### PERFORMANCE ###
GRID_ON=0   # grid computation on [1,0] for on or off
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=27 # minimum read statistic. May wish to set lower for 2x300 reads.
MIN_LEN=80        # minimum read length
MERGE_SECONDARY=1

## MATCH STEP
MATCH_PROC=64     # grid maximum processes for the MATCH
MATCH_PROG="BLAT" # match (all or any match) program [BLAT]
MIN_RP=1          # minimum read pattern count to continue
MIN_RC=15         # minimum read count to continue
MIN_BLAT_MATCH=65 # minimum blat match, default settings within the program practically limit to 30 bp, only useful if set higher.

## SORT STEP
SORT_GROUPS="__ALL__"
SORT_PROG="BLAT" # [LABEL,BLAT]
SORT_PROC=64     # currently not used
NONSEGMENTED=0   # segmented! [0,1]
# LABEL
SECONDARY_SORT=0 # LABEL sorting fast-mode

## ALIGN STEP ##
ALIGN_PROG="BLAT" # rough assembly / alignment to working reference [SAM,BLAT]
ALIGN_PROC=64     # grid maximum processes for the rough align
DEL_TYPE="REF"    # how to handle deletions in the rough alignment: NNN, REF, or DEL (blank = OLD DEFAULTS)

### FINISHING ASSEMBLY ###
ASSEM_PROG="SSW" # assembly program [SSW]
ASSEM_PROC=64    # grid maximum processes for assembly
INS_T=0.55       # minimum frquenncy threshold for insertion refinement
DEL_T=0.55       # minimum frequency threshold for deletion refinement
INS_T_DEPTH=15   # minimum coverage depth for insertion refinement
DEL_T_DEPTH=10   # minimum coverage depth for deletion refinement (in addition to plurality and frequency)
MIN_AMBIG=0.20   # minimum called SNV frequency for mixed base in amended consensus folder
ASSEM_REF=1      # use the same reference(s) for the final assembly as read gathering
# NOTE: uses the default reference seed, any mention of "user supplied reference sorting" is merely perfunctory
ALIGN_AMENDED=1          # align the amended consensus to the HMM profile
PADDED_CONSENSUS=1       # attempt to pad amended_consensus with Ns for amplicaton dropout: requires ALIGN_AMENDED=1 and ASSEM_REF=1
MIN_CONS_SUPPORT=15      # consensus allele minimum count
MIN_CONS_QUALITY=15      # consensus allele minimum average quality
MIN_DROPOUT_EDGE_DEPTH=0 # minimum threshold before dropouts (91+) with flanking regions (6+) are masked during final iterative refinement

### 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).
