* from JE Wigginton 2005 AJHG */

* Return the alignment path(s) for each aligned fragment * Merges overlapping mates * @param graph The graph * @param reads Aligned reads * @retur

* @return set of genotypes for all alignments that were added */

* @brief Retrieve an info field as an integer * * @param result the default to return if the field is not present */

extract chrom / pos / length */

* Extract on-graph variants * @param coordinates graph coordinates and graph information * @param reads list of reads * @param output output JSON

Create the paragraph representation of nodes and edges for this graph :param alleleGraph: create edges between any compatible allele pair (ra

* Get support count from support fraction * @param nums a vector of doubles * @param support_frac the support fraction to fit the MCD * @return an

Genome regions covered by reference nodes

Returns a 3-dimensional matrix of quality-adjusted scores indexed by (qual score) x (ref base) x (query base). */

Assumes that offset has already been removed from read_qual */

for reuse of graph through multiple alignments

Generate query profile rearrange query sequence & calculate the weight of match/mismatch. */

Initiailize a profile with quality adjusted scores. Automatically selects score_size = 1 since adjusted scores should * be maximized to increase sens

Returns a 3-dimensional matrix of quality-adjusted scores indexed by (qual score) x (ref base) x (query base) * that have been scaled up to (at most)

Simple (slow) algorithm for finding greatest common factor of the scores, not performance critical. */

* Check if variant is a single-allelic MNP ie. can be trivially decomposed */

* \brief defines match for the purpose of the alignment. */

check if a variant is a SNP */

STR shifting: left / rightmost positions

load graph description from either vcf or json

* @brief Format int encoded Cigar string * * @param qb for padding with "S" : begin * @param qe for padding with "S" : end * @param altlen for pad

:return: an argument parser

:return: one argument parser

:return: an argument parser

:return: an argument parser