* Initialize the query data structure * * @param size Number of bytes used to store a score; valid valures are 1 or 2 * @param qlen Length of t

* Load manifest file. A manifest contains * * * Sample names * * Sample BAM/CRAM file locations * * Depth estimates, or location of idxdepth ou

* \param matches will be incremented by the number of matches found * \return CIGAR with mismatches clipped on left if first is set * or on

Create graph dictionary from event description :param reference: filename for reference fasta :param event: event description

* Make RefVar */

* Get the raw variance after a distribution has been fit * @return double */

* Get the raw variance after a distribution has been fit * @return double */

* Lower-level read extraction interface * @param max_reads maximum number of reads to load * @param reader Reader that will provide the reads * @pa

* relabel genotypes */

* Getter / setter for the alignment data */

* \brief skip n kmers * * \param n number of would be generated kmers to skip including those containing INVALID_OLIGO */

* Get the support after a distribution has been fit * @return vector of doubles */

* Convert a list of RefVar records to allele strings */

Get nodes and edges in topological sort order :return: sorted_nodes, sorted_edges

* Add a alignment, depth and summary statistics for a sample */

* add mapping stats of a read to an allele: adds reads + counts if mapping contains a path from source to sink; * bases before source and sink are ad

* Add edge counts from paragraph output * @param paragraph_json JSON output from alignAndDisambiguate */

Add mapping stats for a node. will count the read as forward / reverse and * add all types of bases as mapped to the node */

Add one vcfRecord to the graph :param vcf: VCF record :param allele_graph: Use all alleles (from individual VCF entries), rather than

Add variants to one node in the graph

* Append 1 char to RefVar. * * Return false if this is not possible because the variants are incompatible */

Convert VCF file to list of JSON graphs This function converts each record separately (as opposed to all records jointly like convert_vcf) :p

Create a VCFGraph object from a VCF input file :param ref_file_name: Reference Fasta name :param vcf_file_name: VCF file name

* Lower-level read extraction interface for specified target region * @return <num_original_extracted, num_recovered_mates> when finish * @param out

Change ',' to '.' everywhere in buffer. * * We had a sophisticated way, but it did not work in WinCE. * @see https://github.com/open-source-parsers

* Get the canonical allele name for an allele * @param alleleName name of allele on the graph * @return the corresponding canonical allele n

shortcut to get chromosome name */

* @return all contig names */