Add docs regarding bootstraps

[jameshadfield]

We have scant documentation about bootstraps - it's mentioned in a single changelog entry and a one line comment here:

Bootstrap values are allowed, and should be parsed correctly by augur refine.

It'd be good to expand on this a little, including covering:

• Where are bootstraps in the final tree (dataset)?
  • currently under a colouring "confidence"
• Why are some internal nodes missing bootstraps?
  • If augur refine resolves polytomies the newly created internal nodes will be missing bootstraps. A solution is to run with --keep-polytomies
• It's more typical to display bootstraps as branch labels rather than colours. A small script will transfer them over for you:

import argparse
import json

if __name__ == '__main__':
    parser = argparse.ArgumentParser()
    parser.add_argument('--input', type = str, required = True, metavar='JSON', help = "Input dataset JSON with 'confidence' node attrs")
    parser.add_argument('--output', type = str, required = True, metavar='JSON', help = "Output JSON with bootstrap branch labels")
    args = parser.parse_args()

    with open(args.input) as fh:
        dataset = json.load(fh)
    
    nodes = [dataset['tree']]

    while len(nodes):
        node = nodes.pop(0)
        for child in node.get('children', []):
            nodes.append(child)
        bootstrap = node.get('node_attrs', {}).get('confidence', {}).get('value', False)
        if bootstrap is not False:
            if 'branch_attrs' not in node: node['branch_attrs'] = {}
            if 'labels' not in node['branch_attrs']: node['branch_attrs']['labels'] = {}
            node['branch_attrs']['labels']['bootstrap'] = f"{bootstrap:.2f}"

    with open(args.output, 'w') as fh:
        dataset = json.dump(dataset, fh)    

This issue was prompted by this email exchange (private link)