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fix: ensure FORMAT sample order is in-sync with header sample order #671

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merged 8 commits into from
Jan 21, 2025
Merged

fix: ensure FORMAT sample order is in-sync with header sample order #671

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62d79cf
fix: report samples in order of input vcf, not pedigree order
tedil Jan 21, 2025
a14cf69
cosmetic
tedil Jan 21, 2025
07d6c9e
add FIXME for duplicate 'src' FORMAT entry
tedil Jan 21, 2025
50d9f4f
fix: extract samples by name, so order is always in-sync with header
tedil Jan 21, 2025
130197b
unnecessary reference removed
tedil Jan 21, 2025
f3d8cad
More informative error message
tedil Jan 21, 2025
0759b99
add test for checking sample order does not change between in and output
tedil Jan 21, 2025
d623a72
use same seed rng for consistent svuid
tedil Jan 21, 2025
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27 changes: 21 additions & 6 deletions src/annotate/strucvars/mod.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,7 @@
/// Path to the input VCF files.
#[arg(long, required = true)]
pub path_input_vcf: Vec<String>,

#[command(flatten)]
pub output: PathOutput,

Expand Down Expand Up @@ -126,6 +127,7 @@
use noodles::vcf::variant::record::info::field::key::{
END_CONFIDENCE_INTERVALS, END_POSITION, POSITION_CONFIDENCE_INTERVALS, SV_TYPE,
};
use std::collections::HashMap;

use noodles::vcf::variant::record::samples::keys::key::{
CONDITIONAL_GENOTYPE_QUALITY, FILTER, GENOTYPE, GENOTYPE_COPY_NUMBER,
Expand Down Expand Up @@ -358,7 +360,7 @@
Map::<Format>::new(FormatNumber::Count(1), Type::Integer, "Split-end coverage"),
)
.add_format(
"src",
"src", // FIXME this is clearly the same format as above?!
Map::<Format>::new(
FormatNumber::Count(1),
Type::Integer,
Expand Down Expand Up @@ -424,10 +426,21 @@
// Wait for https://github.com/zaeleus/noodles/issues/162#issuecomment-1514444101
// let mut b: record::value::map::Builder<record::value::map::Other> = Map::<noodles::vcf::header::record::value::map::Other>::builder();

for i in pedigree.individuals.values() {
if header.sample_names().contains(&i.name) {
builder = builder.add_sample_name(i.name.clone());
let individuals = pedigree
.individuals
.values()
.map(|i| (i.name.clone(), i))
.collect::<HashMap<_, _>>();

for sample in header.sample_names() {
let individual = individuals.get(sample);
if individual.is_none() {
tracing::debug!("Sample {} not part of the pedigree, skipping.", sample);
continue;
}
let i = individual.unwrap();

builder = builder.add_sample_name(i.name.clone());

// Add SAMPLE entry.
builder = builder.insert(
Expand Down Expand Up @@ -832,15 +845,17 @@
}

// First, create genotype info records.
let mut gt_it = record.samples().values();
for sample_name in header.sample_names() {
tsv_record.genotype.entries.push(GenotypeInfo {
name: sample_name.clone(),
..Default::default()
});

let entry = tsv_record.genotype.entries.last_mut().expect("just pushed");
let sample = gt_it.next().expect("genotype iterator exhausted");
let sample = record
.samples()
.get(&header, sample_name)

Check warning on line 857 in src/annotate/strucvars/mod.rs

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GitHub Actions / clippy

this expression creates a reference which is immediately dereferenced by the compiler 

warning: this expression creates a reference which is immediately dereferenced by the compiler
   --> src/annotate/strucvars/mod.rs:857:22
    |
857 |                 .get(&header, sample_name)
    |                      ^^^^^^^ help: change this to: `header`
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#needless_borrow
    = note: `#[warn(clippy::needless_borrow)]` on by default
.expect("sample not found");
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for (key, value) in sample.keys().as_ref().iter().zip(sample.values().iter()) {
match (key.as_ref(), value) {
Expand Down
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