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// Application includes
#include "Genome.hh"
Genome Genome::genomes[NGS] = {Genome("NCBI36"),Genome("GRCh37"),Genome("GRCh38")};
const string Genome::CHRX = Genome::canonicalChromName("X");
const string Genome::CHRY = Genome::canonicalChromName("Y");
const string Genome::CHRALL = "ALL";
const string Genome::CHRSEX = "SEX";
Genome::Genome(string name) : n_chr_(0)
{
string org_name = name;
for (int i = 0;i < name.length();i++) name[i] = tolower(name[i]);
if (name == "hg18" || name == "ncbi36") {
gname_ = "NCBI36";
other_gname_ = "hg18";
n_chr_ = 24;
cnames_[0] = Genome::canonicalChromName("1"); clens_[0] = 247249719;
cnames_[1] = Genome::canonicalChromName("2"); clens_[1] = 242951149;
cnames_[2] = Genome::canonicalChromName("3"); clens_[2] = 199501827;
cnames_[3] = Genome::canonicalChromName("4"); clens_[3] = 191273063;
cnames_[4] = Genome::canonicalChromName("5"); clens_[4] = 180857866;
cnames_[5] = Genome::canonicalChromName("6"); clens_[5] = 170899992;
cnames_[6] = Genome::canonicalChromName("7"); clens_[6] = 158821424;
cnames_[7] = Genome::canonicalChromName("8"); clens_[7] = 146274826;
cnames_[8] = Genome::canonicalChromName("9"); clens_[8] = 140273252;
cnames_[9] = Genome::canonicalChromName("10"); clens_[9] = 135374737;
cnames_[10] = Genome::canonicalChromName("11"); clens_[10] = 134452384;
cnames_[11] = Genome::canonicalChromName("12"); clens_[11] = 132349534;
cnames_[12] = Genome::canonicalChromName("13"); clens_[12] = 114142980;
cnames_[13] = Genome::canonicalChromName("14"); clens_[13] = 106368585;
cnames_[14] = Genome::canonicalChromName("15"); clens_[14] = 100338915;
cnames_[15] = Genome::canonicalChromName("16"); clens_[15] = 88827254;
cnames_[16] = Genome::canonicalChromName("17"); clens_[16] = 78774742;
cnames_[17] = Genome::canonicalChromName("18"); clens_[17] = 76117153;
cnames_[18] = Genome::canonicalChromName("19"); clens_[18] = 63811651;
cnames_[19] = Genome::canonicalChromName("20"); clens_[19] = 62435964;
cnames_[20] = Genome::canonicalChromName("21"); clens_[20] = 46944323;
cnames_[21] = Genome::canonicalChromName("22"); clens_[21] = 49691432;
cnames_[22] = Genome::canonicalChromName("X"); clens_[22] = 154913754;
cnames_[23] = Genome::canonicalChromName("Y"); clens_[23] = 57772954;
} else if (name == "hg19" || name == "grch37") {
gname_ = "GRCh37";
other_gname_ = "hg19";
n_chr_ = 24;
cnames_[0] = Genome::canonicalChromName("1"); clens_[0] = 249250621;
cnames_[1] = Genome::canonicalChromName("2"); clens_[1] = 243199373;
cnames_[2] = Genome::canonicalChromName("3"); clens_[2] = 198022430;
cnames_[3] = Genome::canonicalChromName("4"); clens_[3] = 191154276;
cnames_[4] = Genome::canonicalChromName("5"); clens_[4] = 180915260;
cnames_[5] = Genome::canonicalChromName("6"); clens_[5] = 171115067;
cnames_[6] = Genome::canonicalChromName("7"); clens_[6] = 159138663;
cnames_[7] = Genome::canonicalChromName("8"); clens_[7] = 146364022;
cnames_[8] = Genome::canonicalChromName("9"); clens_[8] = 141213431;
cnames_[9] = Genome::canonicalChromName("10"); clens_[9] = 135534747;
cnames_[10] = Genome::canonicalChromName("11"); clens_[10] = 135006516;
cnames_[11] = Genome::canonicalChromName("12"); clens_[11] = 133851895;
cnames_[12] = Genome::canonicalChromName("13"); clens_[12] = 115169878;
cnames_[13] = Genome::canonicalChromName("14"); clens_[13] = 107349540;
cnames_[14] = Genome::canonicalChromName("15"); clens_[14] = 102531392;
cnames_[15] = Genome::canonicalChromName("16"); clens_[15] = 90354753;
cnames_[16] = Genome::canonicalChromName("17"); clens_[16] = 81195210;
cnames_[17] = Genome::canonicalChromName("18"); clens_[17] = 78077248;
cnames_[18] = Genome::canonicalChromName("19"); clens_[18] = 59128983;
cnames_[19] = Genome::canonicalChromName("20"); clens_[19] = 63025520;
cnames_[20] = Genome::canonicalChromName("21"); clens_[20] = 48129895;
cnames_[21] = Genome::canonicalChromName("22"); clens_[21] = 51304566;
cnames_[22] = Genome::canonicalChromName("X"); clens_[22] = 155270560;
cnames_[23] = Genome::canonicalChromName("Y"); clens_[23] = 59373566;
} else if (name == "mm9" || name == "mgscv37") {
gname_ = "MGSCv37";
other_gname_ = "mm9";
n_chr_ = 21;
cnames_[0] = Genome::canonicalChromName("1"); clens_[0] = 197195432;
cnames_[1] = Genome::canonicalChromName("2"); clens_[1] = 181748087;
