Document read!(::Reader, ::Record)

[jonathanBieler]

Sorry, I'm a bit confused by the doc (or lack thereof), is that one correct way one has to read a fastq file, say if I want to read N reads (I could use while next !== nothing too) ? I think adding an example in the docs would be good.

reader = FASTQ.Reader(GzipDecompressorStream(open(file)) ; copy=false)

r = first(reader)

for k = 1:N

    # do something here

    next = iterate(reader)
    isnothing(next) && break
    r = next[1]
end

close(reader)

Also the old read!(reader, r) doesn't crash but does nothing, it should be an error now, no ?

[jonathanBieler]

Ha, I though I needed it to go trough paired files at once, but I can use for (r1,r2) in zip(reader1,reader2). Would still be good to document it though.

[jakobnissen]

Dear @jonathanBieler

Indeed, read! is a bug (see #95), which will be fixed in a few hours.
Readers are like any other iterators. To get N elements from an iterator, you can use Iterators.take, or use zip(1:N, reader), or use a normal for loop.

[jonathanBieler]

Thanks, so the read! API is not deprecated ? might be worth mentioning it in the docs then. It was nice to have the same API for XAM, FASTX and VariantCallFormat, so one could write generic code for those.

[jakobnissen]

Hm... I've not deprecated it yet. I don't think it should be deprecated. You're right, it should be in the docs.