Closed frederic-mahe closed 3 years ago
Help entries that could be modified (some suggestions):
-d, --differences INTEGER resolution (1)
-b, --boundary INTEGER min mass of large OTUs (3)
-c, --ceiling INTEGER max memory in MB for the Bloom filter (unlimited)
-i, --internal-structure FILENAME write internal OTU structure to file
-o, --output-file FILENAME output result to file (stdout)
-r, --mothur output using a mothur-like format
-u, --uclust-file FILENAME output using a UCLUST-like format to file
-w, --seeds FILENAME write OTU representatives to FASTA file
swarm's uclust format output: check whether column 3 entry C "cluster size" should be the number of amplicons or the number of reads (sum of abundances)?
EDIT
usearch tallies amplicons, not reads:
printf ">s1;size=2;\nAAAA\n>s2;size=1;\nAAAA\n" > tmp.fas
usearch7 -cluster_fast tmp.fas -minseqlength 1 -id 0.5 -uc tmp.uc
cat tmp.uc
rm tmp.*
usearch reports a cluster size of 2 amplicons, not an abundance of 3. vsearch and swarm behave like usearch.
Made the suggested changes to the help text in commit c07a0d440858309b670a6dd0657e4847c5c2fd73.
Is it ok if I set up Travis CI to compile (and possibly test) Swarm, as done for vsearch?
Is it ok if I set up Travis CI to compile (and possibly test) Swarm, as done for vsearch?
Yes, that sounds like a good idea. Can Travis CI fetch tests from the swarm-tests repository?
Can Travis CI fetch tests from the swarm-tests repository?
Yes, I think so.
Travis CI will now automatically compile and test swarm3 after any commit is pushed or any pull request is submitted.
The status can be seen here: https://travis-ci.org/torognes/swarm
It fails if it compiles with an error or if any of the tests fail.
It is compiled using g++ version 7.4.0 on Ubuntu 18.04.3 (bionic) linux.
The swarm-tests repo is automatically cloned from its source.
It all seems to work fine now after a series of modifications.
There is a badge on the front page (in README.md) showing the latest status.
This only applies to the swarm3 branch.
Changelog for end-users
-d 0
(i.e. the number of differences is set to zero),Under the hood:
d = 1
algorithm,To do
Done
-march=native
vs.-march=x86-64
),-h
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