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vcfpp.h
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/*******************************************************************************
* @file https://github.com/Zilong-Li/vcfpp/vcfpp.h
* @author Zilong Li
* @email [email protected]
* @version v0.6.1
* @breif a single C++ file for manipulating VCF
* Copyright (C) 2022-2023.The use of this code is governed by the LICENSE file.
******************************************************************************/
/*! \mainpage The documentation of the single C++ file *vcfpp.h* for manipulating VCF/BCF
*
* \section intro_sec Introduction
*
* This project https://github.com/Zilong-Li/vcfpp introduces a single C++ file as interface to the basic
* htslib, which can be easily included in a C++ program for scripting high-performance genomic analyses.
*
* - vcfpp.BcfHeader keeps track of the header information in VCF/BCF
* - vcfpp.BcfRecord keeps track of the variants information in VCF/BCF
* - vcfpp.BcfReader streams in variants from VCF/BCF file or stdin
* - vcfpp.BcfWriter streams out variants to VCF/BCF file or stdout
*
* \section install_sec Installation
*
* - <EM> include "vcfpp.h" </EM> to your program and compile it by <EM> g++ my.cpp -std=c++11 -Wall -I. -lhts
* - </EM>
* - make sure you have https://github.com/samtools/htslib installed on your system and the it is in your
* environment.
*
*
* \copyright Copyright (C) 2022 Zilong Li . This project is governed by the LICENSE file in
* https://github.com/Zilong-Li/vcfpp.
*
*
*/
#pragma once
#include <cstddef>
#include <stdexcept>
#ifndef VCFPP_H_
# define VCFPP_H_
# include <iostream>
# include <memory>
# include <string>
# include <type_traits>
# include <vector>
// make sure you have htslib installed
extern "C"
{
# include <htslib/hts.h>
# include <htslib/kstring.h>
# include <htslib/tbx.h>
# include <htslib/vcf.h>
# include <htslib/vcfutils.h>
}
namespace vcfpp
{
template<typename T>
using isValidFMT =
typename std::enable_if<std::is_same<T, std::string>::value || std::is_same<T, std::vector<char>>::value
|| std::is_same<T, std::vector<int>>::value
|| std::is_same<T, std::vector<float>>::value,
bool>::type;
template<typename T>
using isValidInfo =
typename std::enable_if<std::is_same<T, std::string>::value || std::is_same<T, std::vector<int>>::value
|| std::is_same<T, std::vector<float>>::value,
bool>::type;
template<typename T>
using isInfoVector = typename std::enable_if<std::is_same<T, std::vector<int>>::value
|| std::is_same<T, std::vector<float>>::value,
bool>::type;
template<typename T>
using isScalar = typename std::enable_if<std::is_same<T, int>::value || std::is_same<T, float>::value
|| std::is_same<T, double>::value,
bool>::type;
template<typename T>
using isString = typename std::enable_if<std::is_same<T, std::string>::value, bool>::type;
template<typename T>
using isValidGT = typename std::enable_if<std::is_same<T, std::vector<bool>>::value
|| std::is_same<T, std::vector<char>>::value,
bool>::type;
template<typename T>
using isFormatVector = typename std::enable_if<std::is_same<T, std::vector<float>>::value
|| std::is_same<T, std::vector<char>>::value
|| std::is_same<T, std::vector<int>>::value,
bool>::type;
namespace details
{
template<typename T>
isScalar<T> isMissing(T const & v)
{
if(std::is_same<T, float>::value)
{
return bcf_float_is_missing(v);
}
else if(std::is_same<T, int>::value)
{
return bcf_int32_missing(v);
}
}
// test if a string is end with another string
inline bool isEndWith(std::string const & s, std::string const & e)
{
if(s.length() >= e.length())
{
return (0 == s.compare(s.length() - e.length(), e.length(), e));
}
else
{
return false;
}
}
// determinate the mode for read/write the compressed/uncompressed VCF/BCF
inline std::string getMode(std::string const & fname, std::string mode = "r")
{
if(isEndWith(fname, "bcf.gz")) mode += "b";
if(isEndWith(fname, "bcf")) mode += "bu";
