From a190c460555ef8205ab0c732e91a72a066b53a29 Mon Sep 17 00:00:00 2001
From: wdecoster <decosterwouter@gmail.com>
Date: Wed, 14 Feb 2024 00:40:45 +0100
Subject: [PATCH] fix issue with creating karyotype from remote file, passing
 Header object

---
 Cargo.lock       | 2 +-
 Cargo.toml       | 2 +-
 src/karyotype.rs | 6 ++----
 src/main.rs      | 2 +-
 4 files changed, 5 insertions(+), 7 deletions(-)

diff --git a/Cargo.lock b/Cargo.lock
index 753d4c2..b66cadb 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -473,7 +473,7 @@ checksum = "e496a50fda8aacccc86d7529e2c1e0892dbd0f898a6b5645b5561b89c3210efa"
 
 [[package]]
 name = "cramino"
-version = "0.14.1"
+version = "0.14.2"
 dependencies = [
  "arrow",
  "chrono",
diff --git a/Cargo.toml b/Cargo.toml
index b59b568..a1126b2 100644
--- 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 decosterwouter@gmail.com"]
 license = "MIT"
diff --git a/src/karyotype.rs b/src/karyotype.rs
index c150ed6..b77b95e 100644
--- 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
index d31e99a..562bdb7 100644
--- 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();