Fred

My apologies! The `getQueryName() ` involved is line 5974, in `postProcessSearch ` [(here)](https://github.com/rmhubley/RepeatMasker/blob/a58f3130a4fedb7784171a539052277d2cccc690/RepeatMasker#L5974) I've just created a git repository. https://github.com/FredericBGA/trf-repeatmasker (when I clone the repo in another location, I can...

very nice! I'm happy to see that the issue is reproducible. unfortunately I can not easily managed the length of the input filenames (as RepeatMasker is launche in this particular...

Hi, tested with an async tool, it works. I will close this one: https://github.com/galaxyproject/galaxy/pull/9207 Could you please help me to add a test for this?

Hello > Unfortunately while your proposal should work nicely with Galaxy which (in places) understands the # header line convention, this does not match how the NCBI does its own...

Hello I wanted to use gapopen and gapextend options. The simple "text area" is 100% flexible for all other options (not yet available) that a user will need tomorrow !...

Of course. I had updated the tests accordingly. before this PR, with this kind of file: ``` >7 ATGC >7 ATGC ``` the result: ``` >7;7 representing 2 records ATGC...

The failed tests are not related to this PR, right?

you're right, the output is not yet perfect in this case: ``` >1 A >1 A >1 T ```` the output was: ``` >1;1 representing 2 records A >1;1 representing...

@peterjc This new version works for what I was needed. I let you review the code and merge if you want. Thank you for your comments.