if(isEndWith(fname, "vcf.gz")) mode += "z";
return mode;
}
// string split by separator
inline std::vector<std::string> split_string(const std::string & s, const std::string & separators)
{
std::vector<std::string> ret;
bool is_seperator[256] = {false};
for(auto & ch : separators)
{
is_seperator[(unsigned int)ch] = true;
}
int begin = 0;
for(int i = 0; i <= (int)s.size(); i++)
{
if(is_seperator[(uint8_t)s[i]] || i == (int)s.size())
{
ret.push_back(std::string(s.begin() + begin, s.begin() + i));
begin = i + 1;
}
}
return ret;
}
// deleter for htsFile
struct hts_file_close
{
void operator()(htsFile * x)
{
if(x) hts_close(x);
}
};
// deleter for hts iterator
struct hts_iter_close
{
void operator()(hts_itr_t * x)
{
if(x) hts_itr_destroy(x);
}
};
// deleter for hts idx
struct hts_idx_close
{
void operator()(hts_idx_t * x)
{
if(x) hts_idx_destroy(x);
}
};
// deleter for tabix idx
struct tabix_idx_close
{
void operator()(tbx_t * x)
{
if(x) tbx_destroy(x);
}
};
// deleter for variant
struct bcf_line_close
{
void operator()(bcf1_t * x)
{
if(x) bcf_destroy(x);
}
};
// deleter for bcf header
struct bcf_hdr_close
{
void operator()(bcf_hdr_t * x)
{
if(x) bcf_hdr_destroy(x);
}
};
} // namespace details
/**
* @class BcfHeader
* @brief Object represents header of the VCF, offering methods to access and modify the tags
* @note BcfHeader has 3 friends, BcfReader, BcfWriter and BcfRecord.
**/
class BcfHeader
{
friend class BcfRecord;
friend class BcfReader;
friend class BcfWriter;
private:
bcf_hdr_t * hdr = NULL; // bcf header
bcf_hrec_t * hrec = NULL; // populate header
public:
BcfHeader() {}
~BcfHeader()
{
if(hrec) bcf_hrec_destroy(hrec);
if(hdr) bcf_hdr_destroy(hdr);
}
/** @brief stream out the header */
friend std::ostream & operator<<(std::ostream & out, const BcfHeader & h)
{
out << h.asString();
return out;
}
// TODO: check if the value is valid for vcf specification
/** @brief add INFO field to header
* @param id tag name in INFO field
* @param number Number of elements
* @param type Integer, Floast or String
* @param description Description of the tag
* */
inline void addINFO(const std::string & id,
const std::string & number,
const std::string & type,
const std::string & description)
{
addLine("##INFO=<ID=" + id + ",Number=" + number + ",Type=" + type + ",Description=\"" + description
+ "\">");
}
/** @brief add FORMAT field to header
* @param id tag name in FORMAT field
* @param number Number of elements
* @param type Integer, Floast or String
* @param description Description of the tag
* */
inline void addFORMAT(const std::string & id,
const std::string & number,
const std::string & type,
const std::string & description)
{
addLine("##FORMAT=<ID=" + id + ",Number=" + number + ",Type=" + type + ",Description=\"" + description
+ "\">");
}
/**
* @brief add one FILTER line to header
* @param id FILTER name
* @param description Description of the FILTER
* */
inline void addFILTER(const std::string & id, const std::string & description)
{
addLine("##FILTER=<ID=" + id + ",Description=\"" + description + "\">");
}
/** @brief add contig to header
* @param id contig or chromosome name
* */
inline void addContig(const std::string & id)
{
addLine("##contig=<ID=" + id + ">");
}
/**
* @brief add one line to header
* */
inline void addLine(const std::string & str)
{
int ret = 0;
ret = bcf_hdr_append(hdr, str.c_str());
if(ret != 0) throw std::runtime_error("could not add " + str + " to header\n");
ret = bcf_hdr_sync(hdr);
if(ret != 0) throw std::runtime_error("could not add " + str + " to header\n");
}
/** @brief add one sample name to header */
inline void addSample(const std::string & sample) const
{
bcf_hdr_add_sample(hdr, sample.c_str());
if(bcf_hdr_sync(hdr) != 0)
{
throw std::runtime_error("couldn't add the sample.\n");
}
}
/** @brief return header as a string */
inline std::string asString() const
{
kstring_t s = {0, 0, NULL}; // kstring
if(bcf_hdr_format(hdr, 0, &s) == 0) // append header string to s.s! append!
