Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with HTTPS or Subversion.

Download ZIP
branch: master
Commits on Feb 25, 2015
  1. Chris Fields
Commits on Jan 2, 2015
  1. Francisco J. Ossandon

    Moved optimized \n and \r removal subroutine from Bio::DB::Fasta

    fjossandon authored
    to a more central location at Bio::DB::IndexedBase, from where
    its used by Bio::DB::Fasta and Bio::DB::Qual. Also made a small
    tweak to nhx.t and updated Changes.
Commits on Jan 1, 2015
  1. pcantalupo

    Merge branch 'topic/issue86'

    pcantalupo authored
    * topic/issue86:
      fixing issue 86
Commits on Dec 27, 2014
  1. pcantalupo

    fixing issue 86

    pcantalupo authored
Commits on Dec 24, 2014
  1. Francisco J. Ossandon

    Merge pull request #96 from rocky/Inline-C-Fasta

    fjossandon authored
    Speed up Bio::DB::Fasta using compiled regular expressions or Inline::C
Commits on Dec 23, 2014
  1. Brian Osborne
Commits on Dec 20, 2014
  1. Faster, more idiomatic C code. Use stiop_crln() in the other place it…

    Rocky Bernstein authored
    … is used.
  2. Fasta.pm: Add my variable in strip_crnl and rename from strip_nlcr. D…

    Rocky Bernstein authored
    …ocument better
    
    Build.PL: add Inline::C recommended dependency.
    .gitignore: ignore _Inline directories that Inline::C creates.
  3. Francisco J. Ossandon
Commits on Dec 19, 2014
  1. If we have Inline::C around, use that to speed up remove carriage ret…

    Rocky Bernstein authored
    …urns and
    
    line feeds (\n) and (\r).
  2. Francisco J. Ossandon
  3. Francisco J. Ossandon

    Sopma.t: Added -requires_networking requirement up front (in case

    fjossandon authored
    the page or a mirror returns in the future), since its purpose
    was to test a server
  4. Another regular expression which benefits from compiling

    Rocky Bernstein authored
  5. Francisco J. Ossandon

    Inactivated tests for GOR4.t, HNN.t and Sopma.t, since their server

    fjossandon authored
    (*.ibcp.fr) is now defunct (not responding and verified that it
    does not appear in name server records anymore)
  6. Francisco J. Ossandon

    Sopma.pm: Fixed a bug where the server is not responding but the

    fjossandon authored
    reported connection status appears as COMPLETED instead of
    TERMINATED_BY_ERROR (used GOR4 module code as reference)
Commits on Dec 18, 2014
  1. Using compiled regexps in s/// speeds up seq/subseq() by about 7% fro…

    Rocky Bernstein authored
    …m 7.76s to 7.22s over 32358 calls on Variant Effect Prediction data.
Commits on Nov 17, 2014
  1. Francisco J. Ossandon

    Fixed small typo

    fjossandon authored
  2. Francisco J. Ossandon
Commits on Nov 16, 2014
  1. Francisco J. Ossandon

    CodonTable.pm: Fix for issue #90. Added new codon tables 24 & 25 and

    fjossandon authored
    moved special 'Strict' table to ID 0, so it don't interfere with
    new tables in the future. Deleted a dead link and updated other
    tables according to the latest definitions. Since ID 0 now exists
    and is used by 'Strict', the 'id' subroutine now returns 1
    (standard table) for invalid specified ids (besides the warning).
    Also fixed some indentations.
    CodonTable.t: Added tests to cover all the changes plus a few extras
    to improve code coverage after looking Coveralls report.
  2. Francisco J. Ossandon

    Coveralls report finally worked but only some jobs can finish on time,

    fjossandon authored
    which generates an error status. Nevertheless, the coverage report
    is now available at https://coveralls.io/r/bioperl/bioperl-live,
    so I'm deactivating it for now but leaving the badge on the README.
Commits on Nov 13, 2014
  1. Francisco J. Ossandon

    Last try failed probably because I did not specify one of

    fjossandon authored
    the 4 main metrics (statement, branch, condition or path).
    This is the last try. If it can't finish before 50 minutes,
    we probably would need a Travis-CI pro account (120 minutes
    allowed per job) to make it work... Or Devel::Cover author
    help, but he has not replied my email yet.
  2. Francisco J. Ossandon

    In the last try 3 builds almost finished. This last tweak removes

    fjossandon authored
    an unneeded step for cover. Also, change 'statement' option to 'pod',
    which I hope will be faster.
  3. Francisco J. Ossandon

    Argument worked but "-subs_only" actually took longer than

    fjossandon authored
    "-coverage,subroutine", but I have confirmed that "subroutine"
    will cause an error if used alone. This is very tricky...
  4. Francisco J. Ossandon
Commits on Nov 12, 2014
  1. Francisco J. Ossandon

    Make Devel::Cover ignore external module 'prove' and checking

    fjossandon authored
    if -subs_only fixes the "Can't find digest for" error from
    last commit.
  2. Francisco J. Ossandon

    Unfortunately, the complete coverage test could not complete

    fjossandon authored
    in time (10-15 more minutes would be needed). Adjusting to
    only test 'subroutine' and skip other options for now.
  3. Francisco J. Ossandon

    Good news! Reducing the output made it finish much faster,

    fjossandon authored
    but the test suite was executed twice and that's why it reached
    the 50 minutes limit. Taking out '- PERL5OPT' will make it run
    only once and should finally finish. Hope this is the final test.
  4. Francisco J. Ossandon

    I found that the extra verbosity was caused by 'prove',

    fjossandon authored
    not Devel::Cover. I hope this time it will be easier on Travis
  5. Francisco J. Ossandon

    Failed try. Even testing coverage of only subroutines was

    fjossandon authored
    not enough to complete the process under 50 minutes in Travis-CI.
    The feature looks useful but it's really slow. I'll leave the
    code commented for now.
Commits on Nov 10, 2014
  1. Francisco J. Ossandon
  2. Francisco J. Ossandon

    The first attempt of test coverage was working but resulted

    fjossandon authored
    in massive slowdown of the test suite from ~6 min to >50 min,
    so Travis-CI aborted the build. Commenting until I can find
    if it can be run faster to allow Travis-CI to complete tests.
  3. Francisco J. Ossandon
Commits on Nov 8, 2014
  1. Francisco J. Ossandon
Commits on Nov 7, 2014
  1. Francisco J. Ossandon

    Change EMBL entry name (BUM) that is not working for other

    fjossandon authored
    that currently works (HSFOS)
  2. Francisco J. Ossandon
Something went wrong with that request. Please try again.