gobwa

type Arena struct {
	Pointers []uintptr
}

type Chain struct {
	Offset   int64
	Contig   string
	Reversed bool
	// contains filtered or unexported fields
}

type EasyAlignment struct {
	Offset        int64
	Alignment_end int64
	Contig        string
	Reversed      bool
	ChainedHit    *C.mem_alnreg_t
	Score         int
	Secondary     bool
	ReadS         int
	ReadE         int
}

type GoBwaReference struct {
	BWTData unsafe.Pointer // Secret pointer to a *btw_t type
	// contains filtered or unexported fields
}

type GoBwaSettings struct {
	Settings unsafe.Pointer // Secret pointer to a *mem_opt_t type
}

type SingleReadAlignment struct {
	Pos                 int64
	Chrom               string
	Flag                int //what is this?
	Reversed            bool
	Alt                 int
	Mapq                int
	EditDistance        int
	Cigar               []uint32
	AlternativeMappings string
	Score               int
	Sub                 int //what is this?
	AltSC               int //what is this?
	ReadS               int //What part of the read is covered by this alignment
	ReadE               int
	// contains filtered or unexported fields
}