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decompose.cpp
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decompose.cpp
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/* The MIT License
Copyright (c) 2014 Adrian Tan <[email protected]>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
*/
#include "decompose.h"
namespace
{
class Igor : Program
{
public:
///////////
//options//
///////////
std::string input_vcf_file;
std::string output_vcf_file;
std::vector<GenomeInterval> intervals;
std::string ref_fasta_file;
bool smart;
bool debug;
///////
//i/o//
///////
BCFOrderedReader *odr;
BCFOrderedWriter *odw;
//////////
//filter//
//////////
std::string fexp;
Filter filter;
bool filter_exists;
//helper variables
kstring_t s;
kstring_t new_alleles;
kstring_t old_alleles;
/////////
//stats//
/////////
uint32_t no_variants;
uint32_t new_no_variants;
uint32_t no_biallelic;
uint32_t no_multiallelic;
uint32_t no_additional_biallelic;
/////////
//tools//
/////////
VariantManip *vm;
Igor(int argc, char **argv)
{
version = "0.5";
//////////////////////////
//options initialization//
//////////////////////////
try
{
std::string desc = "decomposes multiallelic variants into biallelic in a VCF file.";
TCLAP::CmdLine cmd(desc, ' ', version);
VTOutput my; cmd.setOutput(&my);
TCLAP::ValueArg<std::string> arg_intervals("i", "i", "intervals []", false, "", "str", cmd);
TCLAP::ValueArg<std::string> arg_interval_list("I", "I", "file containing list of intervals []", false, "", "file", cmd);
TCLAP::ValueArg<std::string> arg_output_vcf_file("o", "o", "output VCF file [-]", false, "-", "str", cmd);
TCLAP::ValueArg<std::string> arg_fexp("f", "f", "filter expression []", false, "", "str", cmd);
TCLAP::SwitchArg arg_debug("d", "d", "debug [false]", cmd, false);
TCLAP::SwitchArg arg_smart("s", "s", "smart decomposition [false]", cmd, false);
TCLAP::UnlabeledValueArg<std::string> arg_input_vcf_file("<in.vcf>", "input VCF file", true, "","file", cmd);
cmd.parse(argc, argv);
input_vcf_file = arg_input_vcf_file.getValue();
output_vcf_file = arg_output_vcf_file.getValue();
fexp = arg_fexp.getValue();
smart = arg_smart.getValue();
debug = arg_debug.getValue();
parse_intervals(intervals, arg_interval_list.getValue(), arg_intervals.getValue());
}
catch (TCLAP::ArgException &e)
{
std::cerr << "error: " << e.error() << " for arg " << e.argId() << "\n";
abort();
}
};
void initialize()
{
//////////////////////
//i/o initialization//
//////////////////////
odr = new BCFOrderedReader(input_vcf_file, intervals);
odw = new BCFOrderedWriter(output_vcf_file);
odw->link_hdr(odr->hdr);
//bcf_hdr_append_info_with_backup_naming(odw->hdr, "OLD_MULTIALLELIC", "1", "String", "Original chr:pos:ref:alt encoding", false);
bcf_hdr_append(odw->hdr, "##INFO=<ID=OLD_MULTIALLELIC,Number=1,Type=String,Description=\"Original chr:pos:ref:alt encoding\">\n");
odw->write_hdr();
/////////////////////////
//filter initialization//
/////////////////////////
filter.parse(fexp.c_str(), false);
filter_exists = fexp=="" ? false : true;
//helper variables
s = {0,0,0};
old_alleles = {0,0,0};
new_alleles = {0,0,0};
////////////////////////
//stats initialization//
////////////////////////
no_variants = 0;
no_biallelic = 0;
no_multiallelic = 0;
no_additional_biallelic = 0;
////////////////////////
//tools initialization//
////////////////////////
vm = new VariantManip();
}
/**
* n choose r.