{
std::string out(s.s, s.l);
free(s.s);
return out;
}
else
{
throw std::runtime_error("failed to convert formatted header to string");
}
}
/** @brief return all samples in a string vector */
std::vector<std::string> getSamples() const
{
std::vector<std::string> vec;
for(int i = 0; i < bcf_hdr_nsamples(hdr); i++)
{
vec.push_back(std::string(hdr->samples[i]));
}
return vec;
}
/** @brief return all contig/chromosome names in a string vector */
std::vector<std::string> getSeqnames() const
{
int ret = 0;
const char ** seqs = bcf_hdr_seqnames(hdr, &ret);
if(ret == 0) printf("there is no contig id in the header!\n");
std::vector<std::string> vec;
for(int i = 0; i < ret; i++)
{
vec.push_back(std::string(seqs[i]));
}
free(seqs);
return vec;
}
/**
* @brief get the type of a given tag
* @param tag in the FORMAT
* @return 1: int; 2: float; 3: string; 0: error;
*/
inline int getFormatType(std::string tag) const
{
int tag_id = bcf_hdr_id2int(hdr, BCF_DT_ID, tag.c_str());
if(tag_id < 0) return 0;
if(bcf_hdr_id2type(hdr, BCF_HL_FMT, tag_id) == (BCF_HT_INT & 0xff))
{
return 1;
}
else if(bcf_hdr_id2type(hdr, BCF_HL_FMT, tag_id) == (BCF_HT_REAL & 0xff))
{
return 2;
}
else if(bcf_hdr_id2type(hdr, BCF_HL_FMT, tag_id) == (BCF_HT_STR & 0xff))
{
return 3;
}
else
{
return 0;
}
}
/** @brief remove a contig tag from header */
inline void removeContig(std::string tag) const
{
bcf_hdr_remove(hdr, BCF_HL_CTG, tag.c_str());
}
/** @brief remove a INFO tag from header */
inline void removeInfo(std::string tag) const
{
bcf_hdr_remove(hdr, BCF_HL_INFO, tag.c_str());
}
/** @brief remove a FORMAT tag from header */
inline void removeFormat(std::string tag) const
{
bcf_hdr_remove(hdr, BCF_HL_FMT, tag.c_str());
}
/** @brief remove a FILTER tag from header */
inline void removeFilter(std::string tag) const
{
bcf_hdr_remove(hdr, BCF_HL_FLT, tag.c_str());
}
/**
* @brief update the sample id in the header
* @param samples a comma-separated string for multiple new samples
* @note this only update the samples name in a given sequential order
* */
void updateSamples(const std::string & samples)
{
auto ss = details::split_string(samples, ",");
const int nsamples = nSamples();
if(nsamples != (int)ss.size())
throw std::runtime_error("You provide either too few or too many samples");
kstring_t htxt = {0, 0, 0};
bcf_hdr_format(hdr, 1, &htxt);
// Find the beginning of the #CHROM line
int i = htxt.l - 2, ncols = 0;
while(i >= 0 && htxt.s[i] != '\n')
{
if(htxt.s[i] == '\t') ncols++;
i--;
}
if(i < 0 || strncmp(htxt.s + i + 1, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT", 45))
{
if(i > 0 && !strncmp(htxt.s + i + 1, "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO", 38))
throw std::runtime_error("Error: missing FORMAT fields, cowardly refusing to add samples\n");
throw std::runtime_error("Could not parse the header: " + std::string(htxt.s));
}
ncols = 0;
while(ncols != 9)
{
i++;
if(htxt.s[i] == '\t') ncols++;
}
htxt.l = i;
// Replace all samples
for(i = 0; i < nsamples; i++)
{
kputc('\t', &htxt);
kputs(ss[i].c_str(), &htxt);
}
kputc('\n', &htxt);
// destroy the old and make new header
bcf_hdr_destroy(hdr);
hdr = bcf_hdr_init("r");
if(bcf_hdr_parse(hdr, htxt.s) < 0)
throw std::runtime_error("An error occurred while parsing the header\n");
