# MODULE SPECIFIC
NONSEGMENTED=1        # non-segmented virus
SORT_GROUPS="__ALL__" # Pattern list for sorting

# STAGES
MATCH_PROG="BLAT"
SORT_PROG="BLAT"
ALIGN_PROG="SAM"
ASSEM_PROG="SSW"

# PERFORMANCE
MATCH_PROC=140 # grid maximum processes for the MATCH
ALIGN_PROC=140 # grid maximum processes for the rough align
ASSEM_PROC=140 # grid maximum processes for assembly
GRID_ON=1      # grid computation on
ALLOW_TMP=1    # use TMP for ppath
TMP=/tmp       # temperary space

# VARIANT CALLING HEURISTICS & STATS
MIN_FI=0.0045   # minimum insertion variant frequency
MIN_FD=0.0045   # minimum deletion variant frequency
MIN_F=0.015     # minimum frequency for variants
MIN_C=2         # minimum count for variants
MIN_AQ=24       # minimum average variant quality, does not apply to deletions
MIN_TCC=100     # minimum non-ambiguous column coverage
MIN_CONF=0.80   # minimum confidence not machine error
SIG_LEVEL=0.999 # significance test level for variant calling (.90,.95,.99,.999).

# CONSENSUS REFINEMENT & READ SELECTION
MAX_ROUNDS=5
QUAL_THRESHOLD=30 # average or median threshold for QUALITY reads
MIN_LEN=125       # minimum read length for QUALITY reads
INS_T=0.15        # threshold for insertion refinement
DEL_T=0.50        # threshold for deletion refinement
SKIP_E=1          # skip reference elongation
INCL_CHIM=0       # whether or not to get rid of chimera
MIN_RP=15         # minimum read pattern count to continue
MIN_RC=15         # minimum read count to continue
MIN_AMBIG=0.25    # min SNV freq for ambig nts in final amended consensus
MERGE_SECONDARY=1

# ASSEMBLY
MAX_ITER_SSW=5 # max num of SSW iterations to perform, 3 should be sufficient w/4 to prove
SSW_M=2        # smith-waterman match score
SSW_X=5        # smith-waterman mismatch penalty
SSW_O=10       # smith-waterman gap open penalty
SSW_E=1        # smith-waterman gap extension penalty
