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Question: ShortRead::FastqStreamer() causes segfault
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gravatar for Watal M. Iwasaki
23 months ago by
Japan
Watal M. Iwasaki10 wrote:

Hi all,

I am trying to filter FASTQs with library(ShortRead). One of my FASTQs contains an entry with width=0 and it causes segfault in the following code:

it = FastqStreamer('reads_1.fasta.gz', 10)
srq = yield(it)
as(quality(srq), 'matrix')

I think I could remove those reads in advance with srq[width(srq) > 0], but it seems to spoil the advantage of srFilter() and compose(). Interestingly, I found that an ShortReadQuality object read by readFastq() did not reproduce this error. So splitting FASTQ to small pieces may be another workaround. Do you have any suggestion?

 

Thanks,
Watal

ADD COMMENTlink written 23 months ago by Watal M. Iwasaki10

I wasn't able to reproduce this with a fastq file I created artificially; can you please update your question to include the output of sessionInfo(), as well as providing a way to reproduce your data (e.g., by creating a zero-width record after running example(readFastq), writing out using writeFastq(), or by making your data available via dropbox or referencing it in a public data base or communicating with me martin.morgan at roswellpark dot org directly).

One you have updated your question, please use the 'ADD COMMENT' link to indicate that the question has been updated.

ADD REPLYlink written 23 months ago by Martin Morgan ♦♦ 20k
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