// free everything
free(htxt.s);
}
/**
* @brief explicitly set samples to be extracted
* @param samples samples to include or exclude as a comma-separated string
* */
inline void setSamples(const std::string & samples) const
{
int ret = 0;
ret = bcf_hdr_set_samples(hdr, samples.c_str(), 0);
if(ret != 0)
{
throw std::runtime_error("the " + std::to_string(ret)
+ "-th sample are not in the VCF.\nparameter samples:" + samples);
}
}
/** @brief set the VCF version */
inline void setVersion(const std::string & version) const
{
bcf_hdr_set_version(hdr, version.c_str());
}
/** @brief return the number of samples in the VCF */
inline int nSamples() const
{
return bcf_hdr_nsamples(hdr);
}
};
/**
* @class BcfRecord
* @brief Object represents a variant record in the VCF, offering methods to access and modify fields.
* @note BcfRecord has to be associated with a BcfHeader object and needs to be filled in by calling
*BcfReader.getNextVariant function.
**/
class BcfRecord
{
friend class BcfReader;
friend class BcfWriter;
private:
BcfHeader * header;
std::shared_ptr<bcf1_t> line = std::shared_ptr<bcf1_t>(bcf_init(), details::bcf_line_close()); // variant
bcf_hdr_t * hdr_d = NULL; // a dup header by bcf_hdr_dup(header->hdr)
bcf_fmt_t * fmt = NULL;
bcf_info_t * info = NULL;
int32_t * gts = NULL;
int ndst, ret, nsamples;
bool noneMissing = true; // whenever parsing a tag have to reset this variable
bool isAllPhased = false;
int nploidy = 0; // the number of ploidy
int nvalues = 0; // the number of values for a tag in FORMAT
public:
/// if there is "." in GT for the sample, then it's coded as missing (TRUE)
std::vector<char> isGenoMissing;
public:
/// empty constructor. call init() afterwards
BcfRecord() {}
/// constructor with a given BcfHeader object
BcfRecord(BcfHeader & h)
{
initHeader(h);
}
~BcfRecord()
{
if(gts) free(gts);
if(hdr_d) bcf_hdr_destroy(hdr_d);
}
/// initilize the header associated with BcfRecord object by pointing to another BcfHeader object
void initHeader(BcfHeader & h)
{
header = &h;
if(!header->hdr) throw std::runtime_error("please initial header first\n");
nsamples = header->nSamples();
typeOfGT.resize(nsamples);
gtPhase.resize(nsamples, 0);
}
/// reset the header associated with BcfRecord object by pointing to another BcfHeader object
void resetHeader(BcfHeader & h)
{
header = &h;
}
/** @brief stream out the variant */
friend std::ostream & operator<<(std::ostream & out, const BcfRecord & v)
{
out << v.asString();
return out;
}
/** @brief return current variant as raw string */
inline std::string asString() const
{
kstring_t s = {0, 0, NULL}; // kstring
if(vcf_format(header->hdr, line.get(), &s) == 0)
{
std::string out(s.s, s.l);
free(s.s);
return out;
}
else
{
throw std::runtime_error("couldn't format current record into a string.\n");
}
}
/**
* @brief fill in the input vector with genotypes of 0 and 1. only works for ploidy<=2. Genotypes with
* missing allele is coded as heterozygous
* @param v valid input includes vector<bool> and vector<char> type
* @return bool
* @note use isNoneMissing() to check if all genotypes are with no missingness. Alternatively, one can
* use vector<int> as the input type as noted in the other overloading function getGenotypes().
