address builder pattern

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "oarfish"
-version = "0.6.4"
+version = "0.6.5"
 edition = "2021"
 authors = [
   "Zahra Zare Jousheghani <zzare@umd.edu>",

src/bulk.rs

@@ -261,7 +261,7 @@ fn get_source_type(pb: &std::path::Path) -> InputSourceType {
 #[allow(clippy::too_many_arguments)]
 pub fn quantify_bulk_alignments_raw_reads(
     header: &noodles_sam::Header,
-    aligner: minimap2::Aligner,
+    aligner: minimap2::Aligner<minimap2::Built>,
     filter_opts: AlignmentFilters,
     read_paths: &[std::path::PathBuf],
     txps: &mut [TranscriptInfo],

src/main.rs

@@ -9,8 +9,8 @@ use minimap2_sys as mm_ffi;
 // use minimap2::ffi as mm_ffi;
 //use minimap2_temp as minimap2;
 use num_format::{Locale, ToFormattedString};
-use std::{fs::File, io};
 use std::sync::Arc;
+use std::{fs::File, io};
 
 use tracing::info;
 use tracing_subscriber::{filter::LevelFilter, fmt, prelude::*, EnvFilter};
@@ -36,7 +36,7 @@ use crate::util::{binomial_probability::binomial_continuous_prob, kde_utils};
 type HeaderReaderAligner = (
     noodles_sam::header::Header,
     Option<bam::io::Reader<bgzf::MultithreadedReader<File>>>,
-    Option<minimap2::Aligner>,
+    Option<minimap2::Aligner<minimap2::Built>>,
 );
 
 fn get_aligner_from_args(args: &Args) -> anyhow::Result<HeaderReaderAligner> {