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17:30:45
stassats
hmm, reinitialize-instance on classes doesn't call reinitialize-instance on subclasses, and my update-dependent isn't invoked
18:53:52
sjl_
(with-open-file (f "foo" :element-type 'base-char) (read-line f)) currently returns a simple-string. Is there any way to get it to return simple-base-string's instead?
18:54:43
sjl_
my use case is reading data from large (10-100gb) FASTQ files (data from DNA sequencers)
18:54:59
sjl_
[ClozureCL] COMMON-LISP-USER> (type-of (with-open-file (f "~/.stumpwmrc" :element-type 'base-char) (read-line f)))
18:57:13
stassats
if you're relying on character streams to read 100gb fast, you're already losing, and then adding read-line
18:58:33
stassats
you're not going to just leave the data as lines? so anything read with read-line will be garbage
19:00:47
sjl_
Like, from the perspective of writing a library to handle FASTQs, I'd hope to provide something like (do-fastq (label sequence scores) stream ...)
19:01:31
sjl_
No, FASTQ files can be used for DNA (ATGC), RNA (AUGC), or protein (20 different letters)
19:03:24
sjl_
I still need to read it in. I was hoping that I could get away with something nicer than reading into an octet buffer and parsing it myself. But maybe that's just the best solution.
19:04:21
sjl_
(I already wrote the octet-buffer solution, and it got much messier than the read-line solution)
19:10:48
stassats
i suppose read-line could return a simple-base-string, but that might break some code