libaw

Libaw is a alignment writer library, mainly targeting internal use in nucleotide sequence local alignment programs. The library can handle the SAM format and the Graphical Pairwise Alignment (GPA) format.

Functions

aw_init

Initialize an alignment writer object.

aw_t *aw_init(
	char const *path,
	gref_idx_t const *idx,
	aw_params_t const *params);

aw_clean

Destroy the object.

void aw_clean(aw_t *aw);

aw_append_alignment

Append an alignment result. See libgaba for the details of the struct gaba_result_s container and libgref for the sequence indexer objects.

void aw_append_alignment(
	aw_t *aw,
	gref_idx_t const *ref,
	gref_acv_t const *query,
	struct gaba_result_s const *const *aln,
	int64_t cnt);

License

MIT

Copyright (c) 2016 Hajime Suzuki