Closed GoogleCodeExporter closed 9 years ago
They are not ignored. But I did found and fixed a minor bug not related to
these two options, but related to cd-hit-2d and cd-hit-est-2d. Not sure if that
bug caused problem for you, but it works fine for me now with testing datasets
similar to what you described.
The fix has been push to the repository, you can check it out and see if it
works for you.
Original comment by phooli...@gmail.com
on 13 Sep 2012 at 9:48
Thanks for your reply. I cloned the source trunk and compiled it, then reran
my test. I get the same result. Am I doing something wrong or
misunderstanding the options? Attached are my test nucleotide sequences (one
is a subsequence of the other). Here are my commands/results:
Works as expected:
cd-hit-est-2d -r 1 -i cdk.fa -i2 cdk_subseq.fa -o test.out -c .95 -d 99 -p 1 -g
1 -s2 0.0 -S2 99999;cat test.out.clstr
>Cluster 0
0 1267nt, >gi|300863097|ref|NM_000077.4|... *
1 840nt, >gi|300863097|ref|NM_000077.4|subseq... at 1:840:1:840/+/100.00%
If I switch -i,-i2, I expect the same result, but it does not cluster:
cd-hit-est-2d -r 1 -i2 cdk.fa -i cdk_subseq.fa -o test.out -c .95 -d 99 -p 1 -g
1 -s2 0.0 -S2 99999;cat test.out.clstr
>Cluster 0
0 840nt, >gi|300863097|ref|NM_000077.4|subseq... *
Thanks very much for your help!
Original comment by vanhemer...@gmail.com
on 14 Sep 2012 at 3:17
Attachments:
Thank you for providing testing datasets for reproducing the bug. With these
datasets, I did track down the bug that caused the problem, and it turns out
these two options were not properly handled. Now it is fixed and pushed to the
repository. Thank you again.
Original comment by phooli...@gmail.com
on 14 Sep 2012 at 11:12
Original issue reported on code.google.com by
vanhemer...@gmail.com
on 4 Sep 2012 at 9:17