vcf-c-api.cpp

/*
  C API provides an application binary interface for external use
 */

extern "C" {
#include "vcf-c-api.h"
}

#include "Variant.h"

using namespace std;
using namespace vcflib;

void testme() {
}

void *zig_variant(void *var) {
    return 0L;
}

void *var_parse(const char *line, bool parse_samples) {
    cerr << "HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH" << endl;
    Variant * var = new Variant(); // construct buffer
    // Variant::parse(string& line, bool parseSamples) {
    string s = line;
    var->parse(s, parse_samples);
    cerr << "HEY\n" << s << "{" << var->id << "}" << endl;
    printf("<%p %s>\n",var,var->id.c_str());
    return var;
}

const char *var_id(void *var) {
    auto v = static_cast<Variant*>(var);
    // cout << "BACK IN C++ getname " << v->id << endl;
    return (v->id.data());
}

const long var_pos(void *var) {
    return (static_cast<Variant*>(var)->position);
}

const char *var_ref(void *var) {
    auto v = static_cast<Variant*>(var);
    return (v->ref.data());
}

const unsigned long var_info_num(void *variant, const char *name) {
    auto v = static_cast<Variant*>(variant);
    return v->info[name].size();
}

const char **var_info(void *var, const char *name, const char **ret) {
    auto v = static_cast<Variant*>(var);
    int idx = 0;
    for (auto &a: v->info[name]) {
        ret[idx] = a.c_str();
        idx++;
    }
    return ret;
}

const unsigned long var_alt_num(void *variant) {
    auto v = static_cast<Variant*>(variant);
    return v->alt.size();
}

const char **var_alt(void *variant,const char **ret) {
    auto v = static_cast<Variant*>(variant);
    int idx = 0;
    for (auto &a: v->alt) {
    // auto a = &v->alt[0];
        ret[idx] = a.c_str();
        // printf("ptr=%p:%s,%p:%s:\n",a.c_str(),a.c_str(),ret[idx],ret[idx]);
        // printf("ret=%s,%p,%s\n",ret,*ret,*ret);
        // break;
        idx++;
    }
    return ret;
}

void var_set_id(void *var, const char *id) {
    auto v = static_cast<Variant*>(var);
    v->id = id; // copies content
}

void var_set_ref(void *var, const char *ref) {
    auto v = static_cast<Variant*>(var);
    v->ref = ref; // copies content
}

void var_clear_alt(void *var) {
    auto v = static_cast<Variant*>(var);
    v->alt.clear();
}

void var_set_alt(void *var, const char *alt, long idx) {
    auto v = static_cast<Variant*>(var);
    v->alt.push_back(alt);
}

void var_clear_info(void *var, const char *name) {
    auto v = static_cast<Variant*>(var);
    v->info[name].clear();
}

void var_set_info(void *var, const char *name, const char *value, long idx) {
    auto v = static_cast<Variant*>(var);
    v->info[name].push_back(value);
}

const unsigned long var_samples_num(void *var) {
    auto v = static_cast<Variant*>(var);
    return v->samples.size();
}

const char **var_geno(void *var, const char **ret) {
    auto v = static_cast<Variant*>(var);
    auto samples = v->samples;
    int idx = 0;
    for (auto sname: v->sampleNames) {
        // cout << sname ;
        // cout << samples[sname]["GT"].front() << endl;

        // printf("<%s>\n",samples[sname]["GT"].front());
        ret[idx] = samples[sname]["GT"].front().data();
        idx++;
    }
    return ret;
}

void var_clear_sample(void *var, long idx) {
    auto v = static_cast<Variant*>(var);
    auto sname = v->sampleNames[idx].data();
    v->samples[sname]["GT"].clear();
}

void var_set_sample(void *var, const char *genos, long idx) {
    auto v = static_cast<Variant*>(var);
    //    ret[idx] = samples[sname]["GT"].front().data();
    auto sname = v->sampleNames[idx].data();
    // printf("%i: %s\n",idx,sname);
    // map<string, map<string, vector<string> > > samples;  // vector<string> allows for lists by Genotypes or Alternate
    v->samples[sname]["GT"].push_back(genos);
}