dentist.commands.generateDazzlerOptions source code

1 /**
2     This is the `generateDazzlerOptions` command of `dentist`.
3 
4     Copyright: © 2018 Arne Ludwig <arne.ludwig@posteo.de>
5     License: Subject to the terms of the MIT license, as written in the
6              included LICENSE file.
7     Authors: Arne Ludwig <arne.ludwig@posteo.de>
8 */
9 module dentist.commands.generateDazzlerOptions;
10 
11 import dentist.common : isTesting;
12 import std.stdio : writefln, writeln;
13 
14 /// Execute the `generateDazzlerOptions` command with `options`.
15 void execute(Options)(in Options options)
16 {
17     writeln("# self alignment options (consider using `HPC.daligner`)");
18     writefln!"daligner %-(%s %) <reference> <reference>"(options.selfAlignmentOptions);
19     writeln("# ref vs reads alignment options (consider using `HPC.damapper`)");
20     writefln!"damapper %-(%s %) <reference> <reads>"(options.refVsReadsAlignmentOptions);
21 
22     static if (isTesting)
23     {
24         writeln("# true assembly vs result alignment options (consider using `HPC.damapper`)");
25         writefln!"damapper %-(%s %) <true-assembly> <result>"(options.trueAssemblyVsResultAlignmentOptions);
26     }
27 }