[med-svn] [grinder] branch master updated (3577b3d -> b0b5bd4)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch master
in repository grinder.

      from  3577b3d   Move debian/upstream to debian/upstream/metadata
       new  b0a5b3a   Imported Upstream version 0.5.4
       new  3963ac1   Merge tag 'upstream/0.5.4'
       new  6de4c4e   New upstream version
       new  8992263   cme fix dpkg-control
       new  d1a9879   Remove default gbp.conf file
       new  b89ab91   Adapt packaging to new upstream version
       new  b0b5bd4   Upload to unstable

The 7 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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 +-
 debian/changelog                     |    7 +
 debian/control                       |    5 +-
 debian/gbp.conf                      |    7 -
 debian/rules                         |   23 +-
 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
 59 files changed, 950 insertions(+), 7041 deletions(-)
 rename {script => bin}/grinder (100%)
 rename {script => bin}/grinder.pod (98%)
 delete mode 100644 debian/gbp.conf
 delete mode 100644 lib/Bio/DB/Fasta.pm
 delete mode 100644 lib/Bio/DB/IndexedBase.pm
 delete mode 100644 lib/Bio/PrimarySeq.pm
 delete mode 100644 lib/Bio/PrimarySeqI.pm
 delete mode 100644 lib/Bio/Seq/SeqFastaSpeedFactory.pm
 delete mode 100644 lib/Bio/Seq/SimulatedRead.pm
 delete mode 100644 lib/Bio/SeqFeature/Amplicon.pm
 delete mode 100644 lib/Bio/SeqFeature/Primer.pm
 delete mode 100644 lib/Bio/SeqFeature/SubSeq.pm
 delete mode 100644 lib/Bio/Tools/AmpliconSearch.pm
 delete mode 100644 lib/Bio/Tools/IUPAC.pm
 delete mode 100644 t/data/database_dna.fa.index
 delete mode 100644 t/data/database_mixed.fa.index
 delete mode 100644 t/data/database_protein.fa.index
 delete mode 100644 t/data/database_rna.fa.index
 delete mode 100644 t/data/shotgun_database.fa.index

-- 
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