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Validate bedMethyl merge inputs and preserve row identities #664

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eb81703
Preflight bedMethyl merge inputs
SuhasSrinivasan Aug 5, 2026
ac7ae9d
Preserve bedMethyl identities during merge
SuhasSrinivasan Aug 5, 2026
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155 changes: 112 additions & 43 deletions modkit-core/src/bedmethyl_util/subcommands.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -182,25 +182,62 @@ pub struct EntryMergeBedMethyl {
min_sample_coverage: Option<u64>,
}

type BedMethylChunk = Vec<BedMethylLine>;
#[derive(Debug)]
struct MergeBedMethylLine {
record: BedMethylLine,
name: String,
}

impl ParseBedLine for MergeBedMethylLine {
fn parse(line: &str) -> Result<Self, MkError> {
let record = BedMethylLine::parse(line)?;
let name = line
.split_whitespace()
.nth(3)
.ok_or_else(|| {
MkError::InvalidBedMethyl(format!(
"missing name field in bedMethyl record:\n{line}"
))
})?
.to_string();
Ok(Self { record, name })
}

fn overlaps(&self, strand_rule: StrandRule) -> bool {
self.record.strand.overlaps(&strand_rule)
}

fn to_line(&self) -> String {
let parsed_line = self.record.to_line();
let mut fields = parsed_line.splitn(5, '\t');
let chrom = fields.next().unwrap();
let start = fields.next().unwrap();
let stop = fields.next().unwrap();
let _parsed_name = fields.next().unwrap();
let remaining_fields = fields.next().unwrap();
format!("{chrom}\t{start}\t{stop}\t{}\t{remaining_fields}", self.name)
}
}

type BedMethylChunk = Vec<MergeBedMethylLine>;

fn merge_data(
readers: &[HtsTabixHandler<BedMethylLine>],
readers: &[HtsTabixHandler<MergeBedMethylLine>],
chrom_coordinates: ChromCoordinates,
tid_to_name: &FxHashMap<u32, String>,
io_threads: usize,
min_samples: usize,
min_sample_coverage: u64,
) -> anyhow::Result<BedMethylChunk> {
type Key = (u64, ModCodeRepr, StrandRule);
type Key = (u64, ModCodeRepr, StrandRule, String);
// this is safe because of how we constructed this
let contig = tid_to_name.get(&chrom_coordinates.chrom_tid).unwrap();
let range = (chrom_coordinates.start_pos as u64)
..(chrom_coordinates.end_pos as u64);
// value is the merged record plus a tally of how many inputs contributed to
// it (each input has at most one record per key), used for the
// --min-samples (inner-join) filter below.
let mut merged_data = FxHashMap::<Key, (BedMethylLine, usize)>::default();
// value is the merged record plus a tally of how many requested inputs
// contributed to it, used for the --min-samples filter below.
let mut merged_data =
FxHashMap::<Key, (MergeBedMethylLine, usize)>::default();

// rationale:
// iterate over every possible contig
Expand All @@ -210,30 +247,45 @@ fn merge_data(
// lines in a hashmap write the hashmap to a new bedmethyl
// recreate hashmap and repeat process for next contig/regions
for index in readers.iter() {
let lines = index.read_bedmethyl(&contig, &range, io_threads)?;
let lines = index.fetch_region(
&contig,
&range,
StrandRule::Both,
io_threads,
)?;
let mut contributed_keys = FxHashSet::<Key>::default();

for line in lines {
let line = line?;

// an input only contributes to a position when its record has at
// least the requested valid coverage
if line.valid_coverage < min_sample_coverage {
if line.record.valid_coverage < min_sample_coverage {
continue;
}

let key = (
line.record.start(),
line.record.raw_mod_code,
line.record.strand,
line.name.clone(),
);
let first_for_input = contributed_keys.insert(key.clone());
merged_data
.entry((line.start(), line.raw_mod_code, line.strand))
.entry(key)
// modify the methyl data if an entry is found
.and_modify(|(methyl, n_samples)| {
methyl.count_methylated += line.count_methylated;
methyl.valid_coverage += line.valid_coverage;
methyl.count_canonical += line.count_canonical;
methyl.count_other += line.count_other;
methyl.count_delete += line.count_delete;
methyl.count_fail += line.count_fail;
methyl.count_diff += line.count_diff;
methyl.count_nocall += line.count_nocall;
*n_samples += 1;
methyl.record.count_methylated +=
line.record.count_methylated;
methyl.record.valid_coverage += line.record.valid_coverage;
methyl.record.count_canonical +=
line.record.count_canonical;
methyl.record.count_other += line.record.count_other;
methyl.record.count_delete += line.record.count_delete;
methyl.record.count_fail += line.record.count_fail;
methyl.record.count_diff += line.record.count_diff;
methyl.record.count_nocall += line.record.count_nocall;
if first_for_input {
*n_samples += 1;
}
})
.or_insert((line, 1));
}
Expand All @@ -246,12 +298,21 @@ fn merge_data(
.filter(|(_, n_samples)| *n_samples >= min_samples)
.map(|(methyl, _)| methyl)
.sorted_by(|a, b| {
debug_assert_eq!(a.chrom, b.chrom);
match a.start().cmp(&b.start()) {
Ordering::Equal => match a.strand.cmp(&b.strand) {
Ordering::Equal => a.raw_mod_code.cmp(&b.raw_mod_code),
o @ _ => o,
},
debug_assert_eq!(a.record.chrom, b.record.chrom);
match a.record.start().cmp(&b.record.start()) {
Ordering::Equal => {
match a.record.strand.cmp(&b.record.strand) {
Ordering::Equal => match a
.record
.raw_mod_code
.cmp(&b.record.raw_mod_code)
{
Ordering::Equal => a.name.cmp(&b.name),
o @ _ => o,
},
o @ _ => o,
}
}
o @ _ => o,
}
})
Expand Down Expand Up @@ -282,6 +343,30 @@ impl EntryMergeBedMethyl {
}
let min_sample_coverage: u64 = self.min_sample_coverage.unwrap_or(0);

// Validate every requested input before opening the output. In
// particular, do not silently shrink the reader list: --min-samples
// is resolved against the requested input cardinality above.
let readers = self
.in_bedmethyl
.iter()
.map(|bedmethyl| {
File::open(bedmethyl).with_context(|| {
format!(
"failed to open input bedMethyl file {}",
bedmethyl.display()
)
})?;

HtsTabixHandler::<MergeBedMethylLine>::from_path(bedmethyl)
.with_context(|| {
format!(
"failed to read indexed input bedMethyl file {}",
bedmethyl.display()
)
})
})
.collect::<anyhow::Result<Vec<_>>>()?;

let pool = rayon::ThreadPoolBuilder::new()
.num_threads(self.threads)
.build()?;
Expand Down Expand Up @@ -309,22 +394,6 @@ impl EntryMergeBedMethyl {
writer.write(bedmethyl_header().as_bytes())?;
}

let readers = self
.in_bedmethyl
.iter()
.filter_map(|bedmethyl| {
let index: HtsTabixHandler<BedMethylLine> =
match HtsTabixHandler::from_path(&bedmethyl) {
Ok(reader) => reader,
Err(_) => {
return None;
}
};

Some(index)
})
.collect::<Vec<HtsTabixHandler<BedMethylLine>>>();

// get set of contigs from all files
// done this way in case one file has a set of contigs that the other
// bedmethyl files do not have
Expand Down
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