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structurize the alignment result #13

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structurize the alignment result #13

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99e64cb
structurize the alignment result
Feb 4, 2020
e866d8f
rustfmt build.rs
Feb 4, 2020
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1 change: 0 additions & 1 deletion build.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@ fn libcxx() -> &'static str {
}

fn main() {

cc::Build::new()
.cpp(true)
.static_flag(true)
Expand Down
158 changes: 104 additions & 54 deletions src/lib.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -178,6 +178,12 @@ pub struct StarAligner {

unsafe impl Send for StarAligner {}

/// A container for the primary and secondary alignments
pub struct StarAlignment {
pub primary: bam::Record,
pub secondary: Vec<bam::Record>,
}

impl StarAligner {
fn new(reference: Arc<InnerStarReference>) -> StarAligner {
let aligner = unsafe { bindings::init_aligner_from_ref(reference.as_ref().reference) };
Expand All @@ -190,7 +196,7 @@ impl StarAligner {
}

/// Aligns a given read and produces BAM records
pub fn align_read(&mut self, name: &[u8], read: &[u8], qual: &[u8]) -> Vec<bam::Record> {
pub fn align_read(&mut self, name: &[u8], read: &[u8], qual: &[u8]) -> StarAlignment {
align_read_rust(self.aligner, read, qual, &mut self.aln_buf).unwrap();
self.parse_sam_to_records(name)
}
Expand All @@ -209,21 +215,50 @@ impl StarAligner {
qual1: &[u8],
read2: &[u8],
qual2: &[u8],
) -> (Vec<bam::Record>, Vec<bam::Record>) {
) -> (StarAlignment, StarAlignment) {
align_read_pair_rust(self.aligner, read1, qual1, read2, qual2, &mut self.aln_buf).unwrap();
let full_vec = self.parse_sam_to_records(name);

// Partition the records into first mate and second mate
let mut first_vec: Vec<bam::Record> = Vec::new();
let mut second_vec: Vec<bam::Record> = Vec::new();
for rec in full_vec {
if rec.is_first_in_template() {
first_vec.push(rec);
} else {
second_vec.push(rec);

let mut primary1: Option<bam::Record> = None;
let mut primary2: Option<bam::Record> = None;
let mut secondary1 = Vec::new();
let mut secondary2 = Vec::new();

for slc in self.aln_buf.split(|c| *c == b'\n') {
if slc.len() > 0 {
self.sam_buf.clear();
self.sam_buf.extend_from_slice(name);
self.sam_buf.extend_from_slice(slc);
let record =
bam::Record::from_sam(&self.reference.as_ref().header_view, &self.sam_buf)
.unwrap();
let is_primary = !record.is_secondary();
let is_first = record.is_first_in_template();
if is_primary && is_first && primary1.is_none() {
let _ = primary1.replace(record);
} else if is_primary && !is_first && primary2.is_none() {
let _ = primary2.replace(record);
} else if is_first {
secondary1.push(record);
} else {
secondary2.push(record);
}
}
}
(first_vec, second_vec)

// if we don't have primary alignments, panic
let primary1 = primary1.unwrap();
let primary2 = primary2.unwrap();

(
StarAlignment {
primary: primary1,
secondary: secondary1,
},
StarAlignment {
primary: primary2,
secondary: secondary2,
},
)
}

/// Aligns a given read and return the resulting SAM string
Expand All @@ -242,8 +277,9 @@ impl StarAligner {
/// Given a list of BAM records as a SAM-format string in which records are separated by new
/// lines, add the records to a vector and append the read name to the beginning of them so
/// that they conform with BAM specifications
fn parse_sam_to_records(&mut self, name: &[u8]) -> Vec<bam::Record> {
let mut records = Vec::new();
fn parse_sam_to_records(&mut self, name: &[u8]) -> StarAlignment {
let mut primary: Option<bam::Record> = None;
let mut secondary = Vec::new();
for slc in self.aln_buf.split(|c| *c == b'\n') {
if slc.len() > 0 {
self.sam_buf.clear();
Expand All @@ -252,11 +288,18 @@ impl StarAligner {
let record =
bam::Record::from_sam(&self.reference.as_ref().header_view, &self.sam_buf)
.unwrap();
records.push(record);
if primary.is_none() && !record.is_secondary() {
let _ = primary.replace(record);
} else {
secondary.push(record);
}
}
}

records
// if we're missing a primary alignment, panic
let primary = primary.unwrap();

StarAlignment { primary, secondary }
}
}

Expand Down Expand Up @@ -403,29 +446,32 @@ mod test {
let reference = StarReference::load(settings).unwrap();
let mut aligner = reference.get_aligner();

let recs = aligner.align_read(NAME, ERCC_READ_1, ERCC_QUAL_1);
assert_eq!(recs.len(), 1);
assert_eq!(recs[0].pos(), 50);
assert_eq!(recs[0].tid(), 0);
println!("{:?}", recs);

let recs = aligner.align_read(NAME, ERCC_READ_2, ERCC_QUAL_2);
assert_eq!(recs.len(), 1);
assert_eq!(recs[0].tid(), 0);
assert_eq!(recs[0].pos(), 500);
println!("{:?}", recs);

