* Set the minimum allowable support fraction for a vector of doubles * @param nums a vector of doubles */

shared-pointerize */

Get pairwise variant calls for aligned REF and ALT sequences

Split VCF into parts Store header and records separately :param vcf_path: path to VCF file :param read_length: length of reads = min

Creates a path family with all edges from all paths

* getters for genotypers */

* Reset the raw support fraction * @param raw support_frac double between 0.5 and 1 */

* Getters / setters for BAM statistics */

Read a MSA FASTA file :return: dictionary with sequences :rtype: OrderedDict

* Extract fragments from reads * @param coordinates graph coordinates structure for length calculation * @param reads read buffer * @param output_l

:run the wrapper

Run wrapper for testing

:run the wrapper

set vcf record for the given sample

Split a node at a set of breakpoints and link new (sub-)nodes Used to link to new variant nodes later Modifies graph and deletes node aft

* Get the standard deviation of the fitted distribution * @return double */

* add summary statistics on graph alignments into JSON output */

qual-weighted allele depths for alt

* \brief Constructs a vector of size threads. All memory allocations that are required happen * at this point. * * @param size

* @param genotype_parameters GenotypeParameter class */

* Create breakpoint statistics on graph * @param wgraph graph information * @param node_name name of node * @param forward true to use successor no