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use reference of BcfHeader instead of pointer
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@Zilong-Li
Zilong-Li committed Aug 22, 2022
1 parent d1be817 commit 3104b36
Showing 1 changed file with 79 additions and 73 deletions.
152 changes: 79 additions & 73 deletions vcfpp.h
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Original file line number Diff line number Diff line change
Expand Up @@ -305,10 +305,10 @@ namespace vcfpp
friend class BcfWriter;

public:
/** @brief initilize a BcfRecord object using a given BcfHeader object */
BcfRecord(BcfHeader& h) : header(std::make_shared<BcfHeader>(h))
/** @brief initilize a BcfRecord object using a given BcfHeader object. */
BcfRecord(const BcfHeader& h) : header(h)
{
nsamples = header->nSamples();
nsamples = header.nSamples();
typeOfGT.resize(nsamples);
gtPhase.resize(nsamples);
}
Expand All @@ -328,7 +328,7 @@ namespace vcfpp
inline std::string asString() const
{
kstring_t s = {0, 0, NULL}; // kstring
if (vcf_format(header->hdr, line, &s) == 0)
if (vcf_format(header.hdr, line, &s) == 0)
return std::string(s.s, s.l);
else
throw std::runtime_error("couldn't format current record into a string.\n");
Expand All @@ -343,7 +343,7 @@ namespace vcfpp
isValidGT<T> getGenotypes(T& v)
{
ndst = 0;
ret = bcf_get_genotypes(header->hdr, line, &gts, &ndst);
ret = bcf_get_genotypes(header.hdr, line, &gts, &ndst);
if (ret <= 1)
return false; // gt not present
// if nploidy is not set manually. find the max nploidy using the first variant (eg. 2) resize v as max(nploidy) * nsamples (ret)
Expand All @@ -361,7 +361,7 @@ namespace vcfpp
// work with nploidy == 1, haploid?
int i, j, nphased = 0;
noneMissing = true;
fmt = bcf_get_fmt(header->hdr, line, "GT");
fmt = bcf_get_fmt(header.hdr, line, "GT");
int nploidy_cur = ret / nsamples; // requires nploidy_cur <= nploidy
for (i = 0; i < nsamples; i++)
{
Expand Down Expand Up @@ -402,17 +402,17 @@ namespace vcfpp
template <typename T, typename S = typename T::value_type>
isFormatVector<T> getFORMAT(std::string tag, T& v)
{
fmt = bcf_get_fmt(header->hdr, line, tag.c_str());
fmt = bcf_get_fmt(header.hdr, line, tag.c_str());
nvalues = fmt->n;
ndst = 0;
S* dst = NULL;
int tag_id = bcf_hdr_id2int(header->hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_INT & 0xff))
ret = bcf_get_format_int32(header->hdr, line, tag.c_str(), &dst, &ndst);
else if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_REAL & 0xff))
ret = bcf_get_format_float(header->hdr, line, tag.c_str(), &dst, &ndst);
else if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_STR & 0xff))
ret = bcf_get_format_char(header->hdr, line, tag.c_str(), &dst, &ndst);
int tag_id = bcf_hdr_id2int(header.hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_INT & 0xff))
ret = bcf_get_format_int32(header.hdr, line, tag.c_str(), &dst, &ndst);
else if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_REAL & 0xff))
ret = bcf_get_format_float(header.hdr, line, tag.c_str(), &dst, &ndst);
else if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_STR & 0xff))
ret = bcf_get_format_char(header.hdr, line, tag.c_str(), &dst, &ndst);
if (ret >= 0)
{
// user have to check if there is missing in the return v;
Expand All @@ -433,14 +433,14 @@ namespace vcfpp
* */
bool getFORMAT(std::string tag, std::vector<std::string>& v)
{
fmt = bcf_get_fmt(header->hdr, line, tag.c_str());
fmt = bcf_get_fmt(header.hdr, line, tag.c_str());
nvalues = fmt->n;
// if ndst < (fmt->n+1)*nsmpl; then realloc is involved
ret = -1, ndst = 0;
char** dst = NULL;
int tag_id = bcf_hdr_id2int(header->hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_STR & 0xff))
ret = bcf_get_format_string(header->hdr, line, tag.c_str(), &dst, &ndst);
int tag_id = bcf_hdr_id2int(header.hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_STR & 0xff))
ret = bcf_get_format_string(header.hdr, line, tag.c_str(), &dst, &ndst);
if (ret > 0)
{
v.clear();
Expand All @@ -466,17 +466,17 @@ namespace vcfpp
template <typename T, typename S = typename T::value_type>
isInfoVector<T> getINFO(std::string tag, T& v)
{
info = bcf_get_info(header->hdr, line, tag.c_str());
info = bcf_get_info(header.hdr, line, tag.c_str());
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, tag.c_str(), &dst, &ndst);
ret = bcf_get_info_int32(header.hdr, line, tag.c_str(), &dst, &ndst);
}
else if (info->type == BCF_BT_FLOAT)
{
ret = bcf_get_info_float(header->hdr, line, tag.c_str(), &dst, &ndst);
ret = bcf_get_info_float(header.hdr, line, 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;
Expand All @@ -494,7 +494,7 @@ namespace vcfpp
template <typename T>
isScalar<T> getINFO(std::string tag, T& v)
{
info = bcf_get_info(header->hdr, line, tag.c_str());
info = bcf_get_info(header.hdr, line, tag.c_str());
// scalar value
if (info->len == 1)
{
Expand Down Expand Up @@ -523,7 +523,7 @@ namespace vcfpp
template <typename T>
isString<T> getINFO(std::string tag, T& v)
{
info = bcf_get_info(header->hdr, line, tag.c_str());
info = bcf_get_info(header.hdr, line, tag.c_str());
if (info->type == BCF_BT_CHAR)
v = std::string(reinterpret_cast<char*>(info->vptr), info->vptr_len);
else
Expand All @@ -541,14 +541,14 @@ namespace vcfpp
{
ret = -1;
