FASTA indexing and slicing functionalities

[NickRoz1]

Hello!

Using awesome emi80's contributions, I've included FASTA indexing and slicing functionalities to Sambamba. As BioD submodule was detached since 28ed6e382e commit, merging this pull request will also require either updating BioD version, or manually including fasta.d and fai.d into sambamba/BioD/bio/std/file

[george-githinji]

just a note, @emi80 contribution has already been merged in BioD master branch.

[pjotrp]

Yes, sorry, we are still organising BioD and synchronising with sambamba. Should fix soon (I am building ldc 1.14 first). We should synchronize after.

[pjotrp]

@NickRoz1 great work, btw!

[ycl6]

Hi, just wondering if the FASTA indexing functionality will be added in the near future?

[pjotrp]

We should merge it. @NickRoz1 or @emi80 do you want to add a few test files? Without tests it is probably not a great idea to merge. I think there are some tests in BioD. I can have a look.

[NickRoz1]

For slice.d - I think it would be better to edit BioD fastaRegions function to make it possible to specify FASTA index file separately, e.g.:

auto fastaRegions(string filename, string pathToIndex, string[] queries) {
    File f = File(filename);
    FaiRecord[string] index = makeIndex(readFai(pathToIndex));
    Region[] regions = to!(Region[])(queries);
    return fetchFastaRegions(f, index, regions);
}

Instead of:

auto fastaRegions(string filename, string[] queries) {
    File f = File(filename);
    FaiRecord[string] index = makeIndex(readFai(filename~=".fai"));
    Region[] regions = to!(Region[])(queries);
    return fetchFastaRegions(f, index, regions);
}

I think there are some tests in BioD. I can have a look.

There are tests for underlying FASTA parsers, for example: https://github.com/biod/BioD/blob/7969eb0a847b05874e83ffddead26e193ece8101/bio/std/file/fai.d#L133

[pjotrp]

Thank you @NickRoz1 !