doesn't respect initial proportion values when USE_ORIGINAL_PROPORTIONS=ON
Fastcodeml compiled with USE_ORIGINAL_PROPORTIONS doesn't respect initial parameter values for p0 and p1. Here's an example:
incorrect output with USE_ORIGINAL_PROPORTIONS=ON:
$ ./fast -hy 0 -b 1 -o -p p0=.3 -p p1=.3 ENSGT00390000016702.Primates.01.002.nwk ENSGT00390000016702.Primates.01.phy
Doing branch 1
LnL0: -3156.873153375251150 Function calls: 1
0.5353014 0.1542961 0.3339827 0.3958456 0.3351005 0.2993065 0.2111547 0.3993420
0.4710117 0.5128884 0.4011716
p0: 0.1875000 p1: 0.1875000 p2a: 0.3125000 p2b: 0.3125000
w0: 0.4000000 k: 0.2000000
correct output with USE_ORIGINAL_PROPORTIONS=OFF:
$ ./fast -hy 0 -b 1 -o -p p0=.3 -p p1=.3 ENSGT00390000016702.Primates.01.002.nwk ENSGT00390000016702.Primates.01.phy
Doing branch 1
LnL0: -3225.775431196213958 Function calls: 1
0.4442000 0.5242317 0.2684253 0.5572105 0.4774131 0.4200495 0.4043826 0.4845818
0.1924882 0.1136097 0.5241809
p0: 0.3000000 p1: 0.3000000 p2a: 0.2000000 p2b: 0.2000000
w0: 0.4000000 k: 0.2000000