bump version

Cargo.toml

@@ -63,9 +63,9 @@ csv = "1.3.0"
 mimalloc = { version = "0.1.43", default-features = false }
 num-format = "0.4.4"
 num_cpus = "1.16.0"
-bio-types = { version = "1.0.1", default-features = true, features = ["serde"] }
+bio-types = { version = "1.0.2", default-features = true, features = ["serde"] }
 itertools = "0.13.0"
-thiserror = "1.0.61"
+thiserror = "1.0.62"
 statrs = "0.17.1"
 sce = { git = "https://github.com/parazodiac/SingleCellExperiment", branch = "dev", version = "0.2.0" }
 

src/quant.rs

@@ -319,7 +319,7 @@ pub fn quantify(quant_opts: QuantOpts) -> anyhow::Result<()> {
     if compressed_input {
         let i_file =
             File::open(parent.join("map.collated.rad.sz")).context("run collate before quant")?;
-        let br = BufReader::new(snap::read::FrameDecoder::new(BufReader::new(&i_file)));
+        let br = BufReader::new(snap::read::FrameDecoder::new(&i_file));
 
         info!(
             log,
@@ -544,11 +544,6 @@ pub fn do_quantify<T: BufRead>(mut br: T, quant_opts: QuantOpts) -> anyhow::Resu
     // the number of reference sequences
     let ref_count = hdr.ref_count as u32;
 
-    // TODO -- maybe delete March 5, 2024
-    // the types for the barcodes and umis
-    // let bc_type = rad_types::decode_int_type_tag(bct).expect("unsupported barcode type id.");
-    // let umi_type = rad_types::decode_int_type_tag(umit).expect("unsupported umi type id.");
-
     // the number of genes (different than the number of reference sequences, which are transcripts)
     let num_genes = gene_name_to_id.len();