ngs/convert/
sam.rs

1//! Conversions from a SAM file to other next-generation sequencing file formats.
2
3use std::io;
4use std::num::NonZeroUsize;
5use std::path::PathBuf;
6
7use anyhow::Context;
8use noodles::bam;
9use noodles::bgzf;
10use noodles::bgzf::writer::CompressionLevel;
11use noodles::cram;
12use noodles::fasta;
13use noodles::sam::alignment::Record;
14use noodles::sam::header::record::value::map::ReferenceSequence;
15use noodles::sam::header::record::value::Map;
16use tokio::fs::File;
17use tracing::info;
18
19use crate::utils::args::CompressionStrategy;
20use crate::utils::args::NumberOfRecords;
21use crate::utils::display::RecordCounter;
22use crate::utils::formats;
23use crate::utils::formats::sam::ParsedAsyncSAMFile;
24
25/// Converts a SAM file to a BAM file in an asyncronous fashion.
26pub async fn to_bam_async(
27    from: PathBuf,
28    to: PathBuf,
29    max_records: NumberOfRecords,
30    compression_strategy: CompressionStrategy,
31) -> anyhow::Result<()> {
32    // (1) Open and parse the BAM file.
33    let ParsedAsyncSAMFile { mut reader, header } =
34        formats::sam::open_and_parse_async(from).await?;
35
36    // (2) Determine the compression level.
37    let compression_level: CompressionLevel = compression_strategy.into();
38
39    // (3) Open the SAM file writer.
40    let mut writer = File::create(to)
41        .await
42        .map(|f| {
43            bgzf::r#async::writer::Builder::default()
44                .set_compression_level(compression_level)
45                .build_with_writer(f)
46        })
47        .map(bam::AsyncWriter::from)
48        .with_context(|| "opening output filestream")?;
49
50    // (4) Write the header and the reference sequences.
51    writer.write_header(&header.parsed).await?;
52    writer
53        .write_reference_sequences(header.parsed.reference_sequences())
54        .await?;
55
56    let mut counter = RecordCounter::new();
57    let mut record = Record::default();
58
59    // (5) Write each record in the BAM file to the SAM file.
60    while reader.read_record(&header.parsed, &mut record).await? != 0 {
61        writer
62            .write_alignment_record(&header.parsed, &record)
63            .await?;
64
65        counter.inc();
66
67        if counter.time_to_break(&max_records) {
68            break;
69        }
70    }
71
72    // (6) Shutdown the async writer.
73    writer.shutdown().await?;
74
75    Ok(())
76}
77
78/// Converts a SAM file to a CRAM file in an asyncronous fashion.
79pub async fn to_cram_async(
80    from: PathBuf,
81    to: PathBuf,
82    fasta: PathBuf,
83    max_records: NumberOfRecords,
84) -> anyhow::Result<()> {
85    // (1) Open and parse the SAM file.
86    let ParsedAsyncSAMFile {
87        mut reader,
88        mut header,
89        ..
90    } = formats::sam::open_and_parse_async(from).await?;
91
92    // (2) Builds the FASTA repository and associated index.
93    let mut fasta_reader = formats::fasta::open(fasta)?;
94    let records: Vec<fasta::Record> = fasta_reader
95        .records()
96        .collect::<io::Result<Vec<fasta::Record>>>()?;
97
98    // (3) Modifies the existing SAM header to include the reference sequences provided.
99    let reference_sequences = header.parsed.reference_sequences_mut();
100    for record in records.iter() {
101        let name_as_string = record.name().to_owned();
102        let name = name_as_string.parse()?;
103        let length = record.sequence().len();
104
105        let reference_sequence = Map::<ReferenceSequence>::new(NonZeroUsize::try_from(length)?);
106        reference_sequences.insert(name, reference_sequence);
107    }
108
109    let repository = fasta::Repository::new(records);
110
111    // (4) Open the CRAM file writer.
112    let handle = File::create(to).await?;
113    let mut writer = cram::r#async::writer::Builder::default()
114        .set_reference_sequence_repository(repository)
115        .build_with_writer(handle);
116
117    // (5) Write the CRAM file.
118    info!("Writing the file definition and header to CRAM file.");
119
120    writer.write_file_definition().await?;
121    writer.write_file_header(&header.parsed).await?;
122
123    let mut counter = RecordCounter::new();
124    let mut record = Record::default();
125
126    // (6) Write each record in the SAM file to the CRAM file.
127    info!("Writing records to CRAM file.");
128    while reader.read_record(&header.parsed, &mut record).await? != 0 {
129        let cram_record = cram::Record::try_from_alignment_record(&header.parsed, &record)?;
130        writer
131            .write_record(&header.parsed, cram_record)
132            .await
133            .with_context(|| "Writing CRAM record.")?;
134
135        counter.inc();
136
137        if counter.time_to_break(&max_records) {
138            break;
139        }
140    }
141
142    writer.shutdown(&header.parsed).await?;
143    Ok(())
144}
ngs/convert/sam.rs

ngs/convert/
sam.rs