let recs = aligner.align_read(NAME, ERCC_READ_3, ERCC_QUAL_3);
assert_eq!(recs.len(), 2);
assert_eq!(recs[0].flags(), 0);
assert_eq!(recs[0].tid(), 39);
assert_eq!(recs[0].pos(), 27);
assert_eq!(recs[0].mapq(), 3);
assert_eq!(recs[1].flags(), 0x110); // REVERSE,SECONDARY
assert_eq!(recs[1].tid(), 72);
assert_eq!(recs[1].pos(), 553);
assert_eq!(recs[1].mapq(), 3);
println!("{:?}", recs);
let StarAlignment { primary, secondary } =
aligner.align_read(NAME, ERCC_READ_1, ERCC_QUAL_1);
assert_eq!(secondary.len(), 0);
assert_eq!(primary.pos(), 50);
assert_eq!(primary.tid(), 0);
println!("{:?}", primary);

let StarAlignment { primary, secondary } =
aligner.align_read(NAME, ERCC_READ_2, ERCC_QUAL_2);
assert_eq!(secondary.len(), 0);
assert_eq!(primary.tid(), 0);
assert_eq!(primary.pos(), 500);
println!("{:?}", primary);

let StarAlignment { primary, secondary } =
aligner.align_read(NAME, ERCC_READ_3, ERCC_QUAL_3);
assert_eq!(secondary.len(), 1);
assert_eq!(primary.flags(), 0);
assert_eq!(primary.tid(), 39);
assert_eq!(primary.pos(), 27);
assert_eq!(primary.mapq(), 3);
assert_eq!(secondary[0].flags(), 0x110); // REVERSE,SECONDARY
assert_eq!(secondary[0].tid(), 72);
assert_eq!(secondary[0].pos(), 553);
assert_eq!(secondary[0].mapq(), 3);
println!("{:?}, {:?}", primary, secondary);
}

#[test]
Expand All @@ -437,19 +483,21 @@ mod test {

let t1 = std::thread::spawn(move || {
for _ in 0..100000 {
let recs = aligner1.align_read(NAME, ERCC_READ_1, ERCC_QUAL_1);
assert_eq!(recs.len(), 1);
assert_eq!(recs[0].pos(), 50);
assert_eq!(recs[0].tid(), 0);
let StarAlignment { primary, secondary } =
aligner1.align_read(NAME, ERCC_READ_1, ERCC_QUAL_1);
assert_eq!(secondary.len(), 0);
assert_eq!(primary.pos(), 50);
assert_eq!(primary.tid(), 0);
}
});

let t2 = std::thread::spawn(move || {
for _ in 0..100000 {
let recs = aligner2.align_read(NAME, ERCC_READ_2, ERCC_QUAL_2);
assert_eq!(recs.len(), 1);
assert_eq!(recs[0].pos(), 500);
assert_eq!(recs[0].tid(), 0);
let StarAlignment { primary, secondary } =
aligner2.align_read(NAME, ERCC_READ_2, ERCC_QUAL_2);
assert_eq!(secondary.len(), 0);
assert_eq!(primary.pos(), 500);
assert_eq!(primary.tid(), 0);
}
});

Expand Down Expand Up @@ -510,9 +558,9 @@ mod test {
let read = b"GTGCGGGGAGAAGTTTCAAGAAGGTTCTTATGGAAAAAAGGCTGTGAGCATAGAAAGCAGTCATAGGAGGTTGGGGAACTAGCTTGTCCCTCCCCACC";
let qual = b"GGGAGIGIIIGIIGGGGIIGGIGGAGGAGGAAG.GGIIIG<AGGAGGGIGGGGIIIIIGGIGGGGGIGIIGGAGGGGGIGGGIGIIGGGGIIGGGIIG";
let name = b"gatactaga";
let res = aligner.align_read(name, read, qual);
assert!(res.len() > 0);
assert_eq!(res[0].pos(), 30070473);
let StarAlignment { primary, secondary } = aligner.align_read(name, read, qual);
assert_eq!(secondary.len(), 0);
assert_eq!(primary.pos(), 30070473);
}

#[test]
Expand All @@ -528,9 +576,10 @@ mod test {
let read = b"GTGCGGGGAGAAGTTTCAAGAAGGTTCTTATGGAAAAAAGGCTGTGAGCATAGAAAGCAGTCATAGGAGGTTGGGGAACTAGCTTGTCCCTCCCCACC";
let qual = b"GGGAGIGIIIGIIGGGGIIGGIGGAGGAGGAAG.GGIIIG<AGGAGGGIGGGGIIIIIGGIGGGGGIGIIGGAGGGGGIGGGIGIIGGGGIIGGGIIG";
let name = b"gatactaga";
let res = aligner.align_read(name, read, qual);
for record in res.iter() {
out.write(&record).unwrap();
let StarAlignment { primary, secondary } = aligner.align_read(name, read, qual);
out.write(&primary).unwrap();
for record in &secondary {
out.write(record).unwrap();
}
let bam_wrapped = bam::Reader::from_path(&"test/test.bam");
match bam_wrapped {
Expand All @@ -549,6 +598,7 @@ mod test {
i += 1;
}
*/
std::fs::remove_file(&"test/test.bam").unwrap();
}

/*
Expand Down