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[feat] Merge ibdgl method branch #2

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merged 2 commits into from
Dec 12, 2023
Merged

[feat] Merge ibdgl method branch #2

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9f7dac9
[feat] add ibd gl and ibdseq methods
isinaltinkaya Aug 21, 2023
45b46aa
[fix] Remove redundant readsite directive in gl
isinaltinkaya Aug 21, 2023
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54 changes: 46 additions & 8 deletions argStruct.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -44,6 +44,7 @@ argStruct *argStruct_get(int argc, char **argv) {
// -doDxy <int> : estimate Dxy
// -doPhylo <int> : do neighbor-joining
// -doDist <int> : estimate pairwise distance matrix
// -doIbd <int> : detect IBD segments

// TODO idea multilayer argument reading using LUTs
// e.g. `-doAMOVA` in lut1 -> "args->doAMOVA" in lut2 ->integer in lut3
Expand All @@ -66,7 +67,9 @@ argStruct *argStruct_get(int argc, char **argv) {

} else if (strcasecmp("-doDist", arv) == 0) {
args->doDist = atoi(val);
}
} else if (strcasecmp("-doIbd", arv) == 0) {
args->doIbd = atoi(val);
}

// ################################
// # INPUT FILES [--in-XXX] #
Expand Down Expand Up @@ -345,6 +348,37 @@ argStruct *argStruct_get(int argc, char **argv) {

else if (strcasecmp("--minInd", arv) == 0)
args->minInd = atoi(val);
else if (strcasecmp("--min-af", arv) == 0){
args->min_af = atof(val);
}


else if (strcasecmp("--ibdseq-errorprop", arv) == 0){
args->ibdseq_errorprop = atof(val);
}

else if (strcasecmp("--ibdseq-errormax", arv) == 0){
args->ibdseq_errormax = atof(val);
}

else if (strcasecmp("--ibdseq-minalleles", arv) == 0){
args->ibdseq_minalleles = atoi(val);
if(args->ibdseq_minalleles<2){
ERROR("--ibdseq-minalleles is set to %d. Allowed range of values is 2<value<N");
}
}
else if (strcasecmp("--ibdseq-ibdlod", arv) == 0){
args->ibdseq_ibdlod= atof(val);
if(args->ibdseq_ibdlod<0){
ERROR("--ibdseq-ibdlod must be a positive number.");
}
}
else if (strcasecmp("--ibdseq-ibdtrim", arv) == 0){
args->ibdseq_ibdtrim= atof(val);
if(args->ibdseq_ibdtrim<0){
ERROR("--ibdseq-ibdtrim must be a nonnegative number.");
}
}

else if (strcasecmp("--em-tole", arv) == 0)
args->tole = atof(val);
Expand Down Expand Up @@ -457,10 +491,12 @@ void argStruct::check_arg_dependencies() {
// 2: estimate distance matrix from genotypes
// 3: read distance matrix from file

if (0 == doDist) {
fprintf(stderr, "\n\n-doDist 0: Nothing to do; will exit.\n\n");
exit(0);
} else if (1 == doDist) {
//TODO
// if (0 == doDist) {
// fprintf(stderr, "\n\n-doDist 0: Nothing to do; will exit.\n\n");
// exit(0);
// } else
if (1 == doDist) {
LOG("-doDist 1, will estimate distance matrix from genotype likelihoods.");

IO::requireArgFile(in_vcf_fn, "--in-vcf", "-doDist 1");
Expand All @@ -479,9 +515,11 @@ void argStruct::check_arg_dependencies() {
if (0 != printDistanceMatrix) {
ERROR("-doDist 3 cannot be used with --printDistanceMatrix.\n");
}
} else {
ERROR("-doDist %d is not a valid option.", doDist);
}
}
//TODO
// } else {
// ERROR("-doDist %d is not a valid option.", doDist);
// }

//----------------------------------------------------------------------------------//
// -doAMOVA
Expand Down
19 changes: 19 additions & 0 deletions argStruct.h
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Original file line number Diff line number Diff line change
Expand Up @@ -168,6 +168,7 @@ struct argStruct {
int doDxy = 0;
int doPhylo = 0;
int doDist = 0;
int doIbd = 0;

int printAmovaTable = 0;
int printDistanceMatrix = 0;
Expand All @@ -184,6 +185,24 @@ struct argStruct {
double tole = -1;
int maxEmIter = -1;


// ------------------------------------------------
// VCF filters
double min_af = 0.0;
// ------------------------------------------------



// ------------------------------------------------
// IBDSEQ method implementation
int ibdseq_minalleles=2;
double ibdseq_errormax=0.001;
double ibdseq_errorprop=0.25;
double ibdseq_ibdlod=3.0;
double ibdseq_ibdtrim=0.0;



int nThreads = 1;
int seed = -1;
int nBootstraps = 0;
Expand Down