Exon

https://github.com/wheretrue/exon
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Exon is an execution engine for bioinformatics data, offering SQL-based access, support for various...
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### Run Generic Exon Example

Source: https://github.com/wheretrue/exon/blob/main/exon-examples/README.md

This command provides the general syntax for running any example included in the Exon crate. Users should replace '<example-name>' with the specific example they wish to execute.

```bash
cargo run --example <example-name>
```

--------------------------------

### Run Specific Exon Example (gff_annotation_join)

Source: https://github.com/wheretrue/exon/blob/main/exon-examples/README.md

This command demonstrates how to run a specific example from the Exon crate, in this case, the 'gff_annotation_join' example. It illustrates the concrete application of the generic run command.

```bash
cargo run --example gff_annotation_join
```

--------------------------------

### Install exonr R Package

Source: https://github.com/wheretrue/exon/blob/main/exon-r/README.md

Installs the 'exonr' package from the r-universe repository. The second repository, 'https://cloud.r-project.org', is included as a fallback or for other dependencies.

```R
install.packages('exonr', repos = c('https://wheretrue.r-universe.dev', 'https://cloud.r-project.org'))
```

--------------------------------

### Install Exon Py Library using pip

Source: https://github.com/wheretrue/exon/blob/main/exon-py/README.md

This command installs the `exon-py` Python package from PyPI using pip, the standard package installer for Python.

```console
pip install exon-py
```

--------------------------------

### Example: Rewriting `chrom = 'chr1' AND pos BETWEEN 0 AND 1` (Mermaid)

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

A step-by-step example demonstrating the rewriting process for a complex binary expression equivalent to `chrom = 'chr1' AND pos BETWEEN 0 AND 1`. It shows the initial state and subsequent transformations using a `transform_up` approach.

```mermaid
flowchart TB
    Z[And Binary Expression] --> A[Eq Binary Expression]
    Z --> U[Geq Binary Expression]
    U --> V[Pos Column]
    U --> W[Literal]
    A[And Binary Expression] --> B[Eq Binary Expression]
    A --> C[Leq Binary Expression]
    B --> D[Chrom Column]
    B --> E[Literal]
    C --> F[Pos Column]
    C --> G[Literal]
```

```mermaid
flowchart TB
    Z[And Binary Expression] --> A[Eq Binary Expression]
    Z --> U[IntervalPhysicalExpr]
    A[And Binary Expression] --> B[ChromPhysicalExpr]
    A --> C[IntervalPhysicalExpr]
```

```mermaid
flowchart TB
    Z[And Binary Expression] --> A[RegionPhysicalExpr]
    Z --> U[IntervalPhysicalExpr]
```

```mermaid
flowchart TB
    Z[RegionPhysicalExpr]
```

--------------------------------

### Install Exon with Cargo

Source: https://github.com/wheretrue/exon/blob/main/README.md

This command adds the Exon library as a dependency to your Rust project using Cargo, Rust's package manager. It fetches the latest version from crates.io.

```bash
cargo add exon
```

--------------------------------

### VCF Expression Rewrite: Pos Column Equals Literal

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

An 'equals' binary expression with a position column and a literal is rewritten into an IntervalPhysicalExpr. For example, a literal '5' transforms into a VCF interval '5-5'.

```Mermaid
flowchart TB
    A[Eq Binary Expression] --> B[Pos Column]
    A --> C[Literal]
```

```Mermaid
flowchart TB
    A[IntervalPhysicalExpr]
```

--------------------------------

### VCF Expression Rewrite: Pos Column Greater Than Equal Literal

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

A 'greater than' binary expression with a position column and a literal is rewritten into an IntervalPhysicalExpr. For example, a literal '5' yields a VCF interval '5-'. This expression typically needs to be paired with a 'less than equal' expression to define a bounded interval.

```Mermaid
flowchart TB
    A[Greater Than Binary Expression] --> B[Pos Column]
    A --> C[Literal]
```

```Mermaid
flowchart TB
    A[IntervalPhysicalExpr]
```

--------------------------------

### Push Release Changes and Tag to Origin

Source: https://github.com/wheretrue/exon/blob/main/docs/release-guide.md

Pushes the committed changes to the `main` branch of the remote repository and also pushes the newly created version tag to the remote. This makes the release official and available remotely.

```bash
git push origin main
git push origin v$VERSION
```

--------------------------------

### Commit Version Changes and Tag Release

Source: https://github.com/wheretrue/exon/blob/main/docs/release-guide.md

Stages all modified files, creates a commit message indicating the version bump, and then creates an annotated Git tag for the new release version. This step finalizes the local versioning changes.

```bash
git add -u .
git commit -m "release: bump to version v$VERSION"
git tag -a v$VERSION -m "release: v$VERSION"
```

