* \return number of threads in th pool + 1. This is because the thread calling execute() * is counted as a worker. */

* Get / initialize the logger * @param name name of the logger * @return the spdlog logger */

Number of values in array or object

check if alignment is better than any of the top recorded alignments

const char* Value::CZString::c_str() const { return cstr_; }

* @brief Debug dump, optional */

* Add observation for RefVar allele from a read. * * @param rv the allele * @param is_rev true if observation is on reverse strand * @param left_b

* Helper to aggregate reference variants base by base * * Refpos must be > vars.back().end * */

* Error if given file doesn't exist * @param path_str */

* add read and update length estimate * @param coordinates coordinates and graph for length calculation * @param read read information */

* @brief Get a cigar string */

* Initialize graph from JSON * @param in Input JSON node * @param reference reference fasta name * @param out Output graph to initialize */

* @brief set query sequence */

* @brief set target sequence */

* Write a Json::Value object to string * indent = false also suppresses line breaks */

* Set the graph we genotype on * @param graph our graph to genotype */

* @brief Split a string along separators */

output allele name instead of indexes

* @brief Debug dump, optional */

* @brief Get the alignment score */

* Get variants * * @return consolidated list of variants + depths */