Closed deprekate closed 8 years ago
Like SPACE, TAB is not part of fasta name, either.
Yes, but the SPACE in a sequence header should not be substituted for a TAB. It causes problems downstream, especially for software that relies on the SPACE boundary to get the comment portion (which usually includes functional annotation and taxonomy information).
A TAB also messes up other things like, creating TAB delimited lists, and using the header as one column. It then throws off the column count.
@lh3 I agree with @deprekate that the current behaviour is undesirable.
The vast majority of FASTA/Q files will use a SPACE between the ID and the COMMENT.
I suspect the TAB wasn't intentional in the FASTA/Q output mode, and printing a SPACE would be more compatible:
if (seq->comment.l) printf("\t%s", seq->comment.s);
should be
if (seq->comment.l) printf(" %s", seq->comment.s);
I hope you can make the change, or if you want a pull request I will do it.
Fixed via e5c4fd9. Thanks.
The current version inserts a tab between the header ID and the comment. (I use the @ to show where tabs are)
Line 569 of seqtk.c uses a tab instead of a space.