Is it better that output seq (& qual) not be folded for FASTQ? about kseqpp HOT 7 CLOSED

Sorry, I did not get what you mean by being folded. You mean wrapped?

from kseqpp.

I added an option to disable line wrapping by calling set_nowrapping method before writing any record. Since this is a re-implementation of "kseq" library, I did not change the default behaviour. Please check the develop branch. If it also works for you, I will merge it to master.

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Yes, I mean 'wrapped'. For most FASTQ files, The seq line and qual line are not wrapped. As far as I know, the wrapped FASTQ is not accepted by many downstream softwares, for example: bowtie2.
So my suggestion is, in default manner, the FASTA file should be wrapped while the FASTQ file should not be wrapped.

from kseqpp.

That makes sense. I am going to do the following then:

• add a parameter to SeqStreamOut class to specify the underlying file format (accepting format::fasta, or format::fastq values in klibpp namespace). Actually KStreamOut class which is the base class of SeqStreamOut has already this option which just needs to be forwarded.
• if the format is explicitly set to format::fastq, no-wrapping would be the default behaviour, otherwise it wraps at 60bps.
• just for the record, puts no longer gets wrap parameter and wrapping is determined by the wraplen value. If it is zero, it means no wrap.

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Please check out develop branch (sorry for the forced push!), let me know if it works.

from kseqpp.

Sorry for delayed reply. I am on the vocation due to Chinese national day.

from kseqpp.

No problem, feel free to reopen the issue if the problem persists.

from kseqpp.