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debug: fixed --keep-zeros skip/dup loci #73

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Jul 29, 2024
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debug: fixed --keep-zeros skip/dup loci #73

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153 changes: 140 additions & 13 deletions src/commands/base_depth.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -293,13 +293,14 @@ impl<F: ReadFilter> RegionProcessor for BaseProcessor<F> {
let mut new_result = vec![];
let name = PileupPosition::compact_refseq(&header, tid);
let mut pos = start;
if let Some(position) = result.get(0) {

for position in result.into_iter() {
while pos < (position.pos - self.coord_base) {
new_result.push(PileupPosition::new(name.clone(), pos + self.coord_base));
pos += 1;
}
pos += result.len() as u32;
new_result.extend(result.into_iter());
new_result.push(position);
pos += 1;
}
while pos < stop {
new_result.push(PileupPosition::new(name.clone(), pos + self.coord_base));
Expand Down Expand Up @@ -439,6 +440,49 @@ mod tests {
positions
}

#[fixture]
fn non_mate_aware_keep_zeros_positions(
bamfile: (PathBuf, TempDir),
read_filter: DefaultReadFilter,
) -> HashMap<String, Vec<PileupPosition>> {
let cpus = utils::determine_allowed_cpus(8).unwrap();

// Use the number of cpus available as a proxy for how may ref seqs to hold in memory at one time.
let base_processor = BaseProcessor::new(
bamfile.0.clone(),
None,
false,
true, // keep-zeros
1,
read_filter,
500_000,
cpus,
None,
);

let par_granges_runner = par_granges::ParGranges::new(
bamfile.0,
None,
None,
None,
true,
Some(cpus),
None,
Some(0.001),
base_processor,
);
let mut positions = HashMap::new();
par_granges_runner
.process()
.unwrap()
.into_iter()
.for_each(|p| {
let pos = positions.entry(p.ref_seq.clone()).or_insert_with(Vec::new);
pos.push(p)
});
positions
}

#[fixture]
fn mate_aware_positions(
bamfile: (PathBuf, TempDir),
Expand Down Expand Up @@ -482,6 +526,49 @@ mod tests {
positions
}

#[fixture]
fn mate_aware_keep_zeros_positions(
bamfile: (PathBuf, TempDir),
read_filter: DefaultReadFilter,
) -> HashMap<String, Vec<PileupPosition>> {
let cpus = utils::determine_allowed_cpus(8).unwrap();

// Use the number of cpus available as a proxy for how may ref seqs to hold in memory at one time.
let base_processor = BaseProcessor::new(
bamfile.0.clone(),
None,
false,// mate aware
true, // keep-zeros
1,
read_filter,
500_000,
cpus,
None,
);

let par_granges_runner = par_granges::ParGranges::new(
bamfile.0,
None,
None,
None,
true,
Some(cpus),
None,
Some(0.001),
base_processor,
);
let mut positions = HashMap::new();
par_granges_runner
.process()
.unwrap()
.into_iter()
.for_each(|p| {
let pos = positions.entry(p.ref_seq.clone()).or_insert_with(Vec::new);
pos.push(p)
});
positions
}

fn non_mate_aware_positions_base_qual(
bamfile: (PathBuf, TempDir),
read_filter: DefaultReadFilter,
Expand Down Expand Up @@ -650,16 +737,19 @@ mod tests {