*/
uint32_t choose(uint32_t n, uint32_t r)
{
if (r>n)
{
return 0;
}
else if (r==n)
{
return 1;
}
else if (r==0)
{
return 1;
}
else
{
if (r>(n>>1))
{
r = n-r;
}
uint32_t num = n;
uint32_t denum = 1;
for (uint32_t i=1; i<r; ++i)
{
num *= n-i;
denum *= i+1;
}
return num/denum;
}
}
void decompose()
{
bcf_hdr_t* h = odr->hdr;
bcf1_t* v = bcf_init();
Variant variant;
while (odr->read(v))
{
bcf_unpack(v, BCF_UN_INFO);
if (debug) bcf_print_liten(h, v);
if (filter_exists)
{
vm->classify_variant(h, v, variant);
if (!filter.apply(h, v, &variant, false))
{
continue;
}
}
int32_t n_allele = bcf_get_n_allele(v);
if (n_allele > 2)
{
if (!smart)
{
++no_multiallelic;
no_additional_biallelic += n_allele-2;
old_alleles.l = 0;
bcf_variant2string(odw->hdr, v, &old_alleles);
int32_t rid = bcf_get_rid(v);
int32_t pos1 = bcf_get_pos1(v);
char** allele = bcf_get_allele(v);
int32_t *gt = NULL;
int32_t *pl = NULL;
float *gl = NULL;
int32_t *dp = NULL;
size_t no_samples = bcf_hdr_nsamples(odr->hdr);
bool has_GT = false;
bool has_PL = false;
bool has_GL = false;
bool has_DP = false;
int32_t ploidy = 0;
int32_t n_genotype;
int32_t n_genotype2;
int32_t *gts = NULL;
int32_t *pls = NULL;
float *gls = NULL;
int32_t *dps = NULL;
if (no_samples)
{
bcf_unpack(v, BCF_UN_FMT);
int32_t n = 0;
int32_t ret = bcf_get_genotypes(odr->hdr, v, >, &n);
if (ret>0) has_GT = true;
ploidy = n/bcf_hdr_nsamples(odr->hdr);
n_genotype = bcf_ap2g(n_allele, ploidy);
n_genotype2 = bcf_ap2g(2, ploidy);
if (ret>0) gts = (int32_t*) malloc(no_samples*n_genotype2*sizeof(int32_t));
n=0;
ret = bcf_get_format_int32(odr->hdr, v, "PL", &pl, &n);
if (ret>0)
{
has_PL = true;
pls = (int32_t*) malloc(no_samples*n_genotype2*sizeof(int32_t));
}
n=0;
ret = bcf_get_format_float(odr->hdr, v, "GL", &gl, &n);
if (ret>0)
{
has_GL = true;
gls = (float*) malloc(no_samples*n_genotype2*sizeof(float));
}
n=0;
ret = bcf_get_format_int32(odr->hdr, v, "DP", &dp, &n);
if (ret>0)
{
has_DP = true;
dps = (int32_t*) malloc(no_samples*sizeof(int32_t));
}
}
// std::cerr << "*****************************\n";
// bcf_print(odw->hdr, v);
// std::cerr << "*****************************\n";
for (size_t i=1; i<n_allele; ++i)
{
//bcf_clear(v);
bcf1_t* nv = bcf_dup(v);
new_alleles.l=0;
kputs(allele[0], &new_alleles);
kputc(',', &new_alleles);
kputs(allele[i], &new_alleles);
bcf_update_info_string(odw->hdr, nv, "OLD_MULTIALLELIC", old_alleles.s);
bcf_update_alleles_str(odw->hdr, nv, new_alleles.s);
if (no_samples)
{
//get array genotypes
for (size_t j=0; j<no_samples; ++j)
{
if (has_GT)
{
for (size_t k=0; k<ploidy; ++k)
{
