1. 17 Nov, 2016 3 commits
    • Laros's avatar
      Version bump. · 20db5944
      Laros authored
    • Laros's avatar
      Updated CHANGELOG. · 13f28b36
      Laros authored
    • Laros's avatar
      Merge branch 'master' into 'master' · 9f41922f
      Laros authored
      Fix Windows installation errors once and for all
      After the release of 0.4.1 I still ran into some issues with installing on Windows. I spent today fixing anything that popped up until it installed successfully.
      The changes are:
      * 28488618: Avoided the use of variable length arrays as these are not supported by MSVC. The lengths of arrays must be known at compile-time, else you get an `error C2057: expected constant expression`. (I made this change before I figured MSVC should take the SSE2 route instead, so this is not strictly needed anymore to compile with MSVC, but it will probably fix other non-C99-non-SSE2-compilers anyway.)
      * 8b057ec5: Moved the declarations of `__m128i` variables in the SSE2 code up to the beginning of the function, as MSVC can't cope with them being declared after some function logic. The error you'd get is a rather cryptic `error C2275: '__m128i' : illegal use of this type as an expression`.
      * 96d3195f: Updated the detection of SSE2 capabilities such that SSE2 works with compilers that don't define `__GNUC__`. I made a special case for MSVC as it does not define `__SSE2__` (or any of its family members) either. Instead it 'just works' with MSVC, so if `_MSC_VER` is defined, the code now assumes SSE2 is available.
      * 8ea3ee1f: Apparently the first argument to `distutils.core.Extension`is a module _name_, not a module _path_. Hence, the `/`was supposed to be a `.`. This issue presented itself on Windows as `error LNK2001: unresolved external symbol inittssv/_sg_align`.
      With these fixes in place, TSSV compiles and installs on my 64-bit Windows 10 laptop with 64-bit Python 2.7.12.
      Of course, all of this is tested for regressions with gcc 4.8.4 and Ubuntu 16.04.1 LTS as well.
      See merge request !7
  2. 16 Nov, 2016 1 commit
  3. 02 Nov, 2016 4 commits
  4. 30 Oct, 2016 4 commits
  5. 29 Oct, 2016 3 commits
  6. 26 Oct, 2016 2 commits
    • Hoogenboom, Jerry's avatar
      Fix SWIGging through Setuptools · fcfb98dc
      Hoogenboom, Jerry authored
      When running `python setup.py install`, SWIG is run too late in the
      build process, causing an ImportError when running TSSV. There was a fix
      in place, but it only worked when installing using `pip install tssv`.
      This commit implements the fix from http://stackoverflow.com/a/21236111
    • Hoogenboom, Jerry's avatar
      Change 'inline' to '__inline' for MSVC compiler · b5c51ad3
      Hoogenboom, Jerry authored
      On Windows, Pip (or Setuptools) offers a download link for the
      standalone MSVC 14.0 2015 compiler if no C compiler is installed, which
      does not recognise the inline keyword. Therefore, TSSV's sg_align module
      does not compile on Windows without this change.
      Tested compatibility with GCC 4.8.4: the output is identical.
  7. 13 Oct, 2016 4 commits
  8. 23 Aug, 2016 2 commits
  9. 04 Aug, 2016 1 commit
  10. 02 Aug, 2016 4 commits
  11. 01 Aug, 2016 9 commits
  12. 29 Jul, 2016 2 commits
    • Laros's avatar
      Added ignore file. · fec80b49
      Laros authored
    • Laros's avatar
      Merge branch 'master' into 'master' · a14ef6a6
      Laros authored
      Option to penalise indels more heavily than substitutions
      Made two changes:
      * Added -n/--indel-score argument.  Insertions and deletions in the
        flanking sequences are penalised this number of times more heavily
        than mismatches.  The default is 1, i.e., the penalty for insertions
        and deletions is the same as for mismatches.  Therefore, default
        behaviour has not changed.
        We set this value to 2 in our analysis pipeline because we were having issues with TSSV favoring a deletion in the flanking sequence over a substitution. The result was that some alleles ended with the first base of the right flank attached, which showed up in downstream analysis as an insertion.
      * TSSV will now install the compiled `_sg_align` module inside the tssv
        package directory.  Earlier versions would install this module
        straight into the top-level site-packages or dist-packages directory.
        Installing the new version will leave behind the `_sg_align.so` file of the previous installation in the site-packages or dist-packages directory, but TSSV will use the new file in TSSV's project directory. The old file can safely be deleted.
      This version has been tested over the previous month or so with no issues. I propose to release this as v0.3.1 and have taken the liberty to add this version to the `README.md` as well.
      See merge request !5
  13. 21 Jul, 2016 1 commit