Closed frederic-mahe closed 1 year ago
--db /dev/stdin
works, so the issue really is with --db -
:
## reading explicitely from stdin works for the references
printf ">parentA\nAAAA\n>parentB\nGGGG\n" | \
vsearch \
--uchime_ref <(printf ">query\nAAGG\n") \
--db /dev/stdin \
--quiet \
--uchimeout /dev/null
I think --db
generally does not accept -
as argument meaning read from stdin
. I think this was done intentionally to avoid the use of -
for multiple arguments, which would cause problems.
VSEARCH could be rewritten to accept -
for many/all input file options, but only allowing it used in one at a time.
VSEARCH could be rewritten to accept - for many/all input file options, but only allowing it used in one at a time.
I don't think that's necessary.
I've added a statement in the manpage, and some tests to cover that behavior https://github.com/frederic-mahe/vsearch-tests/commit/7277b1cd74708267c80acd709660f58a75b3b93e
while working on issue #504, I've noticed that
--db -
(reading--db
data fromstdin
) does not work and yields aFatal error
. This could be intended, for instance to avoid reading both queries and references fromstdin
. If not, allowing--db -
would make the user interface more predictable and flexible.