# Original: old ssahaSNP behaviour: best-scorers only,
# discard all if ties
original matchEnds=0 diff=-1
# Meth1: no end-pairing, allow ties but no shortfall
meth1 matchEnds=0
# Meth1_1: as meth1 but limit 1x coverage
meth1_1 matchEnds=0 maxCov=1.0
# Meth1_2: as meth1 but limit 2x coverage
meth1_2 matchEnds=0 maxCov=2.0
# Meth2: strict end-pairing, allow shortfall of 300
meth2 matchEnds=2 diff=300
# Meth3: as meth1 but allow hybrid matches with penalty 50 (was 10)
meth3 matchEnds=0 hybrid=50
# Meth3_pX.Y: as meth3 but select with probability X.Y.
meth3_p0.1 matchEnds=0 hybrid=50 probUse=0.1
meth3_p0.2 matchEnds=0 hybrid=50 probUse=0.2
meth3_p0.3 matchEnds=0 hybrid=50 probUse=0.3
meth3_p0.4 matchEnds=0 hybrid=50 probUse=0.4
meth3_p0.5 matchEnds=0 hybrid=50 probUse=0.5
meth3_p0.6 matchEnds=0 hybrid=50 probUse=0.6
meth3_p0.7 matchEnds=0 hybrid=50 probUse=0.7
meth3_p0.8 matchEnds=0 hybrid=50 probUse=0.8
meth3_p0.9 matchEnds=0 hybrid=50 probUse=0.9
meth3_p1.0 matchEnds=0 hybrid=50
# Meth4: maxCount 1, don't try and match ends
meth4 maxCount=1 matchEnds=0
meth4_01 maxCount=1 matchEnds=0 useBelow=0.01
meth4_99 maxCount=1 matchEnds=0 useAbove=0.01
meth4_10 maxCount=1 matchEnds=0 useBelow=0.1
meth4_90 maxCount=1 matchEnds=0 useAbove=0.1