### PERFORMANCE ###
GRID_ON=0    # grid computation on [1,0] for on or off
GRID_PATH="" # grid path, defaults to the IRMA_RES path if left empty string, do not include quotes for tilde prefix
ALLOW_TMP=1  # if GRID_ON=0, try to use /tmp for working directory
TMP=/tmp     # the scratch/tmpfs for working on the assemblies

### REFERENCE ###
MIN_FA=1         # no alternative reference [0..1]
MIN_CA=20        # minimum count for alternative finished assembly
SKIP_E=1         # skip reference elongation
REF_SET=$DEF_SET # Same as the "consensus.fasta" in the reference folder for the module.

### READ GATHERING ###
MAX_ROUNDS=5             # round of read gathering
USE_MEDIAN=1             # use the median quality or the average [1,0]
QUAL_THRESHOLD=30        # minimum read statistic
MIN_LEN=125              # minimum read length
ENFORCE_CLIPPED_LENGTH=0 # Off. Reads are filtered for minimum length post adapter trimming.

## MATCH STEP
MATCH_PROC=20     # grid maximum processes for the MATCH
MATCH_PROG="BLAT" # match (all or any match) program [BLAT]
MIN_RP=15         # minimum read pattern count to continue
MIN_RC=15         # minimum read count to continue

## SORT STEP
SORT_PROG="BLAT" # [LABEL,BLAT]
SORT_PROC=80     # currently not used
NONSEGMENTED=0
# Pattern list to group gene segment lineages into gene for primary/secondary sorting.
SORT_GROUPS="PB2,PB1,PA,HA,NP,NA,MP,NS"
SEG_NUMBERS="B_PB1:1,B_PB2:2,A_PB2:1,A_PB1:2,PA:3,HA:4,NP:5,NA:6,M:7,NS:8"

# LABEL
SECONDARY_SORT=1                                              # LABEL sorting fast-mode
LABEL_MODULE="irma-FLU"                                       # if LABEL SECONDARY SORT is 0, use LABEL_MODULE
SECONDARY_LABEL_MODULES="irma-FLU-HA,irma-FLU-NA:irma-FLU-OG" # otherwise, search for primary classification from BLAT and use the modules accordingly
GENE_GROUP="HA,NA:OG"                                         # specify primary sorting gene groups for BLAT

## ALIGN STEP ##
ALIGN_PROG="SAM" # rough assembly / alignment to working reference [SAM,BLAT]
ALIGN_PROC=20    # grid maximum processes for the rough align

### FINISHING ASSEMBLY ###
ASSEM_PROG="SSW" # assembly program [SSW]
ASSEM_PROC=20    # grid maximum processes for assembly
INS_T=0.25       # minimum frquenncy threshold for insertion refinement
DEL_T=0.60       # minimum frequency threshold for deletion refinement
MIN_AMBIG=0.20   # minimum called SNV frequency for mixed base in amended consensus folder

### VARIANT CALLING ###
# HEURISTICS
AUTO_F=1      # auto-adjust frequency threshold [1,0]
MIN_FI=0.005  # minimum insertion variant frequency
MIN_FD=0.005  # minimum deletion variant frequency
MIN_F=0.008   # minimum frequency for single nucleotide 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

# CONFIDENCE INTERVALS
SIG_LEVEL=0.999 # significance test level for variant calling (.90,.95,.99,.999).
