The error message that hmmsearch and at least some other tools returns in response to an illegal set of command-line options appears to get cut off in some cases
Example:
/home/npcarter/h3-server/src/hmmsearch --incE 10 --incT 3 Caudal_act.hmm tiny.fasta
Failed to parse command line: Option --incE is incompatible with option(s) --incE,--incT,--cut_ga,-
Hmmsearch has correctly detected the incompatible options, but the list of options that are incompatible with --incE should be (at least according to my read of the code): "--incE,--incT,--cut_ga,--cut_nc,--cut_tc".
Reporting this as an issue because I don't want to be distracted fixing it now, but don't want it to get lost.
The error message that hmmsearch and at least some other tools returns in response to an illegal set of command-line options appears to get cut off in some cases
Example: /home/npcarter/h3-server/src/hmmsearch --incE 10 --incT 3 Caudal_act.hmm tiny.fasta Failed to parse command line: Option --incE is incompatible with option(s) --incE,--incT,--cut_ga,-
Hmmsearch has correctly detected the incompatible options, but the list of options that are incompatible with --incE should be (at least according to my read of the code): "--incE,--incT,--cut_ga,--cut_nc,--cut_tc".
Reporting this as an issue because I don't want to be distracted fixing it now, but don't want it to get lost.