* \brief remembers the original argv array and hands over to the base implementation */

Returns a string with all nodeIDs in a path

* \return best path id * \precondition non-empty candidates list */

* A simple debugging function for printing a RefVar */

Read grmpy output :param grmpyJsonName: input filename :return: grmpy output

Remove nodes without sequence (from deletions / skipped insertions or split ref nodes) Merge in & out edge pairs to keep connections

Remove edge sequence labels that don't add information about haplotypes.

* @brief Replace all instances of find with replace in str */

* \brief clears and repopulates ThreadPool. Use at your own risk. The only reasonable situation you'd might * want to do this is in the se

Wrapper function to run paragraph :param event_and_args: tuple of event to validate and args structure :return:

run vcf2paragraph for one single variant

* \brief executes and stores the exception information so that it can be rethrown on the main thread */

static

update format with single float values. */

update format string for a single sample. */

* Set the genotype for a particular sample * * @param samplename sample name * @param breakpointname name of breakpoint ("" for combined GT) * @pa

* Function to set parameter values in derived classes * @param parameters set of parameters */

* @return The number of samples we have genotypes for */

* \brief skip n kmers on the last generator used. * * \param n number of would be generated kmers to skip including those containing INVALID

* \brief skip n kmers on the last generator used. * * \param n number of would be generated kmers to skip including those containing INVALID

Split long alternate nodes :param graph: graph to work on :param max_len: max length of reference node with no sequences :param paddi

Split long reference nodes :param graph: graph to work on :param max_len: max length of reference node with no sequences :param paddi

* @brief produces a string represent the variant (for printing etc) * * @param rec a points to a bcf1_t * @param hdr the respective header for rec