bool ExtendedReadInfo::UnpackThisRead(InputStructures &global_context, const string &local_contig_sequence, int DEBUG) {
//is_happy_read = CheckHappyRead(global_context, variant_start_pos, int DEBUG);
is_happy_read = true;
// start working to unpack the read data we need
start_flow = 0;
start_pos = alignment.Position;
is_forward_strand = !alignment.IsReverseStrand();
GetUsefulTags(DEBUG);
if (is_happy_read) {
CreateFlowIndex(global_context.flowOrder);
UnpackAlignmentInfo(local_contig_sequence, alignment.Position);
}
return(is_happy_read); // happy to have unpacked this read
}
void UnpackOnLoad(Alignment *rai, const InputStructures &global_context)
{
// No need to waste time if the read is filtered
if (rai->filtered)
return;
rai->is_reverse_strand = rai->alignment.IsReverseStrand();
// Parse read name, run id & flow order index
rai->runid.clear();
if (not rai->alignment.Name.empty()) {
rai->well_rowcol.resize(2);
ion_readname_to_rowcol(rai->alignment.Name.c_str(), &rai->well_rowcol[0], &rai->well_rowcol[1]);
// extract runid while we are at it
rai->runid = rai->alignment.Name.substr(0,rai->alignment.Name.find(":"));
}
if (rai->runid.empty()){
cerr << "WARNING: Unable to determine run id of read " << rai->alignment.Name << endl;
rai->filtered = true;
return;
}
std::map<string,int>::const_iterator fo_it = global_context.flow_order_index_by_run_id.find(rai->runid);
if (fo_it == global_context.flow_order_index_by_run_id.end()){
cerr << "WARNING: No matching flow oder found for read " << rai->alignment.Name << endl;
rai->filtered = true;
return;
}
rai->flow_order_index = fo_it->second;
const ion::FlowOrder & flow_order = global_context.flow_order_vector.at(rai->flow_order_index);
// Retrieve measurements from ZM tag
vector<int16_t> quantized_measurements;
if (not rai->alignment.GetTag("ZM", quantized_measurements)) {
cerr << "ERROR: Normalized measurements ZM:tag is not present in read " << rai->alignment.Name << endl;
exit(1);
}
if ((int)quantized_measurements.size() > global_context.num_flows_by_run_id.at(rai->runid)) {
cerr << "ERROR: Normalized measurements ZM:tag length " << quantized_measurements.size()
<< " exceeds flow order length " << global_context.num_flows_by_run_id.at(rai->runid)
<<" in read " << rai->alignment.Name << endl;
exit(1);
}
rai->measurements.assign(global_context.num_flows_by_run_id.at(rai->runid), 0.0);
for (size_t counter = 0; counter < quantized_measurements.size(); ++counter)
rai->measurements[counter] = (float)quantized_measurements[counter]/256;
rai->measurements_length = quantized_measurements.size();
// Retrieve phasing parameters from ZP tag
if (not rai->alignment.GetTag("ZP", rai->phase_params)) {
cerr << "ERROR: Phasing Parameters ZP:tag is not present in read " << rai->alignment.Name << endl;
exit(1);
}
if (rai->phase_params.size() != 3) {
cerr << "ERROR: Phasing Parameters ZP:tag does not have 3 phase parameters in read " << rai->alignment.Name << endl;
exit(1);
}
if (rai->phase_params[0] < 0 or rai->phase_params[0] > 1 or rai->phase_params[1] < 0 or rai->phase_params[1] > 1
or rai->phase_params[2] < 0 or rai->phase_params[2] > 1) {
cerr << "ERROR: Phasing Parameters ZP:tag outside of [0,1] range in read " << rai->alignment.Name << endl;
exit(1);
}
rai->phase_params[2] = 0.0f; // ad-hoc corrector: zero droop
// Populate read_bases (bases without rev-comp on reverse-mapped reads) and flow_index
rai->read_bases = rai->alignment.QueryBases;
if (rai->is_reverse_strand)
RevComplementInPlace(rai->read_bases);
if (rai->read_bases.empty()){
cerr << "WARNING: Ignoring length zero read " << rai->alignment.Name << endl;
rai->filtered = true;
return;
}
// Unpack alignment
rai->pretty_aln.reserve(global_context.num_flows_by_run_id.at(rai->runid));
UnpackAlignmentInfo(rai);
if (rai->is_reverse_strand)
rai->start_sc = rai->right_sc;
else
rai->start_sc = rai->left_sc;
// Generate flow index
rai->start_flow = 0;
if (not rai->alignment.GetTag("ZF", rai->start_flow)) {
uint8_t start_flow_byte = 0;
if (not rai->alignment.GetTag("ZF", start_flow_byte)) {
cerr << "ERROR: Start Flow ZF:tag not found in read " << rai->alignment.Name << endl;
exit(1);
}
rai->start_flow = (int)start_flow_byte;
}
if (rai->start_flow == 0) {
cerr << "WARNING: Start Flow ZF:tag has zero value in read " << rai->alignment.Name << endl;
rai->filtered = true;
return;
}
CreateFlowIndex(rai, flow_order);
if (global_context.resolve_clipped_bases) {
// Increment start flow to first aligned base
rai->start_flow = rai->flow_index[rai->start_sc];
}
// Check validity of input arguments
if (rai->start_flow < 0 or rai->start_flow >= global_context.num_flows_by_run_id.at(rai->runid)) {
cerr << "ERROR: Start flow outside of [0,num_flows) range in read " << rai->alignment.Name << endl;
cerr << "Start flow: " << rai->start_flow << " Number of flows: " << global_context.flow_order_vector.at(rai->flow_order_index).num_flows();
exit(1);
}
// Retrieve read group name & generate prefix flow
if (not rai->alignment.GetTag("RG",rai->read_group)) {
cerr << "WARNING: No read group found in read " << rai->alignment.Name << endl;
// No big problem, we'll just have to solve the prefix like it's 2013!
rai->read_group.clear();
}
// Get read prefix - hard clipped start of the read: [KS][ZT][ZE]
rai->prefix_flow = -1;
std::map<string,string>::const_iterator key_it = global_context.key_by_read_group.find(rai->read_group);
if (key_it != global_context.key_by_read_group.end()) {
rai->prefix_bases = key_it->second;
string temp_zt, temp_ze;
if (rai->alignment.GetTag("ZT", temp_zt))
rai->prefix_bases += temp_zt;
if (rai->alignment.GetTag("ZE", temp_ze))
rai->prefix_bases += temp_ze;
if (not rai->prefix_bases.empty())
GetPrefixFlow(rai, rai->prefix_bases, flow_order);
}
// Check consistency of prefix_flow and start_flow - maybe we don't have all info about hard clipped bases
if (rai->prefix_flow >= 0) {
int check_start_flow = rai->prefix_flow;
while (check_start_flow < flow_order.num_flows() and flow_order.nuc_at(check_start_flow) != rai->read_bases.at(0))
check_start_flow++;
if (check_start_flow != rai->start_flow) {
rai->prefix_flow = -1;
rai->prefix_bases.clear();
}
}
}