int32_t _a = gt[j*ploidy+k];
if (_a<0)
{
gts[j*ploidy+k] = _a;
}
else
{
int32_t a = bcf_gt_allele(_a);
if (a)
{
a = a==i ? 1 : -1;
}
gts[j*ploidy+k] = ((a+1)<<1) | bcf_gt_is_phased(_a);
}
}
}
if (has_PL)
{
pls[j*n_genotype2] = pl[j*n_genotype];
uint32_t index = 0;
for (uint32_t k = 1; k<n_genotype2; ++k)
{
index += choose(ploidy-(k-1)+i-1,i-1);
pls[j*n_genotype2+k] = pl[j*n_genotype+index];
}
}
if (has_GL)
{
gls[j*n_genotype2] = gl[j*n_genotype];
uint32_t index = 0;
for (uint32_t k = 1; k<n_genotype2; ++k)
{
index += choose(ploidy-(k-1)+i-1,i-1);
gls[j*n_genotype2+k] = gl[j*n_genotype+index];
}
}
if (has_DP)
{
dps[j] = dp[j];
}
}
//remove other format values except for GT, PL, GL and DP
if (i==1)
{
bcf_fmt_t *fmt = v->d.fmt;
for (size_t j = 0; j < v->n_fmt; ++j)
{
const char* tag = odw->hdr->id[BCF_DT_ID][fmt[j].id].key;
if (strcmp(tag,"GT")&&strcmp(tag,"PL")&&strcmp(tag,"GL")&&strcmp(tag,"DP"))
{
bcf_update_format_int32(odw->hdr, nv, tag, 0, 0);
}
}
}
if (has_GT) bcf_update_genotypes(odw->hdr, nv, gts, no_samples*ploidy);
if (has_PL) bcf_update_format_int32(odw->hdr, nv, "PL", pls, no_samples*n_genotype2);
if (has_GL) bcf_update_format_float(odw->hdr, nv, "GL", gls, no_samples*n_genotype2);
if (has_DP) bcf_update_format_int32(odw->hdr, nv, "DP", dps, no_samples);
}
//remove other format values except for GT, PL, GL and DP
bcf_fmt_t *fmt = v->d.fmt;
for (size_t j = 0; j < v->n_fmt; ++j)
{
const char* tag = odw->hdr->id[BCF_DT_ID][fmt[j].id].key;
if (strcmp(tag,"GT")&&strcmp(tag,"PL")&&strcmp(tag,"GL")&&strcmp(tag,"DP"))
{
bcf_update_format_int32(odw->hdr, nv, tag, 0, 0);
}
}
odw->write(nv);
bcf_destroy(nv);
}
if (has_GT) {free(gt); free(gts);}
if (has_PL) {free(pl); free(pls);}
if (has_GL) {free(gl); free(gls);}
if (has_DP) {free(dp); free(dps);}
}
else //smart decomposition
{
++no_multiallelic;
no_additional_biallelic += n_allele-2;
old_alleles.l = 0;
bcf_variant2string(odw->hdr, v, &old_alleles);
int32_t rid = bcf_get_rid(v);
int32_t pos1 = bcf_get_pos1(v);
char** allele = bcf_get_allele(v);
uint32_t no_samples = bcf_hdr_nsamples(odr->hdr);
char** alleles = (char**) malloc(n_allele*sizeof(char*));
for (size_t i=0; i<n_allele; ++i)
{
alleles[i] = strdup(allele[i]);
}
// std::cerr << "=============================\n";
// bcf_print(odr->hdr, v);
// std::cerr << "=============================\n";
//
for (size_t i=1; i<n_allele; ++i)
{
bcf1_t *nv = bcf_dup(v);
bcf_set_rid(nv, rid);
bcf_set_pos1(nv, pos1);
new_alleles.l=0;
kputs(allele[0], &new_alleles);
kputc(',', &new_alleles);
kputs(allele[i], &new_alleles);
//////////////////////