#[rstest(
positions,
awareness_modifier,
case::mate_unaware(non_mate_aware_positions(bamfile(), read_filter()), 0),
case::mate_aware(mate_aware_positions(bamfile(), read_filter()), 0),
case::mate_unaware_bq(non_mate_aware_positions_base_qual(bamfile(), read_filter(), 1), 0),
case::mate_aware_bq(mate_aware_positions_base_qual(bamfile(), read_filter(), 1), 0),
case::mate_unaware_bq(non_mate_aware_positions_base_qual(bamfile(), read_filter(), 3), 0),
case::mate_aware_bq(mate_aware_positions_base_qual(bamfile(), read_filter(), 3), 0)
keep_zeros,
case::mate_unaware(non_mate_aware_positions(bamfile(), read_filter()), false),
case::mate_aware(mate_aware_positions(bamfile(), read_filter()), false),
case::mate_unaware_bq(non_mate_aware_positions_base_qual(bamfile(), read_filter(), 1), false),
case::mate_aware_bq(mate_aware_positions_base_qual(bamfile(), read_filter(), 1), false),
case::mate_unaware_bq(non_mate_aware_positions_base_qual(bamfile(), read_filter(), 3), false),
case::mate_aware_bq(mate_aware_positions_base_qual(bamfile(), read_filter(), 3), false),
case::mate_unaware_keep_zeros(non_mate_aware_keep_zeros_positions(bamfile(), read_filter()), true),
case::mate_aware_keep_zeros(mate_aware_keep_zeros_positions(bamfile(), read_filter()), true),
)]
fn check_depths(positions: HashMap<String, Vec<PileupPosition>>, awareness_modifier: u32) {
fn check_depths(positions: HashMap<String, Vec<PileupPosition>>, keep_zeros: bool) {
assert_eq!(positions.get("chr1").unwrap()[0].depth, 1);
assert_eq!(positions.get("chr1").unwrap()[1].depth, 1);
assert_eq!(positions.get("chr1").unwrap()[4].depth, 2);
assert_eq!(positions.get("chr1").unwrap()[9].depth, 3);
assert_eq!(positions.get("chr1").unwrap()[14].depth, 4);
Expand All @@ -668,8 +758,45 @@ mod tests {
assert_eq!(positions.get("chr1").unwrap()[29].depth, 3);
assert_eq!(positions.get("chr1").unwrap()[34].depth, 2);
assert_eq!(positions.get("chr1").unwrap()[39].depth, 1);
// NB: -6 bc there are 6 positions with no coverage from 44-50
assert_eq!(positions.get("chr1").unwrap()[78 - 6].depth, 4);

if !keep_zeros {
// NB: -6 bc there are 6 positions with no coverage from 44-50
assert_eq!(positions.get("chr1").unwrap()[78 - 6].depth, 4);
} else {
// NB: with --keep-zeros then there should be no skipped loci
assert_eq!(positions.get("chr1").unwrap().len(), 100);

// NB: Since positions[0].pos == 1 for this test data: positions[i].pos == i+1
for (i,p) in positions.get("chr1").unwrap().iter().enumerate() {
assert_eq!(p.pos, (i+1).try_into().unwrap());
}

assert_eq!(positions.get("chr1").unwrap()[43].depth, 1);
assert_eq!(positions.get("chr1").unwrap()[44].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[45].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[46].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[47].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[48].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[49].depth, 1);
assert_eq!(positions.get("chr1").unwrap()[53].depth, 1);
assert_eq!(positions.get("chr1").unwrap()[54].depth, 2);
assert_eq!(positions.get("chr1").unwrap()[55].depth, 2);
assert_eq!(positions.get("chr1").unwrap()[56].depth, 2);
assert_eq!(positions.get("chr1").unwrap()[57].depth, 2);
assert_eq!(positions.get("chr1").unwrap()[58].depth, 2);
assert_eq!(positions.get("chr1").unwrap()[59].depth, 3);
assert_eq!(positions.get("chr1").unwrap()[60].depth, 3);
assert_eq!(positions.get("chr1").unwrap()[61].depth, 3);
assert_eq!(positions.get("chr1").unwrap()[62].depth, 3);
assert_eq!(positions.get("chr1").unwrap()[63].depth, 3);
assert_eq!(positions.get("chr1").unwrap()[64].depth, 4);
assert_eq!(positions.get("chr1").unwrap()[68].depth, 4);
assert_eq!(positions.get("chr1").unwrap()[93].depth, 1);
assert_eq!(positions.get("chr1").unwrap()[94].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[95].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[96].depth, 0);
assert_eq!(positions.get("chr1").unwrap()[99].depth, 0);
}
}

#[rstest(
Expand Down
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