fix issue with creating karyotype from remote file, passing Header ob…

…ject
wdecoster · Feb 13, 2024 · a190c46 · a190c46
1 parent 13500ab
commit a190c46
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Showing 4 changed files with 5 additions and 7 deletions.
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "cramino"
-version = "0.14.1"
+version = "0.14.2"
 edition = "2021"
 authors = ["Wouter De Coster [email protected]"]
 license = "MIT"

diff --git a/src/karyotype.rs b/src/karyotype.rs
@@ -1,9 +1,7 @@
-use rust_htslib::bam::{self, Read};
+use rust_htslib::bam;
 use std::collections::HashMap;
 
-pub fn make_karyotype(tids: &Vec<i32>, bamp: String) {
-    let bam = bam::Reader::from_path(bamp).unwrap();
-    let header = bam::Header::from_template(bam.header());
+pub fn make_karyotype(tids: &Vec<i32>, header: rust_htslib::bam::Header) {
     let head_view = bam::HeaderView::from_header(&header);
 
     let mut tidcount: HashMap<i32, usize> = HashMap::new();

diff --git a/src/main.rs b/src/main.rs
@@ -130,7 +130,7 @@ fn metrics_from_bam(
         None
     };
     if args.karyotype {
-        karyotype::make_karyotype(metrics.tids.as_ref().unwrap(), bam.to_string());
+        karyotype::make_karyotype(metrics.tids.as_ref().unwrap(), header);
     }
     let exon_counts = if let Some(mut exon_counts) = metrics.exons {
         exon_counts.sort_unstable();