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fix: Check for both .csi and .tbi VCF index files by fxwiegand · Pull Request #395 · alignoth/alignoth · GitHub

/ alignoth Public

fix: Check for both .csi and .tbi VCF index files #395

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Merged
fxwiegand merged 3 commits into from
Oct 29, 2025
Conversation 1 Commits 3 Checks 6 Files changed
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fix: Check for both .csi and .tbi VCF index files #395

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c9ece9f
fix: Check for both .csi and .tbi VCF index files
fxwiegand Oct 29, 2025
20bc934
Clarify VCF index error message with tabix instruction
fxwiegand Oct 29, 2025
322ba3f
Refactor error message to use named format arguments
fxwiegand Oct 29, 2025
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12 changes: 7 additions & 5 deletions src/main.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -46,14 +46,16 @@ async fn main() -> Result<()> {
)?;
let mut highlight = opt.highlight.as_ref().cloned().unwrap_or_default();
if let Some(vcf_path) = opt.vcf.as_ref() {
let index = PathBuf::from(&format!("{}.csi", vcf_path.display()));
if index.exists() {
let csi_index = PathBuf::from(&format!("{}.csi", vcf_path.display()));
let tbi_index = PathBuf::from(&format!("{}.tbi", vcf_path.display()));
if csi_index.exists() || tbi_index.exists() {
highlight.extend(VcfHighlight::new(vcf_path.clone()).intervals(region)?);
} else {
bail!(
"VCF/BCF index not found: {}. Please create an index using `bcftools index {}`",
index.display(),
vcf_path.display()
"VCF/BCF index not found: {csi} or {tbi}. Please create an index using `bcftools index {vcf}` or `tabix {vcf}`.",
csi = csi_index.display(),
tbi = tbi_index.display(),
vcf = vcf_path.display()
);
}
}
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