[med-svn] [grinder] 02/07: Merge tag 'upstream/0.5.4'

[Andreas Tille]

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tille pushed a commit to branch master
in repository grinder.

commit 3963ac1d8fc055c198c364bb6943de8bee63f5dd
Merge: 3577b3d b0a5b3a
Author: Andreas Tille <tille at debian.org>
Date:   Sun Jan 24 09:52:51 2016 +0100

    Merge tag 'upstream/0.5.4'
    
    Upstream version 0.5.4

 CHANGES                              |    6 +
 LICENSE                              |    2 +-
 MANIFEST                             |   20 +-
 META.yml                             |   16 +-
 MYMETA.json                          |   18 +-
 MYMETA.yml                           |   39 +-
 Makefile.PL                          |   21 +-
 README                               |   13 +-
 README.htm                           | 1180 +++++++++++++++-------------------
 {script => bin}/grinder              |    0
 {script => bin}/grinder.pod          |   16 +-
 inc/Module/AutoInstall.pm            |   44 +-
 inc/Module/Install.pm                |   22 +-
 inc/Module/Install/AutoInstall.pm    |    2 +-
 inc/Module/Install/Base.pm           |    2 +-
 inc/Module/Install/Can.pm            |    2 +-
 inc/Module/Install/Fetch.pm          |    2 +-
 inc/Module/Install/Include.pm        |    2 +-
 inc/Module/Install/Makefile.pm       |    4 +-
 inc/Module/Install/Metadata.pm       |    6 +-
 inc/Module/Install/ReadmeFromPod.pm  |    2 +-
 inc/Module/Install/Scripts.pm        |    2 +-
 inc/Module/Install/Win32.pm          |    2 +-
 inc/Module/Install/WriteAll.pm       |    2 +-
 lib/Bio/DB/Fasta.pm                  |  455 -------------
 lib/Bio/DB/IndexedBase.pm            | 1104 -------------------------------
 lib/Bio/PrimarySeq.pm                |  951 ---------------------------
 lib/Bio/PrimarySeqI.pm               |  944 ---------------------------
 lib/Bio/Seq/SeqFastaSpeedFactory.pm  |  149 -----
 lib/Bio/Seq/SimulatedRead.pm         |  653 -------------------
 lib/Bio/SeqFeature/Amplicon.pm       |  168 -----
 lib/Bio/SeqFeature/Primer.pm         |  335 ----------
 lib/Bio/SeqFeature/SubSeq.pm         |  208 ------
 lib/Bio/Tools/AmpliconSearch.pm      |  564 ----------------
 lib/Bio/Tools/IUPAC.pm               |  560 ----------------
 lib/Grinder.pm                       |  137 ++--
 lib/Grinder/Database.pm              |    3 +-
 man/average_genome_size.1            |   33 +-
 man/change_paired_read_orientation.1 |   33 +-
 man/grinder.1                        |   69 +-
 t/01-shotgun.t                       |   20 +-
 t/02-mates.t                         |   26 +-
 t/05-forbidden.t                     |    2 +-
 t/15-multiplex.t                     |   14 +-
 t/17-libraries.t                     |    8 +-
 t/20-community-structure.t           |    6 +
 t/21-errors.t                        |   32 +-
 t/29-kmer-collection.t               |   30 +-
 t/32-database.t                      |   13 +-
 t/TestUtils.pm                       |    7 +-
 t/data/database_dna.fa.index         |  Bin 12288 -> 0 bytes
 t/data/database_mixed.fa.index       |  Bin 12288 -> 0 bytes
 t/data/database_protein.fa.index     |  Bin 12288 -> 0 bytes
 t/data/database_rna.fa.index         |  Bin 12288 -> 0 bytes
 t/data/shotgun_database.fa.index     |  Bin 12288 -> 0 bytes
 55 files changed, 940 insertions(+), 7009 deletions(-)

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