Benjamin Buchfink
Benjamin Buchfink
Sorry that I left this. Unfortunately, my private development branch had already diverged a lot from the public master when you posted this, so it wasn't possible to easily merge...
Great thanks, I quickly tested this and everything seems to be working. Should be no problem to have this merged for the next release.
Looks like the `--include-lineage` parameter is causing this, will fix.
Yes I'm afraid the `--max-hsps` logic seems to be broken in blastx mode. The only solution for now is to use the frameshift mode, you will get the correct alignment:...
These columns are not reported by default, you can see them by changing the format e.g. `-f 6 qcovhsp approx_pident`.
I could not reproduce the issue when using `--masking 0`. Please double check that your input sequences don't already contain the X.
Ok, looks like this needs to be fixed. But note that using 2 files like this is not different from just aligning each file separately, the information of paired reads...
> Is there a way to take into account X characters when calculating percentage identity no > why the identities for these two queries are diffefrent? the sequences are different
I tried to reproduce this using swissprot but it works fine, will try full nr now.
I could not reproduce the error using the nr database either. Would it be possible to send me your query file?