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Initial conversion from rejector.org.

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mjobin mjobin
mjobin authored and mjobin committed Aug 15, 2018
1 parent 6581c0a commit 7c17ad1e074c6b3e3a8a604770ebe6cf675583aa
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CXXFLAGS=-O2 -fpermissive -pthread
rejector2source := $(wildcard src/rejector2/*.cpp)
rejector2objects := $(patsubst %.cpp,%.o,$(wildcard src/rejector2/*.cpp))
simcoalrej2_1_2source := $(wildcard src/simcoalrej2_1_2/*.cpp)
simcoalrej2_1_2objects := $(patsubst %.cpp,%.o,$(wildcard src/simcoalrej2_1_2/*.cpp))
rej2runsource := $(wildcard code/rej2run/*.cpp)
rej2runobjects := $(patsubst %.cpp,%.o,$(wildcard code/rej2run/*.cpp))
all : rejector2 simcoalrej2_1_2 rej2run
rejector2 : $(rejector2objects)
$(CXX) $(CXXFLAGS) -o rejector2 $(rejector2objects)
simcoalrej2_1_2 : $(simcoalrej2_1_2objects)
$(CXX) $(CXXFLAGS) -o simcoalrej2_1_2 $(simcoalrej2_1_2objects)
rej2run : $(rej2runobjects)
$(CXX) $(CXXFLAGS) -o rej2run $(rej2runobjects)
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/--Statlist
Heterozygosity 0.1
HeterozygosityAv 0.1
HeterozygositySub 0.1
HeterozygosityAvSub 0.1
DeltaMuSquared 0.1
DeltaMuSquaredSub 0.1
Td 0.1
TdSub 0.1
Dsw 0.1
Beta 0.1
BetaAv 0.1
BetaSub 0.1
BetaAvSub 0.1
LDChiSquare 0.1
RangeofLocus 0.1
SampleSize 0.1
SampleSizeSub 0.1
MaxLength 0.1
MinLength 0.1
MeanLength 0.1
NumDiffAlleles 0.1
CompleteHeterozygotes 0.1
CompleteHomozygotes 0.1
Haplotypes 0.1
Jstatistic 0.1
MicrosatVariance 0.1
DerivedFraction 0.1
NucleotideDiversity 0.1
Nei 0.1
Fst 0.1
MicrosatVarianceAv 0.1
NumDiffAllelesAv 0.1
NucleotideDiversityAv 0.1
FstAv 0.1
JstatisticAv 0.1
ModJstatisticAv 0.1
Istatistic 0.1
IstatisticAv 0.1
ModIstatisticAv 0.1
UBDeltaMuSquared 0.1
UBDeltaMuSquaredSub 0.1
LD 0.1
LDAdj 0.1
Hamming 0.1
HammingBtwn 0.1
NumHaploBlocks 0.1
NumROH 0.1
FROHVar 0.1
SharedHaplotypeBlocks 0.1
MinorAlleleFrequency 0.1
TajimasD 0.1
NumSegSites 0.1
LongSharedBetween 0.1
LongSharedWithin 0.1
BlockLength 0.1
BlockBoundary 0.1
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Locus Type MutRates Ancestral Motif RecombRt Chrom Pos Offset
AGAT084 STR 0.0002 NA 4 0 1 0 NA
GATA135F02P STR 0.0002 NA 4 0 1 0 NA
GATA188F04 STR 0.0002 NA 4 0 1 0 NA
AAT263 STR 0.0002 NA 3 0 1 0 NA
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REJECTOR
Number of Populations
5
/--Priors
Population Sizes
gamma
1000
10
uniform
100
10000
uniform
100
10000
uniform
100
10000
uniform
100
10000
Growth Rates
uniform
0
0.01
uniform
0
0
uniform
0
0.2
uniform
0
0.2
uniform
0
0.2
Number of Migration Matrices
0
Number of Historical Events
4
uniform
3500 0 1 1.0 1 0 0
6500 0 1 1.0 2 0 0
uniform
3500 4 1 1.0 1 0 0
6500 4 1 1.0 2 0 0
uniform
3500 3 1 1.0 1 0 0
6500 3 1 1.0 2 0 0
uniform
500 2 1 1.0 1 0 0
3000 2 1 1.0 1 0 0
Microsat Range Constraint
uniform
5
14
/--Statlist
Heterozygosity 0.1
HeterozygosityAv 0.1
HeterozygositySub 0.1
HeterozygosityAvSub 0.1
DeltaMuSquared 0.1
DeltaMuSquaredSub 0.1
Td 0.1
TdSub 0.1
Dsw 0.1
Beta 0.1
BetaAv 0.1
BetaSub 0.1
BetaAvSub 0.1