//split up INFO fields
//////////////////////
if (nv->n_info)
{
bcf_unpack(v, BCF_UN_INFO);
bcf_hdr_t* hdr = odr->hdr;
bcf_info_t *info = v->d.info;
for (uint32_t j = 0; j < v->n_info; ++j)
{
int32_t key = info[j].key;
if (key<0)
{
fprintf(stderr, "[E::%s] invalid BCF, the INFO key key=%d not present in the header.\n", __func__, key);
abort();
}
const char* tag = hdr->id[BCF_DT_ID][key].key;
int32_t var_len = bcf_hdr_id2length(hdr,BCF_HL_INFO,key);
int32_t type = info[j].type;
if (var_len==BCF_VL_G)
{
// std::cerr << "tag : "<< tag << "\n";
if (type==BCF_BT_INT8||type==BCF_BT_INT16||type==BCF_BT_INT32)
{
int32_t n = 0;
int32_t* g = 0;
int32_t ret = bcf_get_info_int32(odr->hdr, v, tag, &g, &n);
if (ret>0)
{
int32_t n_genotype = n;
int32_t ploidy = bcf_ag2p(n_allele, n_genotype);
int32_t n_genotype2 = bcf_ap2g(2, ploidy);
int32_t* gs = (int32_t*) malloc(n_genotype2*sizeof(int32_t));
gs[0] = g[0];
uint32_t index = 0;
// std::cerr << "no of genotypes : " << n_genotype2 << "\n";
// std::cerr << "allele : "<< i << "\n";
for (uint32_t k = 1; k<n_genotype2; ++k)
{
index += choose(ploidy-(k-1)+i-1,i-1);
// std::cerr << index << "\n";
gs[k] = g[index];
}
bcf_update_info_int32(odw->hdr, nv, tag, gs, n_genotype2);
free(gs);
free(g);
}
}
else if (type==BCF_BT_FLOAT)
{
int32_t n = 0;
float* g = 0;
int32_t ret = bcf_get_info_float(odr->hdr, v, tag, &g, &n);
if (ret>0)
{
int32_t n_genotype = n;
int32_t ploidy = bcf_ag2p(n_allele, n_genotype);
int32_t n_genotype2 = bcf_ap2g(2, ploidy);
float* gs = (float*) malloc(n_genotype2*sizeof(float));
gs[0] = g[0];
uint32_t index = 0;
for (uint32_t k = 1; k<n_genotype2; ++k)
{
index += choose(ploidy-(k-1)+i-1,i-1);
gs[k] = g[index];
}
bcf_update_info_float(odw->hdr, nv, tag, gs, n_genotype2);
free(gs);
free(g);
}
}
else if (type==BCF_BT_CHAR)
{
//not necessary
}
}
else if (var_len == BCF_VL_A)
{
if (type==BCF_BT_INT8||type==BCF_BT_INT16||type==BCF_BT_INT32)
{
int32_t n = 0;
int32_t* a = 0;
int32_t ret = bcf_get_info_int32(odr->hdr, v, tag, &a, &n);
if (ret>0)
{
int32_t as = a[i-1];
bcf_update_info_int32(odw->hdr, nv, tag, &as, 1);
}
free(a);
}
else if (type==BCF_BT_FLOAT)
{
int32_t n = 0;
float* a = 0;
int32_t ret = bcf_get_info_float(odr->hdr, v, tag, &a, &n);
if (ret>0)
{
float as = a[i-1];
bcf_update_info_float(odw->hdr, nv, tag, &as, 1);
}
free(a);
}
else if (type==BCF_BT_CHAR)
{
int32_t n = 0;
char* a = 0;
int32_t ret = bcf_get_info_string(odr->hdr, v, tag, &a, &n);
if (ret>0)
{
char* b = a;
char* c = a;
int32_t e = 0;
while (*b)
{
if (*b==',')
{
*b = 0;
++e;
if (e==i)
{
bcf_update_info_string(odw->hdr, nv, tag, c);
