#91 pipeline_summary.pl getCog returns bad values

[Anonymous]

The getCog function in pipeline_summary.pl will incorrectly assign a COG domain to a sequence that matched a domain in myva, but the matched domain does not belong to a COG in the whog file. The last COG in whog ([K] COG5665 CCR4-NOT transcriptional regulation complex, NOT5 subunit
) is assigned incorrectly to sequences who should not have a COG. The reason is the getCog will loop through the whog file first matching for COG and storing that line as the return value. So, every COG is stored as the return value at some point. Then it will look for the matching myva id in the next lines of the whog. If a matching id is found the loop is broken and the return value sent. However, there is not a proper test to see if a matching myva id is ever truly found. So what happens is the last COG in the file is often incorrectly returned when there was not a matching id. The simple solution would be to store the COG line in a temp variable and only assign it to the return value when a matching id is found.