Hi,

I have had a look at FastqStreamer to stream in successive subsets of a
Fastq file.


My question is whether you can change the number of records to stream on
the fly rather than having to stream 'n' records each time.


For example, I might want to pull in records corresponding to each Illumina
tile from the indices fetched within the Fastq header information,

or just fetch a certain tile with a record index range m:n which does not
nessarily start at m=1 within the Fastq file.


sp <- SolexaPath(system.file('extdata', package='ShortRead'))

fl <- file.path(analysisPath(sp), "s_1_sequence.txt")

length(readFastq(f))

[1] 256


## This fails as n is expected to be a constant amount of streamed records

f <- FastqStreamer(fl, c(100, 50, 100, 6))

Error in FastqStreamer(fl, c(100, 50, 100, 6)) :

  'n' must be finite and >= 0



To fetch a certain tile can you alter the 'added' field position similar to
'seek' in perl so you can grab only that index range  of the Fastq file
without having to go through a while loop?


f <- FastqStreamer(fl, 50)

print(f)

class: FastqStreamer

file: s_1_sequence.txt

status: n=50 current=0 added=0 total=0  ## <- I want to change the
'current/added fields'



cheers,


Marcus

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