* */
template<typename T>
isValidGT<T> getGenotypes(T & v)
{
ndst = 0;
ret = bcf_get_genotypes(header->hdr, line.get(), >s, &ndst);
if(ret <= 0)
{
# if defined(VERBOSE)
std::cerr << "GT not present for current site. did you initilize the variant object?\n";
# endif
return false;
}
// if nploidy is not set manually. find the max nploidy using the first variant (eg. 2) resize v as
// max(nploidy)
// * nsamples (ret) NOTE: if ret == nsamples and only one sample then haploid
if(ret != nploidy * nsamples && nploidy > 0)
{
// rare case if nploidy is set manually. eg. only one sample. the first variant is '1' but the
// second is '1/0'. ret = 1 but nploidy should be 2
v.resize(nploidy * nsamples);
}
else
{
v.resize(ret);
nploidy = ret / nsamples;
}
// work with nploidy == 1, haploid?
isGenoMissing.assign(nsamples, 0);
int i, j, nphased = 0;
noneMissing = true;
fmt = bcf_get_fmt(header->hdr, line.get(), "GT");
int nploidy_cur = ret / nsamples; // requires nploidy_cur <= nploidy
for(i = 0; i < nsamples; i++)
{
// check and fill in typeOfGT; only supports SNPs now. check vcfstats.c for inspiration
typeOfGT[i] = bcf_gt_type(fmt, i, NULL, NULL);
if(typeOfGT[i] == GT_UNKN)
{
noneMissing = false; // set missing as het, user should check if isNoneMissing();
isGenoMissing[i] = 1;
v[i * nploidy + 0] = 1;
for(j = 1; j < nploidy_cur; j++) v[i * nploidy + j] = 0;
continue;
}
for(j = 0; j < nploidy_cur; j++)
{
// TODO: right now only parse 0 and 1, ie max(nploidy)=2; other values 2,3... will be set to 1
v[i * nploidy + j] = bcf_gt_allele(gts[j + i * nploidy_cur]) != 0;
}
if(nploidy == 2)
{
gtPhase[i] = (gts[1 + i * nploidy_cur] & 1) == 1;
nphased += gtPhase[i];
}
}
if(nphased == nsamples)
{
isAllPhased = true;
}
else
{
isAllPhased = false;
}
return true;
}
/**
* @brief fill in the input vector with genotype values, 0, 1 or -9 (missing).
* @param v valid input is vector<int> type
* @return bool
* @note this function provides full capability to handle all kinds of genotypes
* in multi-ploidy data costing more spae than the other function. missing allele is set as -9.
* */
bool getGenotypes(std::vector<int> & v)
{
ndst = 0;
ret = bcf_get_genotypes(header->hdr, line.get(), >s, &ndst);
if(ret <= 0)
{
# if defined(VERBOSE)
std::cerr << "GT not present for current site. did you initilize the variant object?\n";
# endif
return false;
}
v.resize(ret);
isGenoMissing.assign(nsamples, 0);
nploidy = ret / nsamples;
int i, j, nphased = 0;
noneMissing = true;
for(i = 0; i < nsamples; i++)
{
int32_t * ptr = gts + i * nploidy;
int is_phased = 0;
for(j = 0; j < nploidy; j++)
{
// if true, the sample has smaller ploidy
if(ptr[j] == bcf_int32_vector_end) break;
// missing allele
if(bcf_gt_is_missing(ptr[j]))
{
noneMissing = false;
isGenoMissing[i] = 1;
v[i * nploidy + j] = -9;
continue;
}
v[i * nploidy + j] = bcf_gt_allele(ptr[j]);
is_phased += bcf_gt_is_phased(ptr[j]);
}
if(nploidy == is_phased)
{
gtPhase[i] = true;
nphased += gtPhase[i];
}
}
if(nphased == nsamples)
{
isAllPhased = true;
}
else
{
isAllPhased = false;
}
return true;
}
/**
* @brief get tag value in FORMAT
* @param tag valid tag name in FORMAT column declared in the VCF header
* @param v valid input include vector of float, char, int type
* @return bool
* */
template<typename T, typename S = typename T::value_type>
isFormatVector<T> getFORMAT(std::string tag, T & v)
