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Commits on Feb 4, 2016
  1. @cjfields

    Merge pull request #128 from dk/master

    cjfields committed
    don't hang on parsing fasta36 -m 9 output
  2. @cjfields

    Merge pull request #79 from Buuntu/master

    cjfields committed
    Added script to extract DNA sequences (as well as 5' or 3' regions if specified) from a FASTA file using a BLAST output file
Commits on Jan 27, 2016
  1. @cjfields

    don't enforce strict line length for FASTA, it's good practice but no…

    cjfields committed
    …t canonical and breaks things
Commits on Jan 8, 2016
  1. @bosborne
  2. @bosborne
Commits on Dec 30, 2015
  1. @pcantalupo
  2. @majensen

    Merge pull request #136 from bioperl/feat-travis-containers

    majensen committed
    Feat travis containers (#135)
  3. feat(travis-containers) : whitelist master again

    Mark A. Jensen committed
  4. feat(travis-containers) : mods for containers

    Mark A. Jensen committed
    Used addons.apt.packages to bring in reqd pkgs without
    sudo.
    
    Mod whitelist to run on this branch only.
  5. @majensen

    fix #134 : do apt-get **update** first

    majensen committed
    Crap, I'm not Chuck.
  6. @majensen

    fix #134 : do apt-get update first

    majensen committed
    Trying a Chuck Norris fix (but I tried it on a fork and it worked)
Commits on Dec 22, 2015
  1. @majensen

    Update README.md

    majensen committed
Commits on Dec 21, 2015
  1. @fjossandon
  2. @fjossandon
  3. @bosborne
  4. @bosborne

    Remove ctrl M

    bosborne committed
Commits on Dec 14, 2015
  1. @fjossandon
  2. @fjossandon
Commits on Dec 13, 2015
  1. @fjossandon

    Restriction::IO.t: REBASE ftp database is not responding properly,

    fjossandon committed
    so added a line to test file to skip tests if connection is not working
  2. @fjossandon
  3. @fjossandon

    embl & genbank: Standarized their qualifier treatment (removed use of…

    fjossandon committed
    … $_,
    
    avoid not defined $qualifier warning, and added "\s*" just after
    equal sign)
  4. @fjossandon

    hmmer3: Added use of \Q\E on match of alignment lines to avoid errors

    fjossandon committed
    when the string include stop codons
Commits on Dec 11, 2015
  1. @bosborne
Commits on Dec 4, 2015
  1. @bosborne
Commits on Dec 3, 2015
  1. @bosborne
  2. @bosborne
Commits on Nov 29, 2015
  1. @carandraug
Commits on Nov 21, 2015
  1. @hyphaltip

    update docs to reflect what is in the array

    hyphaltip committed
    provide reference and docs to the method and point to paper where this was based on. Can't find link to Corbin and Alisha's code, will have to ask someday
Commits on Oct 21, 2015
  1. typo fix

    Dmitry Karasik committed
  2. don't hang on parsing fasta36 -m 9 output

    Dmitry Karasik committed
Commits on Oct 8, 2015
  1. @muffato @cjfields

    bugfix: make sure there is at least 1 space between the sequence name…

    muffato committed with cjfields
    … and the "AC" tag
    
    With the previous code, the name would be attached to "AC" if the it is 22 (or more) characters long
  2. @cjfields

    Merge pull request #91 from nathanweeks/topic/dbi_sqlite_fts

    cjfields committed
    Support FTS attribute table and WITHOUT ROWID optimization for Bio::DB::SeqFeature::Store::DBI::SQLite.  Travis-CI tests are passing (regardless what Github says)
  3. @cjfields

    Merge pull request #109 from gantzgraf/patch-1

    cjfields committed
    Stop masking $seq variable in entrezgene.pm next_seq.  Thanks @gantzgraf !
Commits on Sep 21, 2015
  1. @bosborne

    Correct test number

    bosborne committed
  2. @bosborne

    Add 'desc' to table format

    bosborne committed
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