v0.1

Major update of strobealign. This version comes with an improvement in accuracy (and the number of aligned reads) around lengths 100-125nt reads, and it is also faster than older versions for these lengths. Most notable changes:

• Algorithm changes

  • Using xxhash instead of no hash for strobes. Gives a better pseudorandom generation of hashes for linking.
  • Linking strobes using bitcount( (h_1 ^ h_2) ^ q) which creates a skewed seed length distribution towards shorter seeds in the window. This improves mapping candidate read detection particularly for shorter reads (100nt).

• Parameters

  • Adding the option to customize sampling window of second strobe with -l and -u.
  • Adding a parameter -r [INT] for approximate read length (default 150). This will make strobealign customize parameters -l -u, and -k

• Also cuts the reference accessions at first space, which fixes issue #4