finish the work I started

Author: clintval

Cargo.toml

@@ -2,7 +2,7 @@
 name = "vartovcf"
 version = "0.1.0"
 authors = ["Clint Valentine <valentine.clint@gmail.com>"]
-edition = "2021"
+edition = "2024"
 license = "MIT"
 readme = "README.md"
 repository = "https://github.com/clintval/vartovcf"
@@ -24,23 +24,26 @@ name = "vartovcf"
 path = "src/main.rs"
 
 [dependencies]
-anyhow = "1.0.86"
-bio-types = "1.0.1"
+anyhow = "1.0.100"
+bio-types = "1.0.4"
 case = "1.0.0"
-chrono = "0.4.38"
-csv = "1.3.0"
-env_logger = "0.11.3"
-log = "0.4.22"
-rust-htslib = "0.47.0"
-serde = { version = "1.0.203", features = ["derive"] }
-serde_with = { version = "3.8.3" }
+csv = "1.4.0"
+env_logger = "0.11.8"
+log = "0.4.28"
+proglog = "0.4.0"
+rust-htslib = "0.51.0"
+serde = { version = "1.0.228", features = ["derive"] }
+serde_with = { version = "3.15.0" }
 structopt = "0.3.26"
-strum = { version = "0.26.3", features = ["derive"] }
+strum = { version = "0.27.2", features = ["derive"] }
 
 [dev-dependencies]
-assert_cmd = "2.0.14"
-env_logger = "0.11.3"
+assert_cmd = "2.0.17"
+env_logger = "0.11.8"
 file_diff = "1.0.0"
-pretty_assertions = "1.4.0"
-rstest = "0.21.0"
-tempfile = "3.10.1"
+pretty_assertions = "1.4.1"
+rstest = "0.26.1"
+tempfile = "3.23.0"
+
+[lints.rust]
+unexpected_cfgs = { level = "warn", check-cfg = ['cfg(tarpaulin_include)'] }

src/lib/fai.rs

@@ -92,7 +92,7 @@ where
     I: AsRef<Path> + Debug,
 {
     match fasta.as_ref().to_str() {
-        Some(path) => header.push_record(format!("##reference={}", path).as_bytes()),
+        Some(path) => header.push_record(format!("##reference={path}").as_bytes()),
         None => return Err("Could not create a string out of the FASTA path".into()),
     };
     Ok(())

src/lib/mod.rs

@@ -13,21 +13,17 @@ use std::io::Read;
 use std::path::{Path, PathBuf};
 use strum::Display;
 use strum::{EnumString, VariantNames};
+use proglog::ProgLogBuilder;
 
 use crate::fai::{fasta_contigs_to_vcf_header, fasta_path_to_vcf_header};
 use crate::io::has_gzip_ext;
-use crate::progress_logger::{ProgressLogger, RecordLogger, DEFAULT_LOG_EVERY};
 use crate::record::tumor_only_header;
 use crate::record::TumorOnlyVariant;
 
 pub mod fai;
 pub mod io;
-pub mod progress_logger;
 pub mod record;
 
-/// The default log level for the `vartovcf` tool.
-pub const DEFAULT_LOG_LEVEL: &str = "info";
-
 /// The valid structural variation (SV) type values for the `SVTYPE` FORMAT field.
 pub const VALID_SV_TYPES: &[&str] = &["BND", "CNV", "DEL", "DUP", "INS", "INV"];
 
@@ -99,7 +95,13 @@ where
     }
     .expect("Could not build a VCF writer!");
 
-    let mut progress = ProgressLogger::new("processed", "variant records", DEFAULT_LOG_EVERY);
+    let progress = ProgLogBuilder::new()
+        .name("main")
+        .verb("Processed")
+        .noun("variant records")
+        .unit(10_000)
+        .build();
+
     let mut carry = csv::StringRecord::new();
     let mut variant = writer.empty_record();
     let mut seen: HashSet<String> = HashSet::new();
@@ -123,7 +125,6 @@ where
 
         if var.sample != sample {
             let message = format!("Expected sample '{}' found '{}'!", sample, var.sample);
-            progress.emit()?;
             return Err(message.into());
         };
 
@@ -197,11 +198,9 @@ where
         variant.push_format_integer(b"VD", &[var.alt_depth])?;
 
         writer.write(&variant)?;
-        progress.observe()?;
+        progress.record();
     }
 
-    progress.emit()?;
-
     Ok(0)
 }
 

src/lib/progress_logger.rs

@@ -79,7 +79,7 @@ impl error::Error for ParsePairBiasError {}
 
 impl fmt::Display for ParsePairBiasError {
     fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        write!(f, "{:?}", self)
+        write!(f, "{self:?}")
     }
 }
 
@@ -91,7 +91,7 @@ impl error::Error for ParseSvInfoError {}
 
 impl fmt::Display for ParseSvInfoError {
     fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        write!(f, "{:?}", self)
+        write!(f, "{self:?}")
     }
 }
 
@@ -111,7 +111,7 @@ pub enum StrandBias {
 
 impl fmt::Display for StrandBias {
     fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
-        write!(f, "{:?}", self)
+        write!(f, "{self:?}")
     }
 }
 
@@ -371,7 +371,7 @@ pub fn tumor_only_header(sample: &str) -> Header {
     let mut header = Header::default();
     header.push_sample(sample.as_bytes());
     header.remove_filter(b"PASS");
-    header.push_record(format!("##source={}", source).as_bytes());
+    header.push_record(format!("##source={source}").as_bytes());
     header.push_record(r#"##INFO=<ID=ADJAF,Number=1,Type=Float,Description="Adjusted allele frequency for indels due to local realignment. Lossy due to rounding.">"#.as_bytes());
     header.push_record(r#"##INFO=<ID=BIAS,Number=1,Type=String,Description="Strand bias flags (UnDetected, Detected, TooFewReads) in the format `reference`:`alternate`.">"#.as_bytes());
     header.push_record(r#"##INFO=<ID=BIASALT,Number=2,Type=Integer,Description="The number of variant call forward and reverse reads in the format `forward`:`reverse`.">"#.as_bytes());

src/lib/record.rs

@@ -44,14 +44,14 @@ struct Opt {
 /// Main binary entrypoint.
 #[cfg(not(tarpaulin_include))]
 fn main() -> Result<(), Error> {
-    let env = Env::default().default_filter_or(vartovcflib::DEFAULT_LOG_LEVEL);
+    let env = Env::default().default_filter_or("info");
     let opt = Opt::from_args();
 
     env_logger::Builder::from_env(env).init();
 
     let input: Box<dyn Read> = match &opt.input {
         Some(path) if path.to_str().unwrap() != "-" => {
-            info!("Input file: {:?}", path);
+            info!("Input file: {path:?}");
             Box::new(BufReader::new(File::open(path)?))
         }
         _ => {
@@ -61,7 +61,7 @@ fn main() -> Result<(), Error> {
     };
 
     match &opt.output {
-        Some(output) if output.to_str().unwrap() != "-" => info!("Output file: {:?}", output),
+        Some(output) if output.to_str().unwrap() != "-" => info!("Output file: {output:?}"),
         _ => info!("Output stream: STDOUT"),
     }