Module bio::data_structures

Various useful data structures.

Modules

bitenc	A fixed-width bit encoding implementation. This allows to store a sequence of values over a reduced alphabet by packing them bit-encoded into a sequence of bytes.
bwt	The Burrows-Wheeler-Transform and related data structures. The implementation is based on the lecture notes "Algorithmen auf Sequenzen", Kopczynski, Marschall, Martin and Rahmann, 2008 - 2015.
fmindex	FM-Index and FMD-Index for finding suffix array intervals matching a given pattern in linear time.
interval_tree
qgram_index	A classical, flexible, q-gram index implementation.
rank_select	Rank/Select data structure based on Gonzalez, Grabowski, Mäkinen, Navarro (2005). This implementation uses only a single level of blocks, and performs well for large n.
smallints	A data structure for a sequence of small integers with a few big integers. Small ints are stored in type S (e.g. a byte), big ints are stored separately (in type B) in a BTree. The implementation provides vector-like operations on the data structure (e.g. retrieve a position, add an integer, etc.).
suffix_array	Suffix arrays and related algorithms. The implementation is based on the lecture notes "Algorithmen auf Sequenzen", Kopczynski, Marschall, Martin and Rahmann, 2008 - 2015.