hmm.out.txt_log

-r allele_count.base_call.txt
-o hmm.out.txt
-t bi
-m 
-z sample_hmm_model
starting probs: 
CC 0.2
LL 0.4
CL 0.4
transition: 
CC -> CC 0.99908720031296
CC -> LL 0.0
CC -> CL 9.12799687040107E-4

LL -> CC 0.0
LL -> LL 0.999725140118787
LL -> CL 2.7485988121273E-4

CL -> CC 4.01832355541268E-4
CL -> LL 1.84842883548983E-4
CL -> CL 0.99941332476091

emission: 
CC -> Discrete distribution --- CC 0, LL 0, CL 0, UN 0.979, CU 0.02, LU 0.001, AA 0, AB 0, AC 0, AL 0, BB 0, BC 0, BL 0, AP 0, BP 0, CP 0, LP 0, OP 0, OC 0, OL 0, OK 0, MP 0, MB 0, ML 0, MJ 0, NP 0, NB 0, NC 0, NI 0, IP 0, IA 0, IL 0, JP 0, JA 0, JC 0, KP 0, KA 0, KB 0, QP 0, QL 0, RP 0, RC 0, TP 0, TA 0, SP 0, SB 0
LL -> Discrete distribution --- CC 0, LL 0, CL 0, UN 0.979, CU 0.001, LU 0.02, AA 0, AB 0, AC 0, AL 0, BB 0, BC 0, BL 0, AP 0, BP 0, CP 0, LP 0, OP 0, OC 0, OL 0, OK 0, MP 0, MB 0, ML 0, MJ 0, NP 0, NB 0, NC 0, NI 0, IP 0, IA 0, IL 0, JP 0, JA 0, JC 0, KP 0, KA 0, KB 0, QP 0, QL 0, RP 0, RC 0, TP 0, TA 0, SP 0, SB 0
CL -> Discrete distribution --- CC 0, LL 0, CL 0, UN 0.978, CU 0.011, LU 0.011, AA 0, AB 0, AC 0, AL 0, BB 0, BC 0, BL 0, AP 0, BP 0, CP 0, LP 0, OP 0, OC 0, OL 0, OK 0, MP 0, MB 0, ML 0, MJ 0, NP 0, NB 0, NC 0, NI 0, IP 0, IA 0, IL 0, JP 0, JA 0, JC 0, KP 0, KA 0, KB 0, QP 0, QL 0, RP 0, RC 0, TP 0, TA 0, SP 0, SB 0