Abstract: In finding associated positions of bases of a read on a reference genome, each base has a position number on the read. A procedure to obtain P sequence parts of the read comprises a first loop to obtain P candidates and extend each of the P candidates by preceding and/or following bases of the read to obtain the P sequence parts. A sequence part matches a part of the reference genome according to predefined criteria at a location on the reference genome. The first loop comprises determining the number of locations on the reference genome that match a partial sequence with a length of M bases, the partial sequence starting at a base with position number S and repeating that action by increasing M as long as the number of locations on the reference genome that match is larger than a predefined number T, where P?T.

Abstract: The invention relates to a computer implemented method of storing/recovering in/from a storage data structure a multitude of sequences that have been aligned with a reference data structure. The information of the sequences is stored in different sections. Each section comprises data streams comprising specific data of the sequences having a reference position in the reference position range associated with the data stream. In a first section, the length of the sequences is stored. In a second section, the mutations of a sequence with respect to the reference sequence are stored. In a third section, consensus based quality values are linked with positions in the reference sequence. In a fourth section, the sequence identifiers are stored. The storage data structure has a format which is optimized for viewer, re-alignment, variant calling and other post-processing tools.

Abstract: The invention relates to a method for finding a position of a data pattern in reference data. For this a reference index data structure comprising a reference data structure, a sorted index and a jump table is generated. The sorted index comprises for each position in the reference data structure an entry. Each entry comprises a position field which value refers to an associated position in the reference data structure. By means of the position a reference data pattern corresponding to said position could be reconstructed from the reference data structure. The entries of the sorted index are sorted according to the reference data pattern associated with the value in the position field. A search is performed through the sorted index by reconstructing a reference data pattern from the reference data structure and comparing it with the data pattern to be matched.

Abstract: A method and apparatus are provided for retrieving data from a table in a database. According to the method one or more indexes arc generated for use in processing a query by selecting values as unique key values from one or more columns in a table in a relational database system. Each unique key corresponds to a row in the table. The condition of whether a row in a table satisfies a search criterion, is represented by a bit in a bitstring or, in cases where the bitstring is segmented, in a segment of bitstring. The unique keys and corresponding segment of bitstring are then stored in an index.