# merge

## What

Merges a user-supplied metadata table with the latest AncientMetagenomeDir master metadata tables, with on-the-fly [validation](/how_to/validate).

## When

This command would be used when you have a local version of an AncientMetagenomeDir table (samples or libraries) of just the new samples or libraries to add, and want to append to the current master table before submitting a pull request.

You typically only do this if preparing a pull request to the AncientMetagenomeDir repository entirely locally.

## How

The following description assumes you have already prepared an AncientMetagenomeDir **samples** or **libraries** table whose rows only consist of the header and new samples to be added.

> ⚠️ _The header, and present columns etc. should match exactly that on the corresponding AncientMetagenomeDir table_

Given a new samples table `samples_for_new_pr.tsv` to be added to the single genome samples table `ancientsinglegenome-hostassociated`, you can run the following command:

```bash
amdirt merge -n ancientsinglegenome-hostassociated -t samples samples_for_new_pr.tsv
```

Note that during merge `merge` will also perform schema validation to ensure the contents of the new rows are valid against the AncientMetagenomeDir schema.

## Output

The output of the `merge` command is a new table with the merged rows named after the table you merged the new rows onto, placed by default in the directory you ran the command from (customisable with `-o`).

In the example above, the file result would be: `ancientsinglegenome-hostassociated_samples.tsv`.

The contents of this file can then theoretically be used to submit a pull request to the AncientMetagenomeDir repository.