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Commits on Dec 12, 2016
  1. Partial codons for SearchIO when parsing Exonerate

    Squashed commit of pull request #815.
    
    Fix for handling protein to nucleic acid mapping in Exonerate, with tests for exonerate protein2genome mode.
    bow committed with peterjc Dec 12, 2016
Commits on Dec 22, 2015
  1. Update documentation on hmmer3-domtab format.

    The `seq_len` attribute was previously missing from the
    documentation.
    bow committed Dec 22, 2015
Commits on Aug 3, 2015
  1. Fix issue #588

    The bug is caused by phmmer outputing an unexpected line at the end
    of the output hmmer3-text file when the `-A` flag is set. This commit
    ensures the line is ignored and adds a test case to check for this
    behavior.
    bow committed Aug 3, 2015
Commits on Aug 2, 2015
  1. Fix hmmer3-text bug where table hit description has preference over f…

    …ull descriptions
    
    Previously, the hit description in the hit table always overwrites the full
    description. This doesn't matter when they are the same, but the description
    in the tables has a maximum length. If the full description exceeds the length,
    a truncated version is shown in the table.
    
    This change ensures that the full description is always used.
    bow committed Aug 2, 2015
Commits on Jul 8, 2015
  1. Fix for issue #525, HmmerIO text parser bug fix.

    HmmerIO text parser broke on sequence hits without individual domain hits
    
    Also with additional tests to ensure the bug does not happen again.
    bow committed with peterjc Jul 8, 2015
  2. Fix for issue #556.

    Instead of relying on raw string splits, we now use regex splits
    to have the parser more robust. We should be able to handle
    cases where descriptions are not present, provided each ID starts
    with the '>' character.
    bow committed Jul 8, 2015
Commits on Nov 11, 2014
Commits on Oct 2, 2014
Commits on Jul 11, 2014
Commits on Jul 10, 2014
  1. Merge pull request #307 from bow/patch_multiple-hit-ids

    Add alternative ID support to SearchIO
    bow committed Jul 10, 2014
  2. Update NEWS

    bow committed Jul 10, 2014
Commits on Jul 9, 2014
  1. Add tox.ini info to documentation (suggested by @msabramo)

    Original issue: #50
    bow committed Jul 9, 2014
Commits on May 27, 2014
  1. Remove append calls

    bow committed May 27, 2014
Commits on May 26, 2014
  1. Update NEWS

    bow committed May 26, 2014
  2. Update test class name

    bow committed May 25, 2014
  3. Update main test class name

    bow committed May 22, 2014