Basic iterator trait, range pushing methods, to coitrees, and more!

 - tests and test utilies
 - rough join stuff
 - interval/range conversion methods
 - new GRanges methods refined
 - iteration methods
 - read_seqlens
 - PathBuf-based arguments in io
 - lazy BED parsing
 - invalid BED tests
 - adjust range operation with tests
 - clippy & fmt
 - GitHub Rust workflow added

.github/workflows/rust.yml

@@ -0,0 +1,22 @@
+name: Rust
+
+on:
+ push:
+ branches: [ "main" ]
+ pull_request:
+ branches: [ "main" ]
+
+env:
+ CARGO_TERM_COLOR: always
+
+jobs:
+ build:
+
+ runs-on: ubuntu-latest
+
+ steps:
+ - uses: actions/checkout@v3
+ - name: Build
+ run: cargo build --verbose
+ - name: Run tests
+ run: cargo test --verbose

Cargo.toml

@@ -1,13 +1,33 @@
 [package]
-name = "granges2"
+name = "granges"
 version = "0.1.0"
 edition = "2021"
-
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+license = "MIT"
+authors = ["Vince Buffalo <[email protected]>"]
+keywords = ["genomics", "bioinformatics", "compbio"]
+categories = ["science"]
+documentation = "https://docs.rs/granges/"
+repository = "https://github.com/vsbuffalo/granges"
+description = "A Rust library and command line tool for genomic range operations."
 
 [dependencies]
+# clap = { version = "4.4.18", features = ["derive"], optional = true }
+clap = { version = "4.4.18", features = ["derive"] }
 coitrees = { version = "0.4.0", features = ["nosimd"] }
-genomap = "0.1.5"
+flate2 = "1.0.28"
+genomap = "0.2.6"
 indexmap = "2.2.3"
+ndarray = "0.15.6"
+noodles = { version = "0.63.0", features = ["core", "bed"] }
 rand = "0.8.5"
 thiserror = "1.0.57"
+
+# [features]
+# cli = [ "clap" ]
+
+[[bin]]
+name = "granges"
+path = "src/main/mod.rs"
+# required-features = ["cli"]
+
+

src/data/mod.rs

@@ -0,0 +1,3 @@
+//! Data container implementations.
+
+pub mod vec;

src/data/ndarray.rs

@@ -0,0 +1,62 @@
+//! Data container implementations for [`ndarray::Array1`] and [`ndarray::Array2`].
+
+use ndarray::{Array1, Array2, ArrayView1};
+use crate::traits::IndexedDataContainer;
+
+impl<'a, U> IndexedDataContainer<'a> for Array1<U>
+where
+ U: Copy + Default + 'a,
+{
+ type Item = U;
+ type Output = Array1<U>;
+
+ fn get_value(&'a self, index: usize) -> Self::Item {
+ self[index]
+ }
+
+ fn len(&self) -> usize {
+ self.len()
+ }
+
+ fn is_valid_index(&self, index: usize) -> bool {
+ index < self.shape()[0]
+ }
+
+ fn new_from_indices(&self, indices: &[usize]) -> Self::Output {
+ Array1::from_iter(indices.iter().map(|&idx| self.get_value(idx)))
+ }
+}
+
+impl<'a, U> IndexedDataContainer<'a> for Array2<U>
+where
+ U: Copy + Default + 'a,
+{
+ type Item = ArrayView1<'a, U>;
+ type Output = Array2<U>;
+
+ fn get_value(&'a self, index: usize) -> Self::Item {
+ self.row(index)
+ }
+
+ fn len(&self) -> usize {
+ self.shape()[0]
+ }
+
+ fn is_valid_index(&self, index: usize) -> bool {
+ index < self.shape()[0]
+ }
+
+ fn new_from_indices(&self, indices: &[usize]) -> Self::Output {
+ let cols = self.shape()[1];
+
+ let rows_data: Vec<U> = indices
+ .iter()
+ .flat_map(|&idx| self.row(idx).iter().cloned().collect::<Vec<_>>())
+ .collect();
+
+ // create a new Array2<U> from the rows
+ // shape is (number of indices, number of columns)
+ Array2::from_shape_vec((indices.len(), cols), rows_data)
+ .expect("Shape and collected data size mismatch")
+ }
+}

src/data/vec.rs

@@ -0,0 +1,33 @@
+//! Data container implementations for [`Vec<U>`].
+
+
+/// Trait methods for the commonly-used `Vec<U>` data container.
+///
+/// Note that the associated `Item` type is always a *reference* to the data elements.
+impl<'a, U> IndexedDataContainer<'a> for Vec<U>
+where
+ U: Clone + 'a,
+{
+ type Item = &'a U;
+ type Output = Vec<U>;
+
+ fn get_value(&'a self, index: usize) -> Self::Item {
+ self.get(index).unwrap()
+ }
+
+ fn len(&self) -> usize {
+ self.len()
+ }
+
+ fn is_valid_index(&self, index: usize) -> bool {
+ self.get(index).is_some()
+ }
+
+ fn new_from_indices(&self, indices: &[usize]) -> Self::Output {
+ Vec::from_iter(indices.iter().map(|&idx| (*self.get_value(idx)).clone()))
+ }
+}
+
+
+
+

src/error.rs

@@ -1,13 +1,33 @@
+use std::num::{ParseIntError, ParseFloatError};
+
+use genomap::GenomeMapError;
 use thiserror::Error;
 
 use crate::Position;
 
 #[derive(Debug, Error)]
 pub enum GRangesError {
+ // IO related errors
+ #[error("File reading eror: {0}")]
+ IOError(#[from] std::io::Error),
+
+ // File parsing related errors
+ #[error("Integer parsing error: {0}")]
+ ParseIntError(#[from] ParseIntError),
+ #[error("Float parsing error: {0}")]
+ ParseFloatError(#[from] ParseFloatError),
+ #[error("Bed-like file has too few columns. The first three columns must be sequence name, and start and end positions.\nLine: {0}")]
+ BedlikeTooFewColumns(String),
+ #[error("File has invalid column type entry: {0}")]
+ InvalidColumnType(String),
+
+ // Invalid genomic range errors
  #[error("Range invalid: start ({0}) must be greater than end ({1})")]
  InvalidGenomicRange(Position, Position),
-
  #[error("Range [{0}, {1}] is invalid for sequence of length {2}")]
  InvalidGenomicRangeForSequence(Position, Position, Position),
-
+ #[error("Sequence name '{0}' is not the ranges container")]
+ MissingSequence(String),
+ #[error("Error encountered in genomap::GenomeMap")]
+ GenomeMapError(#[from] GenomeMapError),
 }