Many updates to the C++ implementation of StrobeMap
- NAM finding is now parallelized (OpenMP).
- StrobeMap can take read query sequences both as fasta and fastq.
- Faster indexing of references (through preallocation of hash table).
- Fixed minor bugs such as seg fault for references where no strobemer could be generated (e.g., reference containing only N's)
- Precompiled binaries added for Linux and Mac OSx.
- Several parameters added, described below.
- Parameter -s to split the output into one file per thread and fw/rc NAMs (to be compatible as seed finder for uLTRA RNA long-read aligner)
- Parameter -L to print at most L NAMs per query [1000]. Will print the NAMs with highest score S = n_strobemer_hits * query_span.
- Parameter -S to sort output NAMs for each query based on score. Default is to sort first by ref ID, then by query coordinate, then by reference coordinate.