<commit_before># GA4GH Reporting

This is a set of scripts to produce variant benchmarking reports.

# Input / Output

## Input

* one or more diploid test VCF files
* Genome in a Bottle or Platinum Genomes truth files

## Output

* a HTML report.

# Basic Usage

There are two scripts in the [bin] folder:

* **run.py** : run hap.py and produce a report 

```bash
python run.py -o test.html test.vcf.gz
```

* **rep.py** : report from hap.py results 

```bash
python run.py -o test.html result.extended.csv
```

See also [share/microbench](share/microbench) for a demo.

# Dependencies

* hap.py v0.3.0+ -- [https://github.com/Illumina/hap.py/tree/dev-0.3](https://github.com/Illumina/hap.py/tree/dev-0.3)
* [optional] rtgtools vcfeval in the GA4GH version: [https://github.com/RealTimeGenomics/rtg-tools/tree/ga4gh-test](https://github.com/RealTimeGenomics/rtg-tools/tree/ga4gh-test)
* A truth set, e.g. Platinum Genomes or Genome in a Bottle
* Python packages in [requirements.txt]:
    - flask
    - jinja2<commit_msg>some README additions<commit_after># GA4GH Reporting

This is a set of scripts to produce variant benchmarking reports.

# Input / Output

## Input

* one or more diploid test VCF files
* Genome in a Bottle or Platinum Genomes truth files

## Output

* a HTML report.

# Basic Usage

There are two scripts in the [bin] folder:

* **run.py** : run hap.py and produce a report

```bash
python run.py -o test.html test.vcf.gz
```

* **rep.py** : report from hap.py results

```bash
python rep.py -o test.html result.extended.csv
```

See also [share/microbench](share/microbench) for a demo.

# Dependencies

* hap.py v0.3.0+ -- [https://github.com/Illumina/hap.py/tree/dev-0.3](https://github.com/Illumina/hap.py/tree/dev-0.3)
* rtgtools vcfeval in the GA4GH version: [https://github.com/RealTimeGenomics/rtg-tools/tree/ga4gh-test](https://github.com/RealTimeGenomics/rtg-tools/tree/ga4gh-test)
* A truth set, e.g. Platinum Genomes or Genome in a Bottle
* Python packages in [requirements.txt]:
    - jinja2
* Included Javascript/CSS packages:
    - D3.js (BSD 3-clause license, see [src/html/lib/d3/LICENSE]() and [https://github.com/mbostock/d3]())
    - bijou CSS styles (MIT license, see [src/html/lib/bijou/LICENSE]() and [https://github.com/andhart/bijou]())
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{'dir': 'git-commits-cleaned', 'id': '4593890', 'n_tokens_mistral': 876, 'n_tokens_neox': 818, 'n_words': 231}