Add read_length() to ShortRead type
unode opened this issue · 2 comments
This was something that was requested in an offline discussion.
Given a Fastq file with variable read length (e.g. after preprocessing):
mapped = select(mapped) using |mr|:
mr = mr.filter(min_match_size={read_length}, action={drop})
if not mr.flag({mapped}): ^^^^^^^^^^^^^
discard
here {read_length}
could be mr.read_length()
.
In a paired-end read, does this apply to both mates?
In a paired-end read, does this apply to both mates?
Tricky question, but I see your point. I'd say read_length() == forward + reverse
.
However from the offline discussion I think the goal was per-read length which would require two methods.
So given this we could have forward_read_length()
and reverse_read_length()
.
However these would not make sense in a single-end context and error'ing there would be inconvenient.
What do you say to return read_length()
for forward_read_length()
and 0
for reverse_read_length()
when in a single-end context?