v2.6.2

Fixed

• segfaults when using stats profile functions

Closed Issues

• segfaults when using (some) profile functions #99
• MAPQ should be 0 for unmapped reads #100

2.6.1

Fixed

• Out-of-bounds memory corruption in tracebacks

Closed Issues

• Out-of-bounds memory corruption #98

2.6

Added

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

Gaps are penalty-free at	Function Name
beginning of s1/query and beginning of s2/database	sg_qb_db
end of s2/database and end of s1/query	sg_qe_de

Fixed

• configure now works correctly when using -Wall

Closed Issues

• sg_qe_de - alignment extension? #95

Merged Pull Requests

• Fix compiler/linker support of SIMD instructions with -Wall #94

2.5

Added

• Position-Specific Scoring Matrix Alignment (see README.md)
  • parasail_matrix_t attributes type, length, alphabet, and query
  • pssm matrix functions
    • parasail_matrix_pssm_create
    • parasail_matrix_pssm_create_case_sensitive
    • parasail_matrix_convert_square_to_pssm

Changed

• Alignment functions now verify inputs as follows
  • input sequences are not null and lengths are greater than zero
  • input matrix is not null
  • open and gap penalties are greater than or equal to zero
• parasail_matrix_from_file can now parse a simple pssm format (see README.md)

Fixed

• Failure linking against OpenMP on macOS [#91] [#92] (jvkersch)

2.4.3

Fixed

• provide action-if-not-found case for PKG_CHECK_MODULES([Z])
  Thanks to ksahlin for the bug report.
• spellcheck parasail_aligner, thanks to nileshpatra.

Closed Issues

• Failed to build parasail on Mac OSx #81

Merged Pull Requests

• Fix spellings #78

2.4.2

Fixed

• Add missing headers to make dist target, use distcheck in Travis.
• Library functions no longer call exit() upon failure, instead returning error to caller.
• Update email address.

Closed Issues

• API request: return NULL from parasail_sequences_from_file upon error? [#71]

Merged Pull Requests

• Fix tarball [#77] (SoapZA)

2.4.1

Fixed

• Bug in CIGAR construction causing incorrect results. Regression from 2.3 release.

Closed Issues

• Bug in CIGAR Construction #67

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]

v2.3

Added

• Support for MSYS and mingw builds.
• parasail_aligner outputs version information in verbose mode.
• Functions parasail_result_get_traceback and parasail_traceback_free to retrieve traceback C strings. See README.md for details.

v2.2

Added

• ARM NEON vectorized functions via the simde project. Also thanks to philres for the hardware donation.

Fixed

• parasail_aligner works again with profile-based functions

Closed Issues

• Support for ARM64? [#59]