break;
}
c = b+1;
}
else if (*(b+1)==0)
{
bcf_update_info_string(odw->hdr, nv, tag, c);
break;
}
++b;
}
if (e>i)
{
bcf_update_info_string(odw->hdr, nv, tag, NULL);
}
free(a);
}
}
}
else if (var_len == BCF_VL_R)
{
if (type==BCF_BT_INT8||type==BCF_BT_INT16||type==BCF_BT_INT32)
{
int32_t n = 0;
int32_t* a = 0;
int32_t ret = bcf_get_info_int32(odr->hdr, v, tag, &a, &n);
if (ret)
{
int32_t* as = (int32_t*) malloc(sizeof(int32_t)*2);
as[0] = a[0];
as[1] = a[i];
bcf_update_info_int32(odw->hdr, nv, tag, as, 2);
free(as);
free(a);
}
}
else if (type==BCF_BT_FLOAT)
{
int32_t n = 0;
float* a = 0;
int32_t ret = bcf_get_info_float(odr->hdr, v, tag, &a, &n);
if (ret>0)
{
float* as = (float*) malloc(sizeof(float)*2);
as[0] = a[0];
as[1] = a[i];
bcf_update_info_float(odw->hdr, nv, tag, as, 2);
free(as);
free(a);
}
}
else if (type==BCF_BT_CHAR)
{
int32_t n = 0;
char* a = 0;
int32_t ret = bcf_get_info_string(odr->hdr, v, tag, &a, &n);
if (ret>0)
{
char* b = a;
char* c = a;
int32_t e = 0;
while (*b)
{
if (*b==',')
{
*b = 0;
++e;
if (e==i)
{
bcf_update_info_string(odw->hdr, nv, tag, c);
break;
}
c = b+1;
}
//last occurrence
else if (*(b+1)==0)
{
bcf_update_info_string(odw->hdr, nv, tag, c);
break;
}
++b;
}
if (e>i)
{
bcf_update_info_string(odw->hdr, nv, tag, NULL);
}
free(a);
}
}
}
else if (var_len == BCF_VL_FIXED)
{
//leave it there
}
else if (var_len == BCF_VL_VAR)
{
//leave it there
}
}
}
////////////////////////
//split up FORMAT fields
////////////////////////
if (no_samples)
{
bcf_unpack(v, BCF_UN_FMT);
if (nv->n_fmt)
{
bcf_hdr_t* hdr = odr->hdr;
bcf_fmt_t *fmt = v->d.fmt;
for (uint32_t j = 0; j < (int32_t)v->n_fmt; ++j)
{
int32_t id = fmt[j].id;
if (id<0)
{
fprintf(stderr, "[E::%s] invalid BCF, the FORMAT tag id=%d not present in the header.\n", __func__, id);
abort();
}
const char* tag = hdr->id[BCF_DT_ID][id].key;
int32_t var_len = bcf_hdr_id2length(hdr,BCF_HL_FMT,id);
int32_t type = fmt[j].type;
if (var_len==BCF_VL_G)
{
if (type==BCF_BT_INT8||type==BCF_BT_INT16||type==BCF_BT_INT32)
{
int32_t n = 0;
int32_t* g = 0;
int32_t ret = bcf_get_format_int32(odr->hdr, v, tag, &g, &n);
int32_t n_genotype = n/no_samples;
int32_t ploidy = bcf_ag2p(n_allele, n_genotype);
int32_t n_genotype2 = bcf_ap2g(2, ploidy);
int32_t* gs = (int32_t*) malloc(no_samples*n_genotype2*sizeof(int32_t));
//get array genotypes
for (uint32_t j=0; j<no_samples; ++j)
{
gs[j*n_genotype2] = g[j*n_genotype];
uint32_t index = 0;
for (uint32_t k = 1; k<n_genotype2; ++k)
{
index += choose(ploidy-(k-1)+i-1,i-1);
gs[j*n_genotype2+k] = g[j*n_genotype+index];
}
}