cnames_[2] = Genome::canonicalChromName("3"); clens_[2] = 159599783;
cnames_[3] = Genome::canonicalChromName("4"); clens_[3] = 155630120;
cnames_[4] = Genome::canonicalChromName("5"); clens_[4] = 152537259;
cnames_[5] = Genome::canonicalChromName("6"); clens_[5] = 149517037;
cnames_[6] = Genome::canonicalChromName("7"); clens_[6] = 152524553;
cnames_[7] = Genome::canonicalChromName("8"); clens_[7] = 131738871;
cnames_[8] = Genome::canonicalChromName("9"); clens_[8] = 124076172;
cnames_[9] = Genome::canonicalChromName("10"); clens_[9] = 129993255;
cnames_[10] = Genome::canonicalChromName("11"); clens_[10] = 121843856;
cnames_[11] = Genome::canonicalChromName("12"); clens_[11] = 121257530;
cnames_[12] = Genome::canonicalChromName("13"); clens_[12] = 120284312;
cnames_[13] = Genome::canonicalChromName("14"); clens_[13] = 125194864;
cnames_[14] = Genome::canonicalChromName("15"); clens_[14] = 103494974;
cnames_[15] = Genome::canonicalChromName("16"); clens_[15] = 98319150;
cnames_[16] = Genome::canonicalChromName("17"); clens_[16] = 95272651;
cnames_[17] = Genome::canonicalChromName("18"); clens_[17] = 90772031;
cnames_[18] = Genome::canonicalChromName("19"); clens_[18] = 61342430;
cnames_[19] = Genome::canonicalChromName("X"); clens_[19] = 166650296;
cnames_[20] = Genome::canonicalChromName("Y"); clens_[20] = 15902555;
} else if (name == "hg38" || name == "grch38") {
gname_ = "GRCh38";
other_gname_ = "hg38";
n_chr_ = 24;
cnames_[0] = Genome::canonicalChromName("1"); clens_[0] = 248956422;
cnames_[1] = Genome::canonicalChromName("2"); clens_[1] = 242193529;
cnames_[2] = Genome::canonicalChromName("3"); clens_[2] = 198295559;
cnames_[3] = Genome::canonicalChromName("4"); clens_[3] = 190214555;
cnames_[4] = Genome::canonicalChromName("5"); clens_[4] = 181538259;
cnames_[5] = Genome::canonicalChromName("6"); clens_[5] = 170805979;
cnames_[6] = Genome::canonicalChromName("7"); clens_[6] = 159345973;
cnames_[7] = Genome::canonicalChromName("8"); clens_[7] = 145138636;
cnames_[8] = Genome::canonicalChromName("9"); clens_[8] = 138394717;
cnames_[9] = Genome::canonicalChromName("10"); clens_[9] = 133797422;
cnames_[10] = Genome::canonicalChromName("11"); clens_[10] = 135086622;
cnames_[11] = Genome::canonicalChromName("12"); clens_[11] = 133275309;
cnames_[12] = Genome::canonicalChromName("13"); clens_[12] = 114364328;
cnames_[13] = Genome::canonicalChromName("14"); clens_[13] = 107043718;
cnames_[14] = Genome::canonicalChromName("15"); clens_[14] = 101991189;
cnames_[15] = Genome::canonicalChromName("16"); clens_[15] = 90338345;
cnames_[16] = Genome::canonicalChromName("17"); clens_[16] = 83257441;
cnames_[17] = Genome::canonicalChromName("18"); clens_[17] = 80373285;
cnames_[18] = Genome::canonicalChromName("19"); clens_[18] = 58617616;
cnames_[19] = Genome::canonicalChromName("20"); clens_[19] = 64444167;
cnames_[20] = Genome::canonicalChromName("21"); clens_[20] = 46709983;
cnames_[21] = Genome::canonicalChromName("22"); clens_[21] = 50818468;
cnames_[22] = Genome::canonicalChromName("X"); clens_[22] = 156040895;
cnames_[23] = Genome::canonicalChromName("Y"); clens_[23] = 57227415;
} else {
cerr<<"Unknown genome '"<<org_name<<"'."<<endl;
}
}
int Genome::getChromosomeIndex(string chr)
{
for (int c = 0;c < n_chr_;c++)
if (chr == cnames_[c]) return c;
return -1;
}
Genome *Genome::get(string name)
{
for(int i = 0;i < name.length();i++) name[i] = tolower(name[i]);
int ind = 0;
while (ind < NGS) {
string tmp = genomes[ind].gname_;
for(int i = 0;i < tmp.length();i++) tmp[i] = tolower(tmp[i]);
if (tmp == name) return &genomes[ind];
tmp = genomes[ind].other_gname_;
for(int i = 0;i < tmp.length();i++) tmp[i] = tolower(tmp[i]);
if (tmp == name) return &genomes[ind];
ind++;
}
return NULL;
}
string Genome::canonicalChromName(string name)
{
string tmp = "";
for (int i = 0;i < name.length();i++) tmp += toupper(name[i]);
string ret = name;
if (tmp.substr(0,10) == "CHROMOSOME") ret = tmp.substr(10);
else if (tmp.substr(0,5) == "CHROM") ret = tmp.substr(5);
else if (tmp.substr(0,3) == "CHR") ret = tmp.substr(3);
return ret;
}
string Genome::extendedChromName(string name)
{
string ret = "chr" + Genome::canonicalChromName(name);
return ret;
}
bool Genome::isSexChrom(string name)
{
string tmp = canonicalChromName(name);
if (tmp == CHRSEX || tmp == CHRX || tmp == CHRY) return true;
return false;
}