[med-svn] [maffilter] branch upstream updated (a78afec -> d8e6558)

[Andreas Tille]

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tille pushed a change to branch upstream
in repository maffilter.

      from  a78afec   Imported Upstream version 1.1.0-1+dfsg
       new  9a5e284   New upstream version 1.2.1
       new  d8e6558   New upstream version 1.2.1+dfsg

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repository and will be described in separate emails.  The revisions
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Summary of changes:
 AUTHORS.txt => AUTHORS                             |   0
 CMakeLists.txt                                     | 277 +++-----
 COPYING.txt                                        | 506 ---------------
 ChangeLog                                          |  44 +-
 INSTALL.txt => INSTALL                             |   2 +-
 LICENSE                                            | 674 ++++++++++++++++++++
 MafFilter/CMakeLists.txt                           |  23 +-
 MafFilter/MafFilter.cpp                            | 605 ++++++++++++++++--
 MafFilter/SystemCallMafIterator.cpp                |  84 +++
 ...aturesMafIterator.h => SystemCallMafIterator.h} |  75 ++-
 ...r.cpp => TreeBuildingSystemCallMafIterator.cpp} |  60 +-
 ...rator.h => TreeBuildingSystemCallMafIterator.h} |  80 ++-
 buildBin.sh                                        |   7 +
 doc/CMakeLists.txt                                 |  80 ++-
 doc/maffilter.texi                                 | 695 +++++++++++++++++----
 ...rojected.chr22.subset.nogap.cleaned_aln.maf.gz} | Bin 20032238 -> 13206362 bytes
 examples/UCSC46ways/MafFilter.bpp                  |   2 +-
 examples/UCSC46ways/README                         |   1 +
 ...Mgraminicolav2.FrozenGeneCatalog20080910.gff.gz | Bin 0 -> 809905 bytes
 examples/Ztritici/tba_refIPO323.maf.gz             | Bin 0 -> 60513136 bytes
 maffilter.spec                                     |  66 +-
 man/CMakeLists.txt                                 |  47 +-
 man/{maffilter.1.txt => maffilter.1}               |   2 +-
 23 files changed, 2290 insertions(+), 1040 deletions(-)
 rename AUTHORS.txt => AUTHORS (100%)
 delete mode 100644 COPYING.txt
 rename INSTALL.txt => INSTALL (88%)
 create mode 100644 LICENSE
 create mode 100644 MafFilter/SystemCallMafIterator.cpp
 copy MafFilter/{OutputAsFeaturesMafIterator.h => SystemCallMafIterator.h} (55%)
 copy MafFilter/{OutputAsFeaturesMafIterator.cpp => TreeBuildingSystemCallMafIterator.cpp} (50%)
 copy MafFilter/{OutputAsFeaturesMafIterator.h => TreeBuildingSystemCallMafIterator.h} (50%)
 create mode 100755 buildBin.sh
 copy examples/{Umaydis/Umaydis.fasta => Gorilla/Compara.epo_5_catarrhini_hsap-projected.chr22.subset.nogap.cleaned_aln.maf.gz} (50%)
 create mode 100644 examples/Ztritici/Mgraminicolav2.FrozenGeneCatalog20080910.gff.gz
 create mode 100644 examples/Ztritici/tba_refIPO323.maf.gz
 rename man/{maffilter.1.txt => maffilter.1} (90%)

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