v2.0.2

Added

• manylinux release builds.

Fixed

• Traceback/cigar now works for non-striped alignment functions. A significant bug caused incorrect cigar strings and tracebacks for any alignment routine besides 'striped'. Thanks to huxihao for the issue report on parasail-python.

Closed Issues

• strdup implicitly declared in parser.c [#37]
• make check fails without zlib [#36]

v2.0.1

Fixed

• SSW emulation seg fault when using score_size flag.

v2.0

Added

• Alignment trace functions for generating SAM CIGAR output.
• SAM CIGAR encode, decode, and accessor functions.
• Support for AltiVec/POWER ISA.
• SSW emulation functions.
• parasail_result_t attribute accessor functions.
• parasail_traceback_generic() function for printing tracebacks to stdout.
• Revamped sequence parsing based on [kseq.h].
  • parasail_sequence_t and parasail_sequences_t objects, used with new parasail_sequences_from_file()
  • Support for FASTA, FASTQ.
  • Optional support for compressed input files if libz is found during the build process.
• parasail_aligner
  • Verbose mode -v. This re-enables output common to v1.x.
  • Output format -O {SAMH,SAM,EMBOSS,SSW}.
    Requires one format argument as well as the use of a trace-enabled alignment function.

Changed

• Reduced size of parasail_result_t object. Users should treat the
  result as an opaque pointer and instead use the new attribute accessor
  functions.

Deprecated

• The 'block' vectorized functions should not be used and will be removed.

Removed

• parasail_aligner 'packed' input files.

Fixed

• parasail_aligner now understands the stop codon.

Closed Issues

• It appears that the -s option to specify SAM is not handled by parasail_aligner [#35]
• Stop Codon Error [#34]
• Understanding Result [#32]
• provide functions that return the full traceback [#12]
• smaller memory footprint of parasail_result_t [#11]

v1.3.1

Fixed

• parasail_aligner option '-s' works again.

v1.3

Changed

• Added parasail_aligner option '-G' for output compatible with [GrappoloTK].
• Changed CMake option BUILD_SHARED_LIBS default to ON.
• Added automatic deployment of CI artifacts to releases.

v1.2

Changed

• Added alignment function
  • parasail_nw_banded (note, different interface than the other alignment functions)
• Added matrices
  • nuc44
  • dnafull
• Added matrix functions
  • parasail_matrix_from_file
  • parasail_matrix_copy
  • parasail_matrix_set_value
• Added parasail_aligner options
  • -m matrix -- can be a built-in matrix name or a filename to be parsed
  • 'packed' input files
• parasail_matrix_t attribute int need_free is now int *user_matrix

Closed Issues

• Needleman-Wunsch with affine gap penalties #26

Closed Pull Requests

• fix #29 -- wontfix

v1.1.2

Fixed

• autoconf build; libparasail now correctly depends on libm where needed
• CMake build; do not incorrectly force libparasail to depend on libpthread

v1.1.1

Fixed

• libparasail now correctly links when pow() not in system C library

Merged Pull Requests

• Allow injection via cmake submodule [#27] (armintoepfer)

v1.1

Changed

• Stats functions are now affine, not linear.
• Semi-global and global alignments now use a more negative value to
  represent negative infinity instead of half the value of the smallest
  representable integer for the given bit width.
• end_query and end_ref reported for all routines.

Fixed

• Stats functions are now affine, not linear.

Closed Issues

• provide Java bindings [#22]
• stats functions should be affine, not linear [#10]
• parasail results off by one error [#4]

v1.0.3

Changed

• Added TravisCI support for autotools Linux and OSX builds.
• Added AppVeyor support for CMake Windows builds.
• PARASAIL_API and PARASAIL_LOCAL removed from all parasail functions.
• CMake build
  • Added BUILD_SHARED_LIBS option.
  • Added parasail.def for MSVC DLL creation.
  • Set CMAKE_POSITION_INDEPENDENT_CODE to ON if BUILD_SHARED_LIBS is ON.
  • /arch:AVX is the correct flag for MSVC, not /arch:AVX2.

Fixed

• parasail_free() was not being used to free ISA-specific sequence profiles. Caused MSVC 64-bit library to crash.
• CMake shared library build was basically not functional on any platform. It now works.