# This script is not intended to be executed directly.  It is sourced by test-runner.sh and most functions you see here are defined in test-tools.sh
# The variables EXENAME, EXEBASE, OKDIR, and EXEDIR are defined externally.

beginTestBlock  # Begin a group of tests.
runMake -r @EXE # run `make` for the main exe and any other listed programs
EXT=.out  # set extension for @OKFILE and @OUTFILE placeholders (defaults for runDiff)

SEQ1=testFiles/testFile_ca5s.fasta
SEQ2=testFiles/testFile_ec5s.fasta

# Test phmm_without_options.
runFullTest 'without_options'  $SEQ1 $SEQ2 @OUT.out

# Test phmm maximum likelihood.
runFullTest 'maximum_likelihood'  $SEQ1 $SEQ2 @OUT.out -m




endTestBlock # End a group of tests. Also cleans up orphaned files etc.
