Converts an unsigned integer to string. * @param value Unsigned integer to convert to string * @param current Input/Output string buffer. *

* Get the variance of the fitted distribution * @return double */

* add an observation * @param is_rev true if obs is on reverse strand */

* Low-level read extraction for mapped reads in target region * @param read_pairs Container for extracted reads * @param reader Reader that will pro

* Clear out reads that end before pos */

:return All haplotype IDs (i.e. vcf sample names) present in graph

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

* @brief Decompose a RefVar into primitive variants (subst / ins / del) * * @param rv the RefVar record * @param vars the primitive records */

* Take apart CIGAR string and collect variant candidates * @param read read after alignment * @param target vector of candidate lists */

qual-weighted allele depths for others

qual-weighted allele depths for reference

Adds reference sequence information to reference nodes

* Run single sample alignment * @param sample sample data structure */

apply and retrieve modified reference sequence between start and end * Note that _start and _end will be extended if they aren't contained withi

Converts a unicode code-point to UTF-8.

* return the non-N padded size of a contig. This is calculated * as the size of the contig minus any N's at the beginning or * at the end. * * Ret

Convert a single VCF file to a graph dictionary :param vcf: file name of the VCF file :param ref: reference FASTA file name :param ta

* main function for alignment and genotyping * * @param graphPath If empty the alignment data of the first sample is used as graph *

* Create a map of all breakpoints in a graph * @param wgraph the graph * @return a breakpoint map for the graph */

* Decode BAM alignment from HTSLib struct. * * @param hts_align_ptr a bam1_t * to initialize from. * Passed as void* to avoid dependency on htslib

Duplicates the specified string value. * @param value Pointer to the string to duplicate. Must be zero-terminated if * length is "unkno

Sorted vector with all edges in the path family

* Estimate index and filtered read depth from a BAM / CRAM file * @param parameters parameters object * @return depth information structure */

* Helper function that extracts cigar strings from * gssw_graph_mapping structs; largely copied from GSSW.c and * modified to print cigar st

Generate a variant ID for a pySAM VCF record :param record: a pysam record :param varIdCounts: defaultdict dictionary of coun

get stats from a cigar string */

* Get the alignment read counts * @param sample_index index of sample (name is in sampleNames[sample_index]) * @param edge_or_allele_name name of ed

* Get index bins * @param bam BAM / CRAM file * @param output output vector for bins */

* \return upercase base. Note that this one will not return N for bcl 0! */

Return paths (list of nodes) covering all edges for one sequence (haplotype) :param graph: graph to work on :param sequence: Haplotype to

Split reference intervals into non-overlapping pieces, preserving haplotypes :return List of reference intervals (sorted by start/stop)

TODO: why is score_matrix even an argument here?

Numerical routine to compute the base of the logarithm that translates alignment scores to log-odds */

Rounds a double to nearest int8_t. */

Striped Smith-Waterman Record the highest score of each reference position. Return the alignment score and ending position of the best alignment

Dictionary with graph in paragraph json representation