void InputStructures::BringUpReferenceData(ExtendParameters ¶meters){
DEBUG = parameters.program_flow.DEBUG;
min_map_qv = parameters.MQL0;
cout << "Loading reference." << endl;
read_fasta(parameters.fasta, reference_contigs);
cout << "Loaded reference. Ref length: " << reference_contigs.size() << endl;
bam_initialize(parameters.bams);
if (parameters.sseMotifsProvided) {
cout << "Loading systematic error contexts." << endl;
read_error_motifs(parameters.sseMotifsFileName);
cout << "Loaded." << endl;
}
}
void InputStructures::BringUpReferenceData(ExtendParameters ¶meters) {
DEBUG = parameters.program_flow.DEBUG;
min_map_qv = parameters.MQL0;
use_SSE_basecaller = parameters.program_flow.use_SSE_basecaller;
do_snp_realignment = parameters.program_flow.do_snp_realignment;
cout << "Loading reference." << endl;
read_fasta(parameters.fasta, reference_contigs);
cout << "Loaded reference. Ref length: " << reference_contigs.size() << endl;
// some recalibration information may be read from bam file header
bam_initialize(parameters.bams);
if (parameters.sseMotifsProvided) {
cout << "Loading systematic error contexts." << endl;
read_error_motifs(parameters.sseMotifsFileName);
cout << "Loaded." << endl;
}
// Load homopolymer recalibration model
// why is recal model using the command line directly? <-- Because the basecaller module is programmed that way.
// initialize only if there's a model file
if (parameters.recal_model_file_name.length()>0){
do_recal.recalModel.Initialize(parameters.opts);
do_recal.use_recal_model_only = true;
do_recal.is_live = true;
}
// finally turn off recalibration if not wanted
// even although we have a nice set of recalibration read-in.
if (parameters.program_flow.suppress_recalibration) {
printf("Recalibration model: suppressed\n");
do_recal.recalModel.suppressEnabled();
do_recal.is_live = false;
}
}
