[INTERNAL] Yara: updated options parsing
[INTERNAL] Yara: split reads store from functions on read seqs
[INTERNAL] Yara: replaced Contigs and Reads classes with SeqStore
[INTERNAL] Yara: renamings
[INTERNAL] Yara: working indexer
[FIX,CLI] Yara: fixed indexer cli options
[INTERNAL] Yara: refactored options
[INTERNAL] Yara: refactored mapper template configuration
[API] SeqFile: added readRecords(..., maxRecords)
[INTERNAL] Yara: ported reads loading to the new I/O
[INTERNAL] Yara: changed open(Pair<TFile>, Pair<...> fileName) to open(Pair<TFile>, fileName1, fileName2)
[NOP] Yara
[INTERNAL] Yara: enabled bam writer
[INTERNAL] Yara: enabled parallel write
[API] Yara: indexer option --output-prefix, first mapper argument is reference index prefix
[NOP] Yara: commented old CUDA index overloads
[INTERNAL] Yara: split store from pair and prefetched file
[INTERNAL] Yara: store config
[INTERNAL] Yara: implemented swap() for SeqStore
[API] Yara: PrefetchedFile implements readRecords()