Merge pull request #18 from COMBINE-lab/develop

Develop

Cargo.toml

@@ -27,14 +27,12 @@ categories = ["command-line-utilities", "science"]
 
 [dependencies]
 snap = "1"
-scroll = "0.11.0"
-num = "0.4.0"
-ahash = "0.8.3"
-serde = { version = "1.0.164", features = ["derive"] }
-dashmap = "^5.4.0"
-bio-types = "1.0.0"
-smallvec = "1.10.0"
-rust-htslib = { version = "0.44.1", default-features = false, features = [
-  "bzip2",
-  "lzma",
-] }
+scroll = "0.12.0"
+num = "0.4.1"
+ahash = "0.8.8"
+serde = { version = "1.0.196", features = ["derive"] }
+dashmap = "^5.5.3"
+bio-types = "1.0.1"
+smallvec = "1.13.1"
+noodles-bam = "0.56.0"
+noodles-sam = "0.53.0"

src/rad_types.rs

@@ -12,7 +12,7 @@ use crate as libradicl;
 use self::libradicl::utils;
 use bio_types::strand::*;
 use num::cast::AsPrimitive;
-use rust_htslib::bam::HeaderView;
+use noodles_sam as sam;
 use scroll::Pread;
 use std::io::Write;
 use std::io::{Cursor, Read};
@@ -471,27 +471,25 @@ impl RadHeader {
         rh.num_chunks = buf.pread::<u64>(0).unwrap();
         rh
     }
-    pub fn from_bam_header(header: &HeaderView) -> RadHeader {
+
+    pub fn from_bam_header(header: &sam::Header) -> RadHeader {
         let mut rh = RadHeader {
             is_paired: 0,
             ref_count: 0,
             ref_names: vec![],
             num_chunks: 0,
         };
 
-        rh.ref_count = header.target_count() as u64;
+        let ref_seqs = header.reference_sequences();
+        rh.ref_count = ref_seqs.len() as u64;
         // we know how many names we will read in.
         rh.ref_names.reserve_exact(rh.ref_count as usize);
-        for (_i, t) in header
-            .target_names()
-            .iter()
-            .map(|a| std::str::from_utf8(a).unwrap())
-            .enumerate()
-        {
-            rh.ref_names.push(t.to_owned());
+        for (k, _v) in ref_seqs.iter() {
+            rh.ref_names.push(k.to_string());
         }
         rh
     }
+
     pub fn get_size(&self) -> usize {
         let mut tot_size = 0usize;
         tot_size += std::mem::size_of::<u8>() + std::mem::size_of::<u64>();