Confirm that use of BLAST's -max_target_seqs is intentional

[armish]

Hi there,

This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's -max_target_seqs parameter:

• alignment/para_rpsblast.pl
• alignment/para_tblastn.pl
• alignment/para_tblastx.pl

Based on the recently published report, Misunderstood parameter of NCBI BLAST impacts the correctness of bioinformatics workflows, there is a strong chance that this parameter is misused in your repository.

If the use of this parameter was intentional, please feel free to ignore and close this issue but I would highly recommend to add a comment to your source code to notify others about this use case. If this is a duplicate issue, please accept my apologies for the redundancy as this simple automation is not smart enough to identify such issues.

Thank you!
-- Arman (armish/blast-patrol)

[dnasko]

The following text has been added to each script's help menu:

NOTE the default max_target_seqs is set to 50. Users should update                                               
this value to >= the number of sequences in the subject database if they want to guarentee                                                     
they get the best hit.