--------------------------------

### Retrieve Exon Version from Cargo Metadata

Source: https://github.com/wheretrue/exon/blob/main/docs/release-guide.md

Retrieves the current version of the 'exon' package from the `Cargo.toml` workspace using `cargo metadata` and `jq`. The extracted version is then stored in the `VERSION` environment variable and printed to the console.

```bash
VERSION=$(cargo metadata --format-version 1 | jq -r '.packages[] | select(.name == "exon") | .version')
echo "Releasing v$VERSION"
```

--------------------------------

### Bump Exon Version with Git CZ

Source: https://github.com/wheretrue/exon/blob/main/docs/release-guide.md

Initiates a version bump for the Exon project using `git cz bump --files-only`. This command modifies version files without creating a commit, allowing Cargo to update its lock file with the new version.

```bash
git cz bump --files-only
```

--------------------------------

### VCF File Type Detection and Scanning Flow

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

This flowchart illustrates the VCF file detection process, showing how the presence of a region filter determines whether an indexed or non-indexed VCF scanner and opener are used, ultimately leading to an asynchronous batch stream for data processing.

```Mermaid
flowchart TB
    A[VCF File Type] --> B[VCF Table Provider]
    B --> C(Detect Region Filter)
    C -- Contains Region --> D[IndexedVCFScanner]
    D --> F[IndexedVCFOpener]
    F --> G[IndexedAsyncBatchStream]

    C -- Missing Filter --> E[VCFScan]
    E --> H[VCFOpener]
    H --> I[AsyncBatchStream]
```

--------------------------------

### Rewriting Region and Interval Binary Expression (Mermaid)

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

Illustrates the transformation of a binary expression combining a RegionPhysicalExpr and an IntervalPhysicalExpr. The region's chromosome remains, and the interval is updated to the intersection of the two original intervals.

```mermaid
flowchart TB
    A[And Binary Expression] --> B[RegionPhysicalExpr]
    A --> C[IntervalPhysicalExpr]
```

```mermaid
flowchart TB
    A[RegionPhysicalExpr]
```

--------------------------------

### VCF Expression Rewrite: Combine Interval and Chrom Expressions

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

An 'AND' binary expression that combines an IntervalPhysicalExpr and a ChromPhysicalExpr is rewritten into a single RegionPhysicalExpr, consolidating the chromosomal and interval constraints.

```Mermaid
flowchart TB
    A[And Binary Expression] --> B[IntervalPhysicalExpr]
    A --> C[Chrom Column]
```

```Mermaid
flowchart TB
    A[RegionPhysicalExpr]
```

--------------------------------

### VCF Expression Rewrite: Intersect Two IntervalPhysicalExpr

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

An 'AND' binary expression involving two IntervalPhysicalExprs is rewritten into a new IntervalPhysicalExpr that represents the intersection of the two original intervals.

```Mermaid
flowchart TB
    A[And Binary Expression] --> B[IntervalPhysicalExpr]
    A --> C[IntervalPhysicalExpr]
```

```Mermaid
flowchart TB
    A[IntervalPhysicalExpr]
```

--------------------------------

### VCF Expression Rewrite: Pos Column Less Than Equal Literal

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

A 'less than' binary expression with a position column and a literal is rewritten into an IntervalPhysicalExpr. For instance, a literal '5' results in a VCF interval '1-5'. Note that strict less than is not supported due to the inclusive nature of VCF intervals.

```Mermaid
flowchart TB
    A[Less Than Binary Expression] --> B[Pos Column]
    A --> C[Literal]
```

```Mermaid
flowchart TB
    A[IntervalPhysicalExpr]
```

--------------------------------

### Rewriting Two Region Physical Expressions (Mermaid)

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

Shows the transformation of a binary expression combining two RegionPhysicalExpr expressions. The chromosome is kept if identical, otherwise the expression is false. The interval becomes the intersection of the two intervals.

```mermaid
flowchart TB
    A[And Binary Expression] --> B[RegionPhysicalExpr]
    A --> C[RegionPhysicalExpr]
```

```mermaid
flowchart TB
    A[RegionPhysicalExpr]
```

--------------------------------

### Rust `Interval` Struct Definition

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

Defines the `Interval` struct in Rust, which represents a genomic interval. It includes a `lower_bound` (u32) and an optional `upper_bound` (Option<u32>), with the lower bound defaulting to 1 if not explicitly known.

```rust
struct Interval {
    lower_bound: u32, // will be 1 if not known
    upper_bound: Option<u32>,
}
```

--------------------------------

### VCF Expression Rewrite: Chrom Column Equals Literal

Source: https://github.com/wheretrue/exon/blob/main/docs/vcf_expression_rewriting.md

When an 'equals' binary expression involves a chromosome column and a literal, it is rewritten into a ChromPhysicalExpr, which represents a specific region defined by the literal.

```Mermaid
flowchart TB
    A[Eq Binary Expression] --> B[Chrom Column]
    A --> C[Literal]
```

```Mermaid
flowchart TB
    A[ChromPhysicalExpr]
```
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