when things go wrong, this gets thrown */

Helper class to write tracebacks to log file

* Alignment statistics for ONE graph element: can be node, edge or allele */

Holds a sequence graph in dict format

* Class to collect single-breakpoint statistics / edge counts * * Future versions may incorporate additional alignment information (mapping qualitie

features.h

* Wrapper for a combination of KmerAligner and GraphAligner */

writer.h

record and modification of one manifest record

exact copy of Features

* Pileup information for a single base */

reader.h

Class to construct a more graph-like representation from VCFs. Each sample specifies one haplotype (if used) Intermediate step used to cr

* A variant candidate list collects variant candidates relative * to a reference sequence. * * It also resolves these candidates into a canonical s

* @brief Sequence alignment class interface */

Alignment result storage */

* @brief BAM reader class * * Extracts alignments from BAM/CRAM file contained in a specified region. * Example: * reader.init("crams/LP6008113-

* structure for passing parameter into breakpoint genotyper */

Scoped enums are not available until C++11.

* Interface class for estimating depth */

writer.h

features.h

* Container for genotypes in multiple samples */

* Wrapper for GSSW graph alignment code */

* Graph genotyper interface and basic functionality */