#TOOLS
hisat2 = hisat2
lastal = lastal
lastsp = last-split
mfcv = maf-convert
reformat = reformat.sh
samtools = samtools
sambamba = sambamba
b2fq = bamToFastq
gcov = genomeCoverageBed
intersectBed = intersectBed 
sortBed = sortBed
clusterBed = clusterBed  
randomBed = randomBed
groupBy = groupBy
bg2bw = bedGraphToBigWig

#DATABASES
hsindex = genome/mm
faindex = genome/mm.fasta.fai
lastindex = genome/mouse_mt
mtfaindex = genome/mouse_mt.fasta.fai
gsize = genome/mm.size
MT_fasta = genome/mouse_mt.fasta

#COMPUTATION
threads = 10

#MITOCHONDRIA FEATURES
refchr = NC_005089.1 #NAME FOR MT GENOME (THIS SHOULD THE NAME IN THE FASTA HEADER OF THE NUCLEAR+MITOCHONDRIAL GENOME FILE)
msize = 16299 #SIZE OF MT GENOME
exclude = 5 #FILTER SPLIT READS IF BOTH FRAGMENTS FALL WITHIN THE REGIONS AT THE START AND END TO AVOID PSEUDO GAPPED ALIGNMENTS DUE TO A CIRCULAR GENOME
orihs = 15423
orihe = 16299
orils = 5159
orile = 5195

#SCORING AND FILTERING FEATURES
score_threshold = 80 #ALIGNMENT SCORE CUT-OFF
evalue_threshold = 0.00001 #ALIGNMENT EVALUE CUT OFF
split_length = 15 #MINIMUM NO OF BASES IN A SPLIT READ FRAGMENT FOR THE READ TO BE CONSIDERED AS POTENTIALLY SPANNING A DELETION
paired_distance = 1000 #THE MAXIMUM DISTANCE OF A PAIRED READ FROM ITS SPLIT COUNTERPART FOR PAIRED SUPPORT TO BE CONSIDERED POSITIVE
deletion_threshold_min = 30 #THE MINIMUM SIZE OF THE GAP BETWEEN FRAGMENTS OF A SPLIT READ FOR THE SPLIT READ TO BE CONSIDERED AS POTENTIALLY SPANNING A DELETION
deletion_threshold_max = 30000 #THE MAXIMUM SIZE OF THE GAP BETWEEN FRAGMENTS OF A SPLIT READ FOR THE SPLIT READ TO BE CONSIDERED AS POTENTIALLY SPANNING A DELETION
breakthreshold = -2 #THE MAXIMUM DEVIATION A GIVEN SET OF SPLIT READ BREAKPOINTS CAN HAVE TO BE CONSIDERED WITHIN THE SAME CLUSTER 
cluster_threshold = 5 #MINIMUM NUMBER OF READS SUPPORTING A CLUSTER
breakspan = 15 #THE MINIMUM NO OF BASES A NON-SPLIT READ MUST SPAN EITHER SIDE OF A BREAKPOINT TO BE CONSIDERED IN THE HETEROPLASMY COUNT
sizelimit = 10000 #MAXIMUM SIZE OF DELETIONS TOLERATED, BEYOND WHICH THEY ARE RECLASSIFIED AS POTENTIAL DUPLICATIONS IN THE REVERSE ORIENTATION
hplimit = 0.01 #DETECTED HETEROPLASMY THRESHOLD
flank = 15 #RECOMMENDED 15
split_distance_threshold = 5 #THE MAXIMUM LENGTH OF UNMAPPED DISTANCE BETWEEN TWO FREGMENTS OF A SPLIT READ

#STEPS
dna = yes
enriched = no #IF THE SEQUENCING IS MITOCHONDRIAL DNA ENRICHED THEN SKIP THE INITIAL NUCLEAR GENOME ALIGNMENT STEP
nu_mt = yes #MAPPING TO NUCLEAR AND MITOCHONDRIAL GENOME WITH HISAT2
rmtmp = yes #REMOVE TEMPORARY FILES
o_mt = yes #MITOCHONDRIAL READ EXTRACTION AND REMAPPING TO ONLY MITOCHONDRIAL GENOME WITH LASTAL
i_del = yes #IDENTIFICATION AND CLUSTERING OF DELETIONS/DUPLICATIONS
cn_mt = yes #ESTIMATION OF MT DNA COPY NUMBER (WORKS ONLY IF SAMPLES ARE NOT ENRICHED FOR MT DNA AND "nu_mt" AS WELL AS "o_mt" STEPS ARE RUNNING)
