int SNPBamProcessor::get_haplotype(BamTools::BamAlignment& aln){
if (!aln.HasTag(HAPLOTYPE_TAG))
return -1;
uint8_t haplotype;
if (!aln.GetTag(HAPLOTYPE_TAG, haplotype)){
char type;
aln.GetTagType(HAPLOTYPE_TAG, type);
printErrorAndDie("Failed to extract haplotype tag");
}
assert(haplotype == 1 || haplotype == 2);
return (int)haplotype;
}
std::string get_library(BamTools::BamAlignment& aln, std::map<std::string, std::string>& rg_to_library){
std::string rg;
std::string rg_tag = "RG";
char tag_type = 'Z';
if (!aln.GetTagType(rg_tag, tag_type))
printErrorAndDie("Failed to retrieve BAM alignment's RG tag");
aln.GetTag("RG", rg);
auto iter = rg_to_library.find(rg);
if (iter == rg_to_library.end())
printErrorAndDie("No library found for read group " + rg + " in BAM file headers");
return iter->second;
}
bool ReadContainer::GetIntBamTag(const BamTools::BamAlignment& aln,
const std::string& tag_name, int* destination) {
char tag_type;
if (!aln.GetTagType(tag_name, tag_type)) {return false;}
switch (tag_type) {
case (BamTools::Constants::BAM_TAG_TYPE_INT32):
return aln.GetTag(tag_name, *destination);
case (BamTools::Constants::BAM_TAG_TYPE_INT8):
int8_t d8;
if (!aln.GetTag(tag_name, d8)) {
return false;
}
*destination = static_cast<int>(d8);
return true;
case (BamTools::Constants::BAM_TAG_TYPE_UINT8):
uint8_t ud8;
if (!aln.GetTag(tag_name, ud8)) {
return false;
}
*destination = static_cast<int>(ud8);
return true;
case (BamTools::Constants::BAM_TAG_TYPE_INT16):
int16_t d16;
if (!aln.GetTag(tag_name, d16)) {
return false;
}
*destination = static_cast<int>(d16);
return true;
case (BamTools::Constants::BAM_TAG_TYPE_UINT16):
uint16_t ud16;
if (!aln.GetTag(tag_name, ud16)) {
return false;
}
*destination = static_cast<int>(ud16);
return true;
case (BamTools::Constants::BAM_TAG_TYPE_UINT32):
uint32_t ud32;
if (!aln.GetTag(tag_name, ud32)) {
return false;
}
*destination = static_cast<int>(ud32);
return true;
default:
stringstream msg;
msg << "Encountered unsupported tag type " << tag_type;
PrintMessageDieOnError(msg.str(), ERROR);
}
return false;
}
bool getTagParanoid(BamTools::BamAlignment &alignment, const std::string &tag, int64_t &value) {
char tagType = ' ';
if(alignment.GetTagType(tag, tagType)) {
switch(tagType) {
case BamTools::Constants::BAM_TAG_TYPE_INT8: {
int8_t value_int8 = 0;
alignment.GetTag(tag, value_int8);
value = value_int8;
} break;
case BamTools::Constants::BAM_TAG_TYPE_UINT8: {
uint8_t value_uint8 = 0;
alignment.GetTag(tag, value_uint8);
value = value_uint8;
} break;
case BamTools::Constants::BAM_TAG_TYPE_INT16: {
int16_t value_int16 = 0;
alignment.GetTag(tag, value_int16);
value = value_int16;
} break;
case BamTools::Constants::BAM_TAG_TYPE_UINT16: {
uint16_t value_uint16 = 0;
alignment.GetTag(tag, value_uint16);
value = value_uint16;
} break;
case BamTools::Constants::BAM_TAG_TYPE_INT32: {
int32_t value_int32 = 0;
alignment.GetTag(tag, value_int32);
value = value_int32;
} break;
case BamTools::Constants::BAM_TAG_TYPE_UINT32: {
uint32_t value_uint32 = 0;
alignment.GetTag(tag, value_uint32);
value = value_uint32;
} break;
default: {
alignment.GetTag(tag, value);
} break;
}
return(true);
} else {
return(false);
}
}
