Skip to content

Fix BED format parsing to accept valid end coordinates at chromosome boundaries #12

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
wdecoster merged 3 commits into from
Jan 3, 2026
+75 −10
Merged

Fix BED format parsing to accept valid end coordinates at chromosome boundaries #12

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
9d3d19c
Initial plan
Copilot Jan 2, 2026
d8bcf09
Fix BED format parsing and improve error messages
Copilot Jan 2, 2026
7c77808
Address code review: use proper 1000bp test sequences
Copilot Jan 2, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
85 changes: 75 additions & 10 deletions src/repeats.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -254,19 +254,24 @@ impl RepeatInterval {
.expect("Failed to read fai file")
.lines()
{
if line.split('\t').collect::<Vec<&str>>()[0] == chrom
&& line.split('\t').collect::<Vec<&str>>()[1]
let parts: Vec<&str> = line.split('\t').collect();
if parts[0] == chrom {
let chrom_length = parts[1]
.parse::<u32>()
.expect("Failed parsing chromosome length from fai file")
> end
{
return Some(Self { chrom, start, end, created: None });
.expect("Failed parsing chromosome length from fai file");
// BED format uses 0-based half-open coordinates, so end is exclusive
// Therefore, end can equal the chromosome length
if chrom_length >= end {
return Some(Self { chrom, start, end, created: None });
} else {
panic!(
"End coordinate {end} is out of bounds for chromosome {chrom} (length: {chrom_length})"
);
}
}
}
// if the chromosome is not in the fai file or the end does not fit the interval, return None
panic!(
"Chromosome {chrom} is not in the fasta file or the end coordinate is out of bounds"
);
// if the chromosome is not in the fai file, panic with clear message
panic!("Chromosome {chrom} is not in the fasta file");
}
pub fn new(chrom: &str, start: u32, end: u32) -> Self {
Self { chrom: chrom.to_string(), start, end, created: None }
Expand Down Expand Up @@ -627,4 +632,64 @@ chr19 45770205 45770266 CAG ATXN1_CAG_61"#;
let result = crate::repeats::RepeatIntervalIterator::pathogenic(&fasta);
assert!(result.num_intervals > 0, "Should have found some pathogenic intervals");
}

#[test]
fn test_bed_end_coordinate_at_chromosome_boundary() {
// Test that BED format end coordinate equal to chromosome length is valid
// BED format uses 0-based half-open coordinates, so end is exclusive
let temp_dir = std::env::temp_dir();
let test_fasta = temp_dir.join("test_bed_boundary.fa");
let test_fai = temp_dir.join("test_bed_boundary.fa.fai");

// Create a sequence of exactly 1000 bp
let sequence = "ATGC".repeat(250); // 4 * 250 = 1000 bp
let fasta_content = format!(">chr1\n{}", sequence);
// Chromosome length is 1000
let fai_content = "chr1\t1000\t6\t60\t61";

std::fs::write(&test_fasta, fasta_content).expect("Failed to write test fasta");
std::fs::write(&test_fai, fai_content).expect("Failed to write test fai");

// Test 1: End coordinate equal to chromosome length should be valid
// This represents the region [900, 1000) which includes positions 900-999
let bed_data_at_boundary = "chr1\t900\t1000\tATGC\tgene1";
let result = RepeatIntervalIterator::from_string_data(
bed_data_at_boundary,
&test_fasta.to_string_lossy(),
);
let intervals: Vec<RepeatInterval> = result.collect();
assert_eq!(intervals.len(), 1);
assert_eq!(intervals[0].end, 1000);

// Clean up
let _ = std::fs::remove_file(&test_fasta);
let _ = std::fs::remove_file(&test_fai);
}

#[test]
#[should_panic(expected = "End coordinate 1001 is out of bounds for chromosome chr1")]
fn test_bed_end_coordinate_beyond_chromosome_boundary() {
// Test that end coordinate beyond chromosome length properly fails
let temp_dir = std::env::temp_dir();
let test_fasta = temp_dir.join("test_bed_oob.fa");
let test_fai = temp_dir.join("test_bed_oob.fa.fai");

// Create a sequence of exactly 1000 bp
let sequence = "ATGC".repeat(250); // 4 * 250 = 1000 bp
let fasta_content = format!(">chr1\n{}", sequence);
// Chromosome length is 1000
let fai_content = "chr1\t1000\t6\t60\t61";

std::fs::write(&test_fasta, fasta_content).expect("Failed to write test fasta");
std::fs::write(&test_fai, fai_content).expect("Failed to write test fai");

// End coordinate beyond chromosome length should panic with clear message
let bed_data_oob = "chr1\t900\t1001\tATGC\tgene1";
let _result =
RepeatIntervalIterator::from_string_data(bed_data_oob, &test_fasta.to_string_lossy());

// Clean up (won't reach here due to panic, but good practice)
let _ = std::fs::remove_file(&test_fasta);
let _ = std::fs::remove_file(&test_fai);
}
}
Loading