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fix: Fix read processing when building consensus reads #199

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merged 6 commits into from
Dec 1, 2021
Merged

fix: Fix read processing when building consensus reads #199

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7274bd3
Several fixes
FelixMoelder Nov 24, 2021
0dee744
introduce groupendidx struct
FelixMoelder Nov 24, 2021
dd39607
Update tests
FelixMoelder Nov 24, 2021
a1587ac
Add umi to read
FelixMoelder Nov 24, 2021
b9f3faf
remove check for softclips
FelixMoelder Nov 24, 2021
89e13cd
Reduce duplicate code
FelixMoelder Dec 1, 2021
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35 changes: 20 additions & 15 deletions src/bam/collapse_reads_to_fragments/calc_consensus.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,22 @@ use bio_types::sequence::SequenceReadPairOrientation;
use derive_new::new;
use itertools::Itertools;
use rust_htslib::bam;
use rust_htslib::bam::record::Aux;
use std::collections::{HashMap, HashSet};
use std::ops::BitOrAssign;

const ALLELES: &[u8] = b"ACGT";

pub fn get_umi_string(rec: &bam::record::Record) -> String {
let umi = match rec.aux(b"RX") {
Ok(Aux::String(value)) => {
format!(" RX:Z:{}", value)
}
_ => String::from(""),
};
umi
}

#[derive(Eq, PartialEq)]
enum StrandObservation {
None,
Expand Down Expand Up @@ -94,12 +105,10 @@ impl<'a> CalcOverlappingConsensus<'a> {
if let Some(mut read_orientations) = read_orientations_opt {
consensus_strand.append(&mut read_orientations)
}
let consensus_rec = fastq::Record::with_attrs(
&name,
Some(&String::from_utf8(consensus_strand).unwrap()),
&consensus_seq,
&consensus_qual,
);
let umi = get_umi_string(&self.recs1()[0]);
let description = format!("{}{}", String::from_utf8(consensus_strand).unwrap(), umi);
let consensus_rec =
fastq::Record::with_attrs(&name, Some(&description), &consensus_seq, &consensus_qual);
(consensus_rec, consensus_lh)
}

Expand Down Expand Up @@ -141,9 +150,7 @@ impl<'a> CalcOverlappingConsensus<'a> {
StrandObservation::Forward => consensus_strand.push(b'+'),
StrandObservation::Reverse => consensus_strand.push(b'-'),
StrandObservation::Both => consensus_strand.push(b'*'),
StrandObservation::None => {
unreachable!()
}
StrandObservation::None => consensus_strand.push(b'.'),
}
}
fn build_read_orientation_string(&self) -> Option<Vec<u8>> {
Expand Down Expand Up @@ -282,12 +289,10 @@ impl<'a> CalcNonOverlappingConsensus<'a> {
self.seqids().len(),
)
};
let consensus_rec = fastq::Record::with_attrs(
&name,
Some(&String::from_utf8(consensus_strand).unwrap()),
&consensus_seq,
&consensus_qual,
);
let umi = get_umi_string(&self.recs()[0]);
let description = format!("{}{}", String::from_utf8(consensus_strand).unwrap(), umi);
let consensus_rec =
fastq::Record::with_attrs(&name, Some(&description), &consensus_seq, &consensus_qual);
(consensus_rec, consensus_lh)
}
pub fn recs(&self) -> &[bam::Record] {
Expand Down
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