// 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, tag.c_str(), &v, 1);
else if (bcf_hdr_id2type(header->hdr, BCF_HL_INFO, tag_id) == (BCF_HT_REAL & 0xff))
// 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, 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, tag.c_str(), &v2, 1);
ret = bcf_update_info_float(header.hdr, line, tag.c_str(), &v2, 1);
}
if (ret < 0)
{
Expand All @@ -570,14 +570,14 @@ namespace vcfpp
isValidInfo<T> setINFO(std::string tag, const T& v)
{
ret = -1;
// 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, 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, 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, tag.c_str(), v.data());
// 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, 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, 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, tag.c_str(), v.data());
if (ret < 0)
throw std::runtime_error("couldn't set " + tag + " for this variant.\nplease add the tag in header first.\n");
else
Expand All @@ -588,13 +588,13 @@ namespace vcfpp
void removeINFO(std::string tag)
{
ret = -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, 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, 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, tag.c_str(), NULL);
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, 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, 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, tag.c_str(), NULL);
if (ret < 0)
{
throw std::runtime_error("couldn't remove " + tag + " for this variant.\n");
Expand All @@ -611,7 +611,7 @@ namespace vcfpp
{
// bcf_gt_type
ndst = 0;
ret = bcf_get_genotypes(header->hdr, line, &gts, &ndst);
ret = bcf_get_genotypes(header.hdr, line, &gts, &ndst);
if (ret <= 0)
return false; // gt not present
assert(ret == v.size());
Expand All @@ -628,7 +628,7 @@ namespace vcfpp
gts[k] = bcf_gt_unphased(v[k]);
}
}
if (bcf_update_genotypes(header->hdr, line, gts, ret) < 0)
if (bcf_update_genotypes(header.hdr, line, gts, ret) < 0)
throw std::runtime_error("couldn't set genotypes correctly.\n");
else
return true;
Expand All @@ -654,13 +654,13 @@ namespace vcfpp
isValidFMT<T> setFORMAT(std::string tag, const T& v)
{
ret = -1;
int tag_id = bcf_hdr_id2int(header->hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_INT & 0xff))
ret = bcf_update_format_int32(header->hdr, line, tag.c_str(), v.data(), v.size());
else if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_STR & 0xff))
ret = bcf_update_format_char(header->hdr, line, tag.c_str(), v.data(), v.size());
else if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_REAL & 0xff))
ret = bcf_update_format_float(header->hdr, line, tag.c_str(), v.data(), v.size());
int tag_id = bcf_hdr_id2int(header.hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_INT & 0xff))
ret = bcf_update_format_int32(header.hdr, line, tag.c_str(), v.data(), v.size());
else if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_STR & 0xff))
ret = bcf_update_format_char(header.hdr, line, tag.c_str(), v.data(), v.size());
else if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_REAL & 0xff))
ret = bcf_update_format_float(header.hdr, line, tag.c_str(), v.data(), v.size());
if (ret < 0)
throw std::runtime_error("couldn't set format " + tag + " correctly.\n");
return true;
Expand All @@ -678,11 +678,11 @@ namespace vcfpp
{
ret = -1;
float v2 = v;
int tag_id = bcf_hdr_id2int(header->hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_INT & 0xff))
ret = bcf_update_format_int32(header->hdr, line, tag.c_str(), &v, 1);
else if (bcf_hdr_id2type(header->hdr, BCF_HL_FMT, tag_id) == (BCF_HT_REAL & 0xff))
ret = bcf_update_format_float(header->hdr, line, tag.c_str(), &v2, 1);
int tag_id = bcf_hdr_id2int(header.hdr, BCF_DT_ID, tag.c_str());
if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_INT & 0xff))
ret = bcf_update_format_int32(header.hdr, line, tag.c_str(), &v, 1);
else if (bcf_hdr_id2type(header.hdr, BCF_HL_FMT, tag_id) == (BCF_HT_REAL & 0xff))
ret = bcf_update_format_float(header.hdr, line, tag.c_str(), &v2, 1);
if (ret < 0)
throw std::runtime_error("couldn't set format " + tag + " correctly.\n");
return true;
Expand All @@ -694,20 +694,20 @@ namespace vcfpp
std::vector<char> str(vcfline.begin(), vcfline.end());
str.push_back('\0'); // don't forget string has no \0;
kstring_t s = {vcfline.length(), vcfline.length(), &str[0]}; // kstring
ret = vcf_parse(&s, header->hdr, line);
ret = vcf_parse(&s, header.hdr, line);
if (ret > 0)
throw std::runtime_error("error parsing: " + vcfline + "\n");
if (line->errcode == BCF_ERR_CTG_UNDEF)
{
std::string contig(bcf_hdr_id2name(header->hdr, line->rid));
hdr_d = bcf_hdr_dup(header->hdr);
header->hrec = bcf_hdr_id2hrec(hdr_d, BCF_DT_CTG, 0, line->rid);
if (header->hrec == NULL)
std::string contig(bcf_hdr_id2name(header.hdr, line->rid));
hdr_d = bcf_hdr_dup(header.hdr);
header.hrec = bcf_hdr_id2hrec(hdr_d, BCF_DT_CTG, 0, line->rid);
if (header.hrec == NULL)
throw std::runtime_error("contig" + contig + " unknow and not found in the header.\n");
ret = bcf_hdr_add_hrec(header->hdr, header->hrec);
ret = bcf_hdr_add_hrec(header.hdr, header.hrec);
if (ret < 0)
throw std::runtime_error("error adding contig " + contig + " to header.\n");
ret = bcf_hdr_sync(header->hdr);
ret = bcf_hdr_sync(header.hdr);
}
}