{
fmt = bcf_get_fmt(header->hdr, line.get(), tag.c_str());
if(!fmt)
{
throw std::invalid_argument("no FORMAT=" + tag + " in the VCF header.\n");
}
nvalues = fmt->n;
ndst = 0;
S * dst = NULL;
int tagid = header->getFormatType(tag);
if(tagid == 1)
{
ret = bcf_get_format_int32(header->hdr, line.get(), tag.c_str(), &dst, &ndst);
}
else if(tagid == 2)
{
ret = bcf_get_format_float(header->hdr, line.get(), tag.c_str(), &dst, &ndst);
}
else if(tagid == 3)
{
ret = bcf_get_format_char(header->hdr, line.get(), tag.c_str(), &dst, &ndst);
}
else
{
ret = -1;
}
if(ret >= 0)
{
// user have to check if there is missing in the return v;
v = std::vector<S>(dst, dst + ret);
free(dst);
return true;
}
else
{
free(dst);
return false;
}
}
/**
* @brief get tag value in FORMAT
* @param tag valid tag name in FORMAT column declared in the VCF header
* @param v vector of string
* @return bool
* */
bool getFORMAT(std::string tag, std::vector<std::string> & v)
{
fmt = bcf_get_fmt(header->hdr, line.get(), tag.c_str());
if(!fmt)
{
throw std::invalid_argument("no FORMAT=" + tag + " in the VCF header.\n");
}
nvalues = fmt->n;
// if ndst < (fmt->n+1)*nsmpl; then realloc is involved
ret = -1, ndst = 0;
char ** dst = NULL;
if(header->getFormatType(tag) == 3)
ret = bcf_get_format_string(header->hdr, line.get(), tag.c_str(), &dst, &ndst);
if(ret > 0)
{
v.clear();
for(int i = 0; i < nsamples; i++)
{
// Ugly: GT field is considered to be a string by the VCF header but BCF represents it as INT.
v.emplace_back(dst[i]);
};
free(dst[0]);
free(dst);
return true;
}
else
{
free(dst[0]);
free(dst);
return false;
}
}
/**
* @brief get tag value in INFO
* @param tag valid tag name in INFO column declared in the VCF header
* @param v valid input include vector of float, int type
* @return bool
* */
template<typename T, typename S = typename T::value_type>
isInfoVector<T> getINFO(std::string tag, T & v)
{
info = bcf_get_info(header->hdr, line.get(), tag.c_str());
if(!info)
{
throw std::invalid_argument("no INFO=" + tag + " in the VCF header.\n");
}
S * dst = NULL;
ndst = 0;
ret = -1;
if(info->type == BCF_BT_INT8 || info->type == BCF_BT_INT16 || info->type == BCF_BT_INT32)
{
ret = bcf_get_info_int32(header->hdr, line.get(), tag.c_str(), &dst, &ndst);
}
else if(info->type == BCF_BT_FLOAT)
{
ret = bcf_get_info_float(header->hdr, line.get(), tag.c_str(), &dst, &ndst);
}
if(ret >= 0)
{
v = std::vector<S>(dst, dst + ret); // user have to check if there is missing in the return v;
free(dst);
return true;
}
else
{
free(dst);
return false;
}
}
/**
* @brief get tag value in INFO
* @param tag valid tag name in INFO column declared in the VCF header
* @param v valid input include scalar value of float or int type
* @return bool
* */
template<typename T>
isScalar<T> getINFO(std::string tag, T & v)
{
info = bcf_get_info(header->hdr, line.get(), tag.c_str());
if(!info)
{
throw std::invalid_argument("no INFO=" + tag + " in the VCF header.\n");
}
// scalar value
if(info->len == 1)
{
if(info->type == BCF_BT_INT8 || info->type == BCF_BT_INT16 || info->type == BCF_BT_INT32)
{
v = info->v1.i;
}
else if(info->type == BCF_BT_FLOAT)
{
v = info->v1.f;
}
return true;
}
else
{
# if defined(VERBOSE)
std::cerr << "there are multiple values for " + tag
+ " in INFO for current site. please use vector instead\n";
# endif
return false;
}
}
/**
