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2024/10/24-10:34:24 (Linux cray unknown)
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@pbenner
pbenner committed Oct 24, 2024
1 parent 071d8eb commit 53acd0d
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Showing 2 changed files with 30 additions and 35 deletions.
3 changes: 1 addition & 2 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,13 +21,12 @@ Please find the API documentation [here](https://docs.rs/rustynetics/latest/rust
use crate::bam::BamReaderOptions;
use crate::granges::GRanges;

let mut granges = GRanges::default();
let mut options = BamReaderOptions::default();

options.read_cigar = true;
options.read_qual = true;

if Ok(_) = granges.import_bam_single_end("tests/test_bam_2.bam", Some(options)) {
if Ok(granges) = GRanges::import_bam_single_end("tests/test_bam_2.bam", Some(options)) {
println!("{}", granges);
}
```
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62 changes: 29 additions & 33 deletions src/granges_bam.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,7 @@ const BUFSIZE : usize = 10000;

impl GRanges {

pub fn read_bam_single_end<R: Read>(&mut self, reader: R, options_arg: Option<BamReaderOptions>) -> Result<(), Box<dyn Error>> {
pub fn read_bam_single_end<R: Read>(reader: R, options_arg: Option<BamReaderOptions>) -> Result<Self, Box<dyn Error>> {

let options = options_arg.unwrap_or_default();

Expand Down Expand Up @@ -99,23 +99,23 @@ impl GRanges {
flag .shrink_to_fit();
qual .shrink_to_fit();

*self = GRanges::new(seqnames, from, to, strand);
self.meta.add("flag", MetaData::IntArray(flag))?;
self.meta.add("mapq", MetaData::IntArray(mapq))?;
let mut granges = GRanges::new(seqnames, from, to, strand);
granges.meta.add("flag", MetaData::IntArray(flag))?;
granges.meta.add("mapq", MetaData::IntArray(mapq))?;
if options.read_sequence {
self.meta.add("sequence", MetaData::StringArray(sequence))?;
granges.meta.add("sequence", MetaData::StringArray(sequence))?;
}
if options.read_cigar {
self.meta.add("cigar", MetaData::StringArray(cigar))?;
granges.meta.add("cigar", MetaData::StringArray(cigar))?;
}
if options.read_qual {
self.meta.add("qual", MetaData::StringArray(qual))?;
granges.meta.add("qual", MetaData::StringArray(qual))?;
}

Ok(())
Ok(granges)
}

pub fn read_bam_paired_end<R: Read>(&mut self, reader: R, options_arg: Option<BamReaderOptions>) -> Result<(), Box<dyn Error>> {
pub fn read_bam_paired_end<R: Read>(reader: R, options_arg: Option<BamReaderOptions>) -> Result<Self, Box<dyn Error>> {

let mut options = options_arg.unwrap_or_default();

Expand Down Expand Up @@ -225,26 +225,26 @@ impl GRanges {
qual1 .shrink_to_fit();
qual2 .shrink_to_fit();

*self = GRanges::new(seqnames, from, to, strand);
self.meta.add("flag1", MetaData::IntArray(flag1))?;
self.meta.add("flag2", MetaData::IntArray(flag2))?;
self.meta.add("mapq1", MetaData::IntArray(mapq1))?;
self.meta.add("mapq2", MetaData::IntArray(mapq2))?;
let mut granges = GRanges::new(seqnames, from, to, strand);
granges.meta.add("flag1", MetaData::IntArray(flag1))?;
granges.meta.add("flag2", MetaData::IntArray(flag2))?;
granges.meta.add("mapq1", MetaData::IntArray(mapq1))?;
granges.meta.add("mapq2", MetaData::IntArray(mapq2))?;

if options.read_sequence {
self.meta.add("sequence1", MetaData::StringArray(sequence1))?;
self.meta.add("sequence2", MetaData::StringArray(sequence2))?;
granges.meta.add("sequence1", MetaData::StringArray(sequence1))?;
granges.meta.add("sequence2", MetaData::StringArray(sequence2))?;
}
if options.read_cigar {
self.meta.add("cigar1", MetaData::StringArray(cigar1))?;
self.meta.add("cigar2", MetaData::StringArray(cigar2))?;
granges.meta.add("cigar1", MetaData::StringArray(cigar1))?;
granges.meta.add("cigar2", MetaData::StringArray(cigar2))?;
}
if options.read_qual {
self.meta.add("qual1", MetaData::StringArray(qual1))?;
self.meta.add("qual2", MetaData::StringArray(qual2))?;
granges.meta.add("qual1", MetaData::StringArray(qual1))?;
granges.meta.add("qual2", MetaData::StringArray(qual2))?;
}

Ok(())
Ok(granges)
}

}
Expand All @@ -253,14 +253,14 @@ impl GRanges {

impl GRanges {

pub fn import_bam_single_end(&mut self, filename: &str, options: Option<BamReaderOptions>) -> Result<(), Box<dyn Error>> {
pub fn import_bam_single_end(filename: &str, options: Option<BamReaderOptions>) -> Result<Self, Box<dyn Error>> {
let file = NetFile::open(filename)?;
self.read_bam_single_end(file, options)
Self::read_bam_single_end(file, options)
}

pub fn import_bam_paired_end(&mut self, filename: &str, options: Option<BamReaderOptions>) -> Result<(), Box<dyn Error>> {
pub fn import_bam_paired_end(filename: &str, options: Option<BamReaderOptions>) -> Result<Self, Box<dyn Error>> {
let file = NetFile::open(filename)?;
self.read_bam_paired_end(file, options)
Self::read_bam_paired_end(file, options)
}
}

Expand All @@ -279,15 +279,13 @@ mod tests {

let n = 4891;

let mut granges = GRanges::default();
let mut options = BamReaderOptions::default();

options.read_cigar = true;
options.read_qual = true;

assert!(
granges.import_bam_single_end("tests/test_bam_2.bam", Some(options)).is_ok()
);
let granges = GRanges::import_bam_single_end("tests/test_bam_2.bam", Some(options)).unwrap();

assert_eq!(
granges.num_rows(), n
);
Expand Down Expand Up @@ -328,16 +326,14 @@ mod tests {

let n = 2335;

let mut granges = GRanges::default();
let mut options = BamReaderOptions::default();

options.read_cigar = true;
options.read_qual = true;
options.read_sequence = true;

assert!(
granges.import_bam_paired_end("tests/test_bam_2.bam", Some(options)).is_ok()
);
let granges = GRanges::import_bam_paired_end("tests/test_bam_2.bam", Some(options)).unwrap();

assert_eq!(
granges.num_rows(), n
);
Expand Down

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