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?