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Add DownsampleVcf tool #974

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Add DownsampleVcf tool #974

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06065c6
Add DownsampleVcf tool
TedBrookings Mar 29, 2024
9d1aa06
make changes suggested in PR
jdidion Apr 2, 2024
9ccb1e6
fix tests
jdidion Apr 3, 2024
f6052af
test proportion argument
jdidion Apr 3, 2024
6eb1762
test
jdidion Apr 3, 2024
9a2d510
add more tests
jdidion Apr 3, 2024
8f7a4eb
add tests
jdidion Apr 3, 2024
81e39d1
add more tests
jdidion Apr 4, 2024
f57f1e8
add more tests, fix some tests
jdidion Apr 4, 2024
0232972
cleanup
jdidion Apr 4, 2024
75de344
Merge pull request #976 from fulcrumgenomics/multiallelic-likelihoods
jdidion Apr 15, 2024
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27 changes: 16 additions & 11 deletions README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -14,16 +14,21 @@ A set of tools to analyze genomic data with a focus on Next Generation Sequencin
Detailed user documentation is available on the [project website](http://fulcrumgenomics.github.io/fgbio/) including [tool usage](http://fulcrumgenomics.github.io/fgbio/tools/latest) and [documentation of metrics produced](http://fulcrumgenomics.github.io/fgbio/metrics/latest). Detailed developer documentation can be found [here](http://javadoc.io/doc/com.fulcrumgenomics/fgbio_2.13).

<!---toc start-->
* [Goals](#goals)
* [Overview](#overview)
* [List of tools](#list-of-tools)
* [Building](#building)
* [Command line](#command-line)
* [Include fgbio in your project](#include-fgbio-in-your-project)
* [Contributing](#contributing)
* [Authors](#authors)
* [License](#license)
* [Sponsorship](#sponsorship)
- [fgbio](#fgbio)
- [Goals](#goals)
- [Overview](#overview)
- [List of tools](#list-of-tools)
- [Building](#building)
- [Cloning the Repository](#cloning-the-repository)
- [Running the build](#running-the-build)
- [Command line](#command-line)
- [Include fgbio in your project](#include-fgbio-in-your-project)
- [Contributing](#contributing)
- [Authors](#authors)
- [License](#license)
- [Sponsorship](#sponsorship)
- [Become a sponsor](#become-a-sponsor)
- [Sponsors](#sponsors)
Comment on lines +17 to +31
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GitHub has TOC support so we could consider removing this maintenance burden.

https://github.blog/changelog/2021-04-13-table-of-contents-support-in-markdown-files/

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VS code also automatically updates the TOC. I don't care either way.


<!---toc end-->

Expand Down Expand Up @@ -76,7 +81,7 @@ Below we highlight a few tools that you may find useful.
[Git LFS](https://git-lfs.github.com/) is used to store large files used in testing fgbio. In order to compile and run tests it is necessary to [install git lfs](https://git-lfs.github.com/). To retrieve the large files either:

1. Clone the repository _after_ installing git lfs, or
2. In a previously cloned repository run `git lfs pull` once
2. In a previously cloned repository run the follwing once: `git lfs install && git lfs pull`

After initial setup regular git commands (e.g. `pull`, `fetch`, `push`) will also operate on large files and no special handling is needed.

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