fix: Check for both .csi and .tbi VCF index files (#395) · alignoth/alignoth@dd5059f · GitHub

alignoth / alignoth Public

• Notifications You must be signed in to change notification settings
• Fork 6
• Star 135

• Code
• Issues 4
• Pull requests 1
• Actions
• Projects
• Security and quality
• Insights

Additional navigation options

Commit dd5059f

Browse filesBrowse the repository at this point in the historyBrowse files

fxwiegand

authored

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

* fix: Check for both .csi and .tbi VCF index files * Clarify VCF index error message with tabix instruction * Refactor error message to use named format arguments

1 parent 148a653 commit dd5059f
Copy full SHA for dd5059f

1 file changed

+7-5Lines changed: 7 additions & 5 deletions

File tree

Expand file treeCollapse file tree

Open diff view settings

Filter options

• src
  • main.rs

Expand file treeCollapse file tree

Open diff view settings

Collapse file

‎src/main.rs‎

Copy file name to clipboardExpand all lines: src/main.rs

+7-5Lines changed: 7 additions & 5 deletions

Original file line number	Diff line number	Diff line change
@@ -46,14 +46,16 @@ async fn main() -> Result<()> {
46	46	)?;
47	47	let mut highlight = opt.highlight.as_ref().cloned().unwrap_or_default();
48	48	if let Some(vcf_path) = opt.vcf.as_ref() {
49		- let index = PathBuf::from(&format!("{}.csi", vcf_path.display()));
50		- if index.exists() {
	49	+ let csi_index = PathBuf::from(&format!("{}.csi", vcf_path.display()));
	50	+ let tbi_index = PathBuf::from(&format!("{}.tbi", vcf_path.display()));
	51	+ if csi_index.exists() || tbi_index.exists() {
51	52	highlight.extend(VcfHighlight::new(vcf_path.clone()).intervals(region)?);
52	53	} else {
53	54	bail!(
54		- "VCF/BCF index not found: {}. Please create an index using `bcftools index {}`",
55		- index.display(),
56		- vcf_path.display()
	55	+ "VCF/BCF index not found: {csi} or {tbi}. Please create an index using `bcftools index {vcf}` or `tabix {vcf}`.",
	56	+ csi = csi_index.display(),
	57	+ tbi = tbi_index.display(),
	58	+ vcf = vcf_path.display()
57	59	);
58	60	}
59	61	}

0 commit comments

Comments

0 (0)