bcf_update_format_int32(odw->hdr, nv, tag, gs, no_samples*n_genotype2);
free(gs);
free(g);
}
else if (type==BCF_BT_FLOAT)
{
int32_t n = 0;
float* g = 0;
int32_t ret = bcf_get_format_float(odr->hdr, v, tag, &g, &n);
int32_t n_genotype = n/no_samples;
int32_t ploidy = bcf_ag2p(n_allele, n_genotype);
int32_t n_genotype2 = bcf_ap2g(2, ploidy);
float* gs = (float*) malloc(no_samples*n_genotype2*sizeof(float));
for (uint32_t j=0; j<no_samples; ++j)
{
gs[j*n_genotype2] = g[j*n_genotype];
uint32_t index = 0;
for (uint32_t k = 1; k<n_genotype2; ++k)
{
index += choose(ploidy-(k-1)+i-1,i-1);
gs[j*n_genotype2+k] = g[j*n_genotype+index];
}
}
bcf_update_format_float(odw->hdr, nv, tag, gs, no_samples*n_genotype2);
free(gs);
free(g);
}
else if (type==BCF_BT_CHAR)
{
//to be implemented
}
}
else if (var_len == BCF_VL_A)
{
if (type==BCF_BT_INT8||type==BCF_BT_INT16||type==BCF_BT_INT32)
{
int32_t n = 0;
int32_t* a = 0;
int32_t ret = bcf_get_format_int32(odr->hdr, v, tag, &a, &n);
int32_t* as = (int32_t*) malloc(no_samples*sizeof(int32_t));
if (ret!=(n_allele-1)*no_samples)
{
for (uint32_t j=0; j<no_samples; ++j)
{
as[j] = bcf_int32_missing;
}
}
else
{
for (uint32_t j=0; j<no_samples; ++j)
{
if (a[j*(n_allele-1)+(i-1)]==bcf_int32_missing ||
a[j*(n_allele-1)+(i-1)]==bcf_int32_vector_end)
{
as[j] = bcf_int32_missing;
}
else
{
as[j] = a[j*(n_allele-1)+(i-1)];
}
}
}
bcf_update_format_int32(odw->hdr, nv, tag, as, no_samples);
free(as);
free(a);
}
else if (type==BCF_BT_FLOAT)
{
int32_t n = 0;
float* a = 0;
int32_t ret = bcf_get_format_float(odr->hdr, v, tag, &a, &n);
float* as = (float*) malloc(no_samples*sizeof(float));
if (ret!=(n_allele-1)*no_samples)
{
for (uint32_t j=0; j<no_samples; ++j)
{
bcf_float_set_missing(as[j]);;
}
}
else
{
for (uint32_t j=0; j<no_samples; ++j)
{
if (bcf_float_is_missing(a[j*(n_allele-1)+(i-1)]) ||
bcf_float_is_vector_end(a[j*(n_allele-1)+(i-1)]))
{
bcf_float_set_missing(as[j]);
}
else
{
as[j] = a[j*(n_allele-1)+(i-1)];
}
}
}
bcf_update_format_float(odw->hdr, nv, tag, as, no_samples);
free(as);
free(a);
}
else if (type==BCF_BT_CHAR)
{
//to be implemented
}
}
else if (var_len == BCF_VL_R)
{
if (type==BCF_BT_INT8||type==BCF_BT_INT16||type==BCF_BT_INT32)
{
int32_t n = 0;
int32_t* a = 0;
int32_t ret = bcf_get_format_int32(odr->hdr, v, tag, &a, &n);
int32_t* as = (int32_t*) malloc(no_samples*sizeof(int32_t)*2);
if (ret!=n_allele*no_samples)
{
for (uint32_t j=0; j<no_samples; ++j)
{
as[j*2] = bcf_int32_missing;
as[j*2+1] = bcf_int32_vector_end;
}
}
else
{
for (uint32_t j=0; j<no_samples; ++j)
{
as[j*2] = a[j*n_allele];
as[j*2+1] = a[j*n_allele+i];
