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reduce exception throwing
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@Zilong-Li
Zilong-Li committed Jun 28, 2024
1 parent f2d9726 commit f2b4429
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Showing 2 changed files with 44 additions and 32 deletions.
3 changes: 3 additions & 0 deletions .github/workflows/mac.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -23,5 +23,8 @@ jobs:
- name: test
run: |
cd test
export LIBRARY_PATH="${LIBRARY_PATH}:$(brew --prefix)/lib"
export C_INCLUDE_PATH="${C_INCLUDE_PATH}:$(brew --prefix)/include"
export CPPFLAGS="-I"$(brew --prefix)/include
make
make test
73 changes: 41 additions & 32 deletions vcfpp.h
View file
Original file line number Diff line number Diff line change
Expand Up @@ -79,7 +79,7 @@ using isScalar = typename std::enable_if<std::is_same<T, int>::value || std::is_
bool>::type;

template<typename T>
using isString = typename std::enable_if<std::is_same<T, std::string>::value, void>::type;
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
Expand Down Expand Up @@ -559,8 +559,8 @@ class BcfRecord
* @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 handl all kinds of genotypes in multi-ploidy data with
* the cost of more spae than the other function. missing allele is set as -9.
* @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)
{
Expand Down Expand Up @@ -624,8 +624,7 @@ class BcfRecord
fmt = bcf_get_fmt(header->hdr, line.get(), tag.c_str());
if(!fmt)
{
std::cerr << "no " + tag + " presents in FORMAT for current site\n";
return false;
throw std::invalid_argument("no FORMAT=" + tag + " in the VCF header.\n");
}
nvalues = fmt->n;
ndst = 0;
Expand Down Expand Up @@ -658,7 +657,7 @@ class BcfRecord
else
{
free(dst);
throw std::runtime_error("can not find the type of " + tag + " in the header file.\n");
return false;
}
}

Expand All @@ -673,8 +672,7 @@ class BcfRecord
fmt = bcf_get_fmt(header->hdr, line.get(), tag.c_str());
if(!fmt)
{
std::cerr << "no " + tag + " presents in FORMAT for current site\n";
return false;
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
Expand All @@ -698,7 +696,7 @@ class BcfRecord
{
free(dst[0]);
free(dst);
throw std::runtime_error("couldn't parse the " + tag + " FORMAT of this variant.\n");
return false;
}
}

Expand All @@ -714,8 +712,7 @@ class BcfRecord
info = bcf_get_info(header->hdr, line.get(), tag.c_str());
if(!info)
{
std::cerr << "no " + tag + " presents in INFO for current site\n";
return false;
throw std::invalid_argument("no INFO=" + tag + " in the VCF header.\n");
}
S * dst = NULL;
ndst = 0;
Expand All @@ -737,7 +734,7 @@ class BcfRecord
else
{
free(dst);
throw std::runtime_error("couldn't parse the " + tag + " format of this variant.\n");
return false;
}
}

Expand All @@ -753,8 +750,7 @@ class BcfRecord
info = bcf_get_info(header->hdr, line.get(), tag.c_str());
if(!info)
{
std::cerr << "no " + tag + " presents in INFO for current site\n";
return false;
throw std::invalid_argument("no INFO=" + tag + " in the VCF header.\n");
}
// scalar value
if(info->len == 1)
Expand All @@ -771,8 +767,8 @@ class BcfRecord
}
else
{
std::cerr << "there are multiple values for " + tag + " in INFO for current site\n"
<< "please feed a vector instead\n";
std::cerr << "there are multiple values for " + tag
+ " in INFO for current site. please use vector instead\n";
return false;
}
}
Expand All @@ -789,18 +785,17 @@ class BcfRecord
info = bcf_get_info(header->hdr, line.get(), tag.c_str());
if(!info)
{
std::cerr << "no " + tag + " presents in INFO for current site\n";
return false;
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
{
throw std::runtime_error(tag + " has to be of string type\n");
return false;
}
return true;
}

/**
Expand All @@ -812,7 +807,6 @@ class BcfRecord
template<typename T>
isScalar<T> setINFO(std::string tag, const T & v)
{
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());
Expand All @@ -825,9 +819,13 @@ class BcfRecord
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)
{
std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in header first.\n";
std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
return false;
}
return true;
Expand All @@ -837,12 +835,11 @@ class BcfRecord
* @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 boolean
* @return bool
* */
template<typename T>
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))
Expand All @@ -857,10 +854,14 @@ class BcfRecord
{
ret = bcf_update_info_string(header->hdr, line.get(), tag.c_str(), v.data());
}
else
{
ret = -1;
}

if(ret < 0)
{
std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in header first.\n";
std::cerr << "couldn't set " + tag + " for this variant.\nplease add the tag in headerfirst.\n";
return false;
}
return true;
Expand All @@ -869,7 +870,6 @@ class BcfRecord
/// remove the given tag from INFO of the variant
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))
{
Expand All @@ -883,6 +883,10 @@ class BcfRecord
{
ret = bcf_update_info_string(header->hdr, line.get(), tag.c_str(), NULL);
}
else
{
ret = -1;
}

if(ret < 0)
{
Expand Down Expand Up @@ -970,7 +974,6 @@ class BcfRecord
template<typename T>
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))
{
Expand All @@ -984,10 +987,14 @@ class BcfRecord
{
ret = bcf_update_format_float(header->hdr, line.get(), tag.c_str(), v.data(), v.size());
}
else
{
ret = -1;
}

if(ret < 0)
{
std::cerr << "couldn't set format " + tag + " correctly.\n";
std::cerr << "couldn't set format " + tag + " corectly.\n";
return false;
}
return true;
Expand All @@ -998,12 +1005,11 @@ class BcfRecord
* one sample in the vcf
* @param tag valid tag name in FORMAT column declared in the VCF header
* @param v valid input include int, float or double
* @return bool
* @return void
* */
template<typename T>
isScalar<T> setFORMAT(std::string tag, const T & v)
{
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))
Expand All @@ -1014,10 +1020,13 @@ class BcfRecord
{
ret = bcf_update_format_float(header->hdr, line.get(), tag.c_str(), &v2, 1);
}

else
{
ret = -1;
}
if(ret < 0)
{
std::cerr << "couldn't set format " + tag + " correctly.\n";
std::cerr << "couldn't set format " + tag + " corectly.\n";
return false;
}
return true;
Expand Down

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