[med-svn] [bppsuite] branch master updated (b307988 -> 39e54c5)

[Andreas Tille]

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tille pushed a change to branch master
in repository bppsuite.

      from  b307988   Take over to Debian Med team maintenance
       new  e9422c1   cme fix dpkg-control
       new  38fe236   debhelper 10
       new  4442ddd   DEP5
       new  415f1d8   Add watch file
       new  457ddcd   use dh
       new  616ba6c   New upstream version 2.3.1
       new  7177225   Updated version 2.3.1 from 'upstream/2.3.1'
       new  4ff487c   New upstream version
       new  962b011   Fix manpage debhelper input
       new  39e54c5   Adjust Build-Depends

The 10 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:
 AUTHORS.txt                                        |   2 +
 CMakeLists.txt                                     | 302 +++------------
 ChangeLog                                          |  31 ++
 Examples/MaximumLikelihood/Codons/M1/ML.bpp        |   4 +-
 Examples/MaximumLikelihood/Codons/M2/ML.bpp        |   4 +-
 Examples/PhylogeneticSampling/PhySamp.bpp          |  54 ---
 Examples/PopStats/PopStats.bpp                     |  11 +
 Examples/PopStats/PopStatsCodonSites.bpp           |  19 +
 Examples/README                                    |   1 -
 INSTALL.txt                                        |  13 +-
 bppSuite/CMakeLists.txt                            |  86 ++--
 bppSuite/bppAlnScore.cpp                           |  44 ++-
 bppSuite/bppAncestor.cpp                           |  43 +-
 bppSuite/bppConsense.cpp                           |   8 +-
 bppSuite/bppDist.cpp                               |  24 +-
 bppSuite/bppML.cpp                                 |  61 +--
 bppSuite/bppMixedLikelihoods.cpp                   |  75 ++--
 bppSuite/bppPars.cpp                               |  11 +-
 bppSuite/bppPhyloSampler.cpp                       | 282 --------------
 bppSuite/bppPopStats.cpp                           | 421 ++++++++++++++++++++
 bppSuite/bppReRoot.cpp                             |  10 +-
 bppSuite/bppSeqGen.cpp                             | 208 +++++++---
 bppSuite/bppSeqMan.cpp                             |  77 ++--
 bppSuite/bppTreeDraw.cpp                           |  20 +-
 bppsuite.spec                                      |  80 ++--
 buildBin.sh                                        |   5 +-
 debian/bppsuite.manpages                           |  12 +-
 debian/changelog                                   |  10 +-
 debian/compat                                      |   2 +-
 debian/control                                     |  22 +-
 debian/copyright                                   |  80 ++--
 debian/rules                                       | 153 +-------
 debian/watch                                       |   3 +
 doc/CMakeLists.txt                                 |  76 +++-
 doc/bppsuite.texi                                  | 431 ++++++++++++++++-----
 man/CMakeLists.txt                                 |  54 ++-
 man/{bppalnscore.1.txt => bppalnscore.1}           |   0
 man/{bppancestor.1.txt => bppancestor.1}           |   0
 man/{bppconsense.1.txt => bppconsense.1}           |   0
 man/{bppdist.1.txt => bppdist.1}                   |   0
 ...ixedlikelihoods.1.txt => bppmixedlikelihoods.1} |   0
 man/{bppml.1.txt => bppml.1}                       |   0
 man/{bpppars.1.txt => bpppars.1}                   |   0
 man/bppphysamp.1.txt                               |  37 --
 man/{bpppars.1.txt => bpppopstats.1}               |  10 +-
 man/{bppreroot.1.txt => bppreroot.1}               |   0
 man/{bppseqgen.1.txt => bppseqgen.1}               |   0
 man/{bppseqman.1.txt => bppseqman.1}               |   0
 man/{bpptreedraw.1.txt => bpptreedraw.1}           |   0
 49 files changed, 1526 insertions(+), 1260 deletions(-)
 delete mode 100755 Examples/PhylogeneticSampling/PhySamp.bpp
 create mode 100644 Examples/PopStats/PopStats.bpp
 create mode 100644 Examples/PopStats/PopStatsCodonSites.bpp
 delete mode 100755 bppSuite/bppPhyloSampler.cpp
 create mode 100644 bppSuite/bppPopStats.cpp
 create mode 100644 debian/watch
 rename man/{bppalnscore.1.txt => bppalnscore.1} (100%)
 rename man/{bppancestor.1.txt => bppancestor.1} (100%)
 rename man/{bppconsense.1.txt => bppconsense.1} (100%)
 rename man/{bppdist.1.txt => bppdist.1} (100%)
 rename man/{bppmixedlikelihoods.1.txt => bppmixedlikelihoods.1} (100%)
 rename man/{bppml.1.txt => bppml.1} (100%)
 copy man/{bpppars.1.txt => bpppars.1} (100%)
 delete mode 100644 man/bppphysamp.1.txt
 rename man/{bpppars.1.txt => bpppopstats.1} (59%)
 rename man/{bppreroot.1.txt => bppreroot.1} (100%)
 rename man/{bppseqgen.1.txt => bppseqgen.1} (100%)
 rename man/{bppseqman.1.txt => bppseqman.1} (100%)
 rename man/{bpptreedraw.1.txt => bpptreedraw.1} (100%)

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