* @brief get tag value in INFO
* @param tag valid tag name in INFO column declared in the VCF header
* @param v valid input is std::string
* @return bool
* */
template<typename T>
isString<T> getINFO(std::string tag, T & v)
{
info = bcf_get_info(header->hdr, line.get(), tag.c_str());
if(!info)
{
throw std::invalid_argument("no INFO=" + tag + " in the VCF header.\n");
}
if(info->type == BCF_BT_CHAR)
{
v = std::string(reinterpret_cast<char *>(info->vptr), info->vptr_len);
return true;
}
else
{
return false;
}
}
/**
* @brief set tag value for INFO
* @param tag valid tag name in INFO column declared in the VCF header
* @param v valid input include scalar value of float or int type
* @return bool
* */
template<typename T>
isScalar<T> setINFO(std::string tag, const T & v)
{
// bcf_hrec_set_val
// bcf_update_info_flag(header.hdr, line, tag.c_str(), NULL, 1);
int tag_id = bcf_hdr_id2int(header->hdr, BCF_DT_ID, tag.c_str());
if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_INT & 0xff))
{
ret = bcf_update_info_int32(header->hdr, line.get(), tag.c_str(), &v, 1);
}
else if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_REAL & 0xff))
{
float v2 = static_cast<float>(v);
ret = bcf_update_info_float(header->hdr, line.get(), tag.c_str(), &v2, 1);
}
else
{
ret = -1;
}
if(ret < 0)
{
# if defined(VERBOSE)
std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
# endif
return false;
}
return true;
}
/**
* @brief set tag value for INFO
* @param tag valid tag name in INFO column declared in the VCF header
* @param v valid input include vector<int> vector<float> std::string
* @return bool
* */
template<typename T>
isValidInfo<T> setINFO(std::string tag, const T & v)
{
// bcf_update_info_flag(header.hdr, line, tag.c_str(), NULL, 1);
int tag_id = bcf_hdr_id2int(header->hdr, BCF_DT_ID, tag.c_str());
if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_INT & 0xff))
{
ret = bcf_update_info_int32(header->hdr, line.get(), tag.c_str(), v.data(), v.size());
}
else if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_REAL & 0xff))
{
ret = bcf_update_info_float(header->hdr, line.get(), tag.c_str(), v.data(), v.size());
}
else if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_STR & 0xff))
{
ret = bcf_update_info_string(header->hdr, line.get(), tag.c_str(), v.data());
}
else
{
ret = -1;
}
if(ret < 0)
{
# if defined(VERBOSE)
std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
# endif
return false;
}
return true;
}
/// remove the given tag from INFO of the variant
void removeINFO(std::string tag)
{
int tag_id = bcf_hdr_id2int(header->hdr, BCF_DT_ID, tag.c_str());
if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_INT & 0xff))
{
ret = bcf_update_info_int32(header->hdr, line.get(), tag.c_str(), NULL, 0);
}
else if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_REAL & 0xff))
{
ret = bcf_update_info_float(header->hdr, line.get(), tag.c_str(), NULL, 0);
}
else if(bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_STR & 0xff))
{
ret = bcf_update_info_string(header->hdr, line.get(), tag.c_str(), NULL);
}
else
{
ret = -1;
}
if(ret < 0)
{
throw std::runtime_error("couldn't remove " + tag + " for this variant.\n");
}
}
/**
* @brief set genotypes from scratch even if genotypes not present
* @param v the genotypes of vector<int> type
* @return bool
* */
bool setGenotypes(const std::vector<int> & v)
{