Check if variant is an indel or complex event */

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

return number of reference padding bases */

* @brief returns true if rv is representing the reference * * TODO change signature to move chr before rv * * @param ref refererence sequence fast

* @brief List functions making sure variants aren't pushed past each other. * * variants in the input list must be sorted by starting position * *

push/pop_heap will result in the element with largest number of mismatches evicted.

Construct graph object from JSON representation :param json: Dictionary of JSON file contents

load manifest from file. One line for one record

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

Make a small deletion graph :param chrom: chromosome name :param start: start coordinate (first deleted base) :param end: end coordin

Make a long deletion graph :param chrom: chromosome name :param start: start coordinate (first deleted base) :param end: end coordina

Make a small deletion graph :param chrom: chromosome name :param start: start coordinate (first deleted base) :param end: end coordin

Make a small deletion graph :param chrom: chromosome name :param start: start coordinate (last base before insertion) :param ins: ins

Make a long deletion graph :param chrom: chromosome name :param start: start coordinate (first deleted base) :param end: end coordina

* @return iterator to the lowest allele non-zero minor allele count */

* @return True if need to use Fisher's exact test for HWE P * For multi-alleles, always use chisq * For bi-allelic: * if * N<=30, or

* simple getters */

* Returns true if query is a substring of str. */

return true when successful */

* @brief Extract GT from Format field * */