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Commits on Jul 21, 2016
  1. @nds

    Merge pull request #64 from nds/nds_change_to_dist_zilla_starter_bundle

    nds change to dist zilla starter bundle
    nds committed on GitHub Jul 21, 2016
  2. @nds

    change to dist zilla starter bundle

    nds committed Jul 21, 2016
  3. @nds
Commits on Feb 10, 2016
  1. @martinghunt

    Merge pull request #63 from aslett1/master

    BUG: missing semicolon in get_emm_sequence_type script
    martinghunt committed Feb 10, 2016
Commits on Feb 9, 2016
  1. @aslett1
Commits on Feb 2, 2016
  1. @andrewjpage

    Merge pull request #62 from bewt85/bt5_fix_concatenation

    Order alleles consistently when concatonating
    andrewjpage committed Feb 2, 2016
  2. @bewt85

    Fix allele order in concatenated fa

    Also update test data
    bewt85 committed Feb 2, 2016
  3. @bewt85

    Fix file comparison

    Actual and expected files were in the wrong order
    bewt85 committed Feb 1, 2016
  4. @bewt85

    Check that concatenated alleles sorted consistently

    Alleles should be sorted by name and not by their sequence when concatenating mlst genes
    bewt85 committed Feb 1, 2016
Commits on Dec 7, 2015
  1. @martinghunt

    Merge pull request #61 from bewt85/bt5_488940_ignore_metadata

    Ignore metadata column headings in profiles
    martinghunt committed Dec 7, 2015
Commits on Dec 4, 2015
  1. @bewt85
  2. @bewt85

    Use common allele_blacklist

    bewt85 committed Dec 4, 2015
  3. @bewt85
Commits on Dec 3, 2015
  1. @bewt85
Commits on Sep 9, 2015
  1. @martinghunt

    Merge pull request #60 from sanger-pathogens/BT5_463456_fix_blastn_ma…

    …tching
    
    [468141,463456]: Cope better with small changes to alleles
    martinghunt committed Sep 9, 2015
Commits on Sep 7, 2015
  1. @bewt85

    Bump minor version

    bewt85 committed Sep 7, 2015
Commits on Sep 4, 2015
  1. @bewt85

    Add note about potential BUG from word sizes

    bewt85 committed Sep 4, 2015
  2. @bewt85
  3. @bewt85

    Fix fake blast output in tests

    bewt85 committed Sep 4, 2015
  4. @bewt85

    Remove trailing whitespace

    bewt85 committed Sep 4, 2015
  5. @jgtate

    Merge pull request #59 from sanger-pathogens/bt5_fix_travis_badge

    Travis badge should just report master
    jgtate committed Sep 4, 2015
  6. @bewt85

    Travis badge should just report master

    This was giving the impression that master was broken, which it isn't
    bewt85 committed Sep 4, 2015
  7. @bewt85

    Tested against all STs

    Run against synthetic data containing every single pneumo ST and it got them all right
    bewt85 committed Aug 6, 2015
  8. @bewt85

    Use correct allignment length

    bewt85 committed Jul 29, 2015
  9. @bewt85

    WIP: Use length of alelle match

    Rather than using the length of the match on the sample which may include indels, use the length of the match on the allele
    bewt85 committed Jul 29, 2015
  10. @bewt85

    Merge hits which are mostly overlapping

    Uses a hack to output fake blast results
    bewt85 committed Jul 28, 2015
  11. @bewt85

    Refactor: group hits outputs bins

    bewt85 committed Jul 28, 2015
  12. @bewt85
  13. @bewt85

    Reduce match accuracy

    This should not always find a match unless the contigs are shorter than
    the alleles they're being matched against
    bewt85 committed Jul 23, 2015
  14. @bewt85

    Add imperfect allele match tests

    Add some tests for cases where some alleles are imperfectly matched
    bewt85 committed Jul 23, 2015
  15. @bewt85

    Fix tests for ambiguous ST types

    Fixes some of the tests to add a tilde to the ST name where no ST is a
    perfect match
    bewt85 committed Jul 23, 2015
  16. @bewt85

    Allele and Genomic CSVs clarify matches

    The Allele and Genomics CSV outputs not make it clearer that an ST match
    is only approximate by appending a tilde (~) to the name.
    bewt85 committed Jul 23, 2015
  17. @bewt85

    BUGFIX: test data was wrong

    bewt85 committed Jul 23, 2015
  18. @bewt85

    Genomic CSV shows results for near matches

    It also has less biased / more accurate approximations for ST
    bewt85 committed Jul 23, 2015
  19. @bewt85

    Allele CSV shows closest matches

    Alleles are shown with a ~ if they are less than 100% matches and ST
    matches use these to come up with better approximations.
    bewt85 committed Jul 22, 2015