2.4

Added

• Specific semi-global routines for various beginning and end gap penalty combinations.

Gaps are penalty-free at	Function Name
beginning of s1/query	sg_qb
end of s1/query	sg_qe
beginning and end of s1/query	sg_qx
beginning of s2/database	sg_db
end of s2/database	sg_de
beginning and end of s2/database	sg_dx
beginning of s1/query and end of s2/database	sg_qb_de
beginning of s2/database and end of s1/query	sg_qe_db
beginning and end of both sequences	sg (original, unchanged for backwards compatibility)

• parasail_aligner
  • case-sensitive mode
  • alphabet aliases, for example to support T/U as matches
• New functions, to support case-sensitivity and alphabet aliases
  • parasail_matrix_create_case_sensitive
  • parasail_matrix_from_file_case_sensitive
  • parasail_traceback_generic_extra2
  • parasail_result_get_cigar_extra
  • parasail_result_get_traceback_extra

Changed

• parasail_matrix_from_file matrix format must have a null last row and column (see README.md)

Fixed

• Bug in ARM NEON 64-bit comparison functions causing incorrect results.
• Bug in parasail_matrix_from_file.

Closed Issues

• Question about gap open penalty for different vectorizations. [#64]
• T and U are treated as mismatching nucleotides. [#58]