Expand All @@ -720,7 +720,7 @@ namespace vcfpp
/** @brief return boolean value indicates if current variant is Structual Variant or not */
inline bool isSV() const
{
if (bcf_get_info(header->hdr, line, "SVTYPE") == NULL)
if (bcf_get_info(header.hdr, line, "SVTYPE") == NULL)
return false;
else
return true;
Expand Down Expand Up @@ -793,7 +793,7 @@ namespace vcfpp
/** @brief return CHROM name */
inline std::string CHROM() const
{
return std::string(bcf_hdr_id2name(header->hdr, line->rid));
return std::string(bcf_hdr_id2name(header.hdr, line->rid));
}

/** @brief return ID field */
Expand Down Expand Up @@ -862,14 +862,14 @@ namespace vcfpp
}
else if (line->d.n_flt == 1)
{
return std::string(bcf_hdr_int2id(header->hdr, BCF_DT_ID, line->d.flt[0]));
return std::string(bcf_hdr_int2id(header.hdr, BCF_DT_ID, line->d.flt[0]));
}
else
{
std::string s;
for (int i = 1; i < line->d.n_flt; i++)
{
s += std::string(bcf_hdr_int2id(header->hdr, BCF_DT_ID, line->d.flt[i])) + ",";
s += std::string(bcf_hdr_int2id(header.hdr, BCF_DT_ID, line->d.flt[i])) + ",";
}
s.pop_back();
return s;
Expand Down Expand Up @@ -916,7 +916,7 @@ namespace vcfpp
int nvalues = 0;

private:
std::shared_ptr<BcfHeader> header;
BcfHeader header;
bcf1_t* line = bcf_init(); // current bcf record
bcf_hdr_t* hdr_d; // a dup header by bcf_hdr_dup(header->hdr)
bcf_fmt_t* fmt = NULL;
Expand Down Expand Up @@ -985,6 +985,12 @@ namespace vcfpp
SamplesName = header.getSamples();
}

/// return a BcfHeader object
const BcfHeader& getHeader() const
{
return header;
}

/// open a VCF/BCF/STDIN file for streaming in
void Open(const std::string& file)
{
Expand Down Expand Up @@ -1070,15 +1076,15 @@ namespace vcfpp
int slen = tbx_itr_next(fp, tidx, itr, &s);
if (slen > 0)
{
ret = vcf_parse(&s, r.header->hdr, r.line); // ret > 0, error
ret = vcf_parse(&s, r.header.hdr, r.line); // ret > 0, error
bcf_unpack(r.line, BCF_UN_ALL);
}
return (ret <= 0) && (slen > 0);
}
}
else
{
ret = bcf_read(fp, r.header->hdr, r.line);
ret = bcf_read(fp, r.header.hdr, r.line);
// unpack record immediately. not lazy
bcf_unpack(r.line, BCF_UN_ALL);
return (ret == 0);
Expand Down Expand Up @@ -1235,7 +1241,7 @@ namespace vcfpp
{
if (!isHeaderWritten)
writeHeader();
if (bcf_write(fp, v.header->hdr, v.line) < 0)
if (bcf_write(fp, v.header.hdr, v.line) < 0)
return false;
else
return true;
Expand Down

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