BAM2)
.unwrap();
let header = reader.read_header().unwrap();
let region = CHROM.parse().unwrap();
let mut query = reader.query(&header, ®ion).unwrap().into_reader();
let mut i_iter = 0..MAX_ITER;
let mut record = Record::default();
while let (Ok(true), Some(_)) =
(query.read_record(&mut record).map(|n| n > 0), i_iter.next())
{
std::str::from_utf8(record.name().unwrap().as_bytes()).unwrap();
record.alignment_start().unwrap().unwrap();
record.template_length();
} |
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Answered by
zaeleus
May 16, 2024
Replies: 1 comment 1 reply
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Rust features are additive. You can select the flate2 backend by adding it as a dependency to your application and enabling the desired feature set, i.e., flate2 = { version = "1.0.30", default-features = false, features = ["zlib-ng"] }Also note that noodles-bgzf supports linking to libdeflate via the noodles-bgzf = { version = "0.29.0", features = ["libdeflate"] } |
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1 reply
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Sorry, I missed libdeflate feature. Thanks for your response. |
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Answer selected by
Crispy13
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Rust features are additive. You can select the flate2 backend by adding it as a dependency to your application and enabling the desired feature set, i.e.,
Also note that noodles-bgzf supports linking to libdeflate via the
libdeflatefeature. This will typically yield better performance than general-purpose DEFLATE implementations.