LD 0.1
LDChiSquare 0.1
RangeofLocus 0.1
SampleSize 0.1
SampleSizeSub 0.1
MaxLength 0.1
MinLength 0.1
MeanLength 0.1
NumDiffAlleles 0.1
CompleteHeterozygotes 0.1
CompleteHomozygotes 0.1
Haplotypes 0.1
Jstatistic 0.1
MicrosatVariance 0.1
DerivedFraction 0.1
NucleotideDiversity 0.1
Nei 0.1
Fst 0.1
MicrosatVarianceAv 0.1
NumDiffAllelesAv 0.1
NucleotideDiversityAv 0.1
FstAv 0.1
JstatisticAv 0.1
ModJstatisticAv 0.1
Istatistic 0.1
IstatisticAv 0.1
ModIstatisticAv 0.1
UBDeltaMuSquared 0.1
UBDeltaMuSquaredSub 0.1
/--Data
Vnaught 0
Loci SNP STR DNA UEP STR
MutRates 1.00E-09 2.80E-04 1.00E-08 1.00E-08 2.80E-04
Ancestral "T,C" -1 AGCT L -1
RecombRt 0.000042 0 0 0 0.00005
NumLoci 1 1 1 1 2
Length 1 2 4 1 5
Tag Population
0 A T 25 AGCT L 10000 2
1 A -1 23 AGCT L 10000 2
2 A C -1 AGCT L 22 3
3 A C -1 AGCT L 34 5
4 A C 22 AGCT S 22 3
5 A T 22 AGCT -1 22 7
6 B T 80 AGCT L 80 7
7 B C 21 AGCT L 21 8
8 E T 24 AGCT S 24 8
9 B T 25 AGCT S 25 7
10 C C 22 AGCT L 22 9
11 C C 24 AGCC L 24 6
12 E C 24 AGCT L 24 8
13 C C 22 AGCT S 22 4
14 E C 20 AGCC L 20 9
15 C C 19 AGCT S 19 3
16 D C 45 AGCT L 45 5
17 D T 21 AGCT L 21 2
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REJECTOR
Number of Populations
5
/--Priors
Population Sizes
gamma
1000
10
uniform
100
10000
uniform
100
10000
uniform
100
10000
uniform
100
10000
Growth Rates
uniform
0
0.01
uniform
0
0
uniform
0
0.2
uniform
0
0.2
uniform
0
0.2
Number of Migration Matrices
0
Number of Historical Events
4
uniform
3500 0 1 1.0 1 0 0
6500 0 1 1.0 2 0 0
uniform
3500 4 1 1.0 1 0 0
6500 4 1 1.0 2 0 0
uniform
3500 3 1 1.0 1 0 0
6500 3 1 1.0 2 0 0
uniform
500 2 1 1.0 1 0 0
3000 2 1 1.0 1 0 0
Microsat Range Constraint
uniform
5
14
/--Statlist
Heterozygosity 0.1
HeterozygosityAv 0.1
HeterozygositySub 0.1
HeterozygosityAvSub 0.1
DeltaMuSquared 0.1
DeltaMuSquaredSub 0.1
Td 0.1
TdSub 0.1
Dsw 0.1
Beta 0.1
BetaAv 0.1
BetaSub 0.1
BetaAvSub 0.1
LD 0.1
LDChiSquare 0.1
RangeofLocus 0.1
SampleSize 0.1
SampleSizeSub 0.1
MaxLength 0.1
MinLength 0.1
MeanLength 0.1
NumDiffAlleles 0.1
CompleteHeterozygotes 0.1
CompleteHomozygotes 0.1
Haplotypes 0.1
Jstatistic 0.1
MicrosatVariance 0.1
DerivedFraction 0.1
NucleotideDiversity 0.1
Nei 0.1
Fst 0.1
MicrosatVarianceAv 0.1
NumDiffAllelesAv 0.1
NucleotideDiversityAv 0.1
FstAv 0.1
JstatisticAv 0.1
ModJstatisticAv 0.1
Istatistic 0.1
IstatisticAv 0.1
ModIstatisticAv 0.1
UBDeltaMuSquared 0.1
UBDeltaMuSquaredSub 0.1
/--Data
Vnaught 0
Loci SNP STR DNA DNA STR
MutRates 1.00E-09 2.80E-04 1.00E-08 1.00E-08 2.80E-04
Ancestral "T,C" -1 AGCT AGCT -1
RecombRt 0.000042 0 0 0 0.00005
NumLoci 1 1 1 1 2
Length 1 2 4 4 5
Tag Population
0 A T 25 AGCT AGCT 10000 2
1 A -1 23 AGCT AGCT 10000 2
2 A C -1 AGCT AGCT 22 3
3 A C -1 AGCT AGCT 34 5
4 A C 22 AGCT AGCT 22 3
5 A T 22 AGCT AGCT 22 7
6 B T 80 AGCT ATTT 80 7
7 B C 21 AGCT AGCT 21 8
8 E T 24 AGCT AGCT 24 8
9 B T 25 AGCT AGCT 25 7
10 C C 22 AGCT AGCT 22 9
11 C C 24 AGCC AGCC 24 6
12 E C 24 AGCT AGCT 24 8
13 C C 22 AGCT AGCT 22 4
14 E C 20 AGCC AGCC 20 9
15 C C 19 AGCT AGCT 19 3
16 D C 45 AGCT AGCT 45 5
17 D T 21 AGCT AGCT 21 2
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