! \internal Default constructor initialization must be equivalent to: * memset( this, 0, sizeof(Value) ) * This optimization is used in ValueInterna

Summarize graph contents

Parse remote breakend info from BND VCF record :param record: VCF record :param alt: Alt allele from VCF record (BND) :return

* Add a read to the pileup * @param readinfo Read info object */

return number of reference padding bases */

* @brief adds an ALT=<*> variant to bcf record * * @param rec a points to a bcf1_t * @param hdr the respective header for rec * */

Add simple breakend allele to the graph :param pos: Base of breakend :param ref_seq: Sequence of ref allele :param end: Coord

Add all nodes, edges and paths from graph2 to graph1 (inplace)

Add 'REF' haplotype to all REF edges. Create paths covering all 'REF' edges

add source and sink if necessary and link to exising nodes without in/out edges :param graph: graph to work on :param source_name: name o

Add variants to a graph as new nodes and edges :param graph: The graph object to modify :param variants: 'variants' entry from the paragr

* Align a read to the graph and update the graph_* fields. * * We will align both the forward and the reverse strand and return * the alignment whi

Assumes that DP matrix has been filled out. */

get the best possible score for comparing two sequences of length len */

push/pop_heap will result in the element with worst score evicted.

Combine adjacent nodes with the same sequence labels

* Compare bcf records by position * @param hdr bcf header * @param a first bcf record * @param b second bcf record * @return true if a < b else fa

* 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.

* Return the first position that is not an N character */

* return the size of a contig. Sum of all contig sizes if contig == 0 * @param contig name of contig, or empty * @return number of bases in

count the number of samples in manifest with missing depth or read length