}
}
bcf_update_format_int32(odw->hdr, nv, tag, as, no_samples*2);
free(as);
free(a);
}
else if (type==BCF_BT_FLOAT)
{
int32_t n = 0;
float* a = 0;
int32_t ret = bcf_get_format_float(odr->hdr, v, tag, &a, &n);
float* as = (float*) malloc(no_samples*sizeof(float));
if (ret!=n_allele*no_samples)
{
for (uint32_t j=0; j<no_samples; ++j)
{
bcf_float_set_missing(as[j*2]);
bcf_float_set_vector_end(as[j*2+1]);
}
}
else
{
for (uint32_t j=0; j<no_samples; ++j)
{
as[j*2] = a[j*n_allele];
as[j*2+1] = a[j*n_allele+i];
}
}
bcf_update_format_float(odw->hdr, nv, tag, as, no_samples*2);
free(as);
free(a);
}
else if (type==BCF_BT_CHAR)
{
//to be implemented
}
}
else if (var_len == BCF_VL_FIXED)
{
if (strcmp(tag,"GT")==0)
{
int32_t n = 0;
int32_t* gt = 0;
int32_t ret = bcf_get_genotypes(odr->hdr, v, >, &n);
int32_t ploidy = n/bcf_hdr_nsamples(odr->hdr);
int32_t n_genotype = bcf_ap2g(n_allele, ploidy);
int32_t n_genotype2 = bcf_ap2g(2, ploidy);
int32_t* gts = (int32_t*) malloc(no_samples*n_genotype2*sizeof(int32_t));
for (uint32_t j=0; j<no_samples; ++j)
{
for (size_t k=0; k<ploidy; ++k)
{
int32_t a = gt[j*ploidy+k];
if (a<0)
{
gts[j*ploidy+k] = a;
}
else
{
int32_t na = bcf_gt_allele(a);
if (na)
{
na = na==i ? 1 : -1;
}
gts[j*ploidy+k] = ((na+1)<<1) | bcf_gt_is_phased(a);
}
}
}
bcf_update_genotypes(odw->hdr, nv, gts, no_samples*ploidy);
free(gts);
free(gt);
}
else
{
//leave it there...
}
}
else if (var_len == BCF_VL_VAR)
{
//leave it there
}
}
}
}
bcf_update_info_string(odw->hdr, nv, "OLD_MULTIALLELIC", old_alleles.s);
bcf_update_alleles_str(odw->hdr, nv, new_alleles.s);
odw->write(nv);
bcf_destroy(nv);
}
}
}
else
{
odw->write(v);
++no_biallelic;
}
++no_variants;
}
odr->close();
odw->close();
};
void print_options()
{
std::clog << "decompose v" << version << "\n";
std::clog << "\n";
std::clog << "options: input VCF file " << input_vcf_file << "\n";
std::clog << " [s] smart decomposition " << (smart ? "true" : "false") << " (experimental)\n";
std::clog << " [o] output VCF file " << output_vcf_file << "\n";
print_int_op(" [i] intervals ", intervals);
std::clog << "\n";
}
void print_stats()
{
std::clog << "\n";
std::clog << "stats: no. variants : " << no_variants << "\n";
std::clog << " no. biallelic variants : " << no_biallelic << "\n";
std::clog << " no. multiallelic variants : " << no_multiallelic << "\n";
std::clog << "\n";
std::clog << " no. additional biallelics : " << no_additional_biallelic << "\n";
std::clog << " total no. of biallelics : " << no_additional_biallelic + no_variants << "\n";
std::clog << "\n";
};
~Igor() {};
private:
};
}