[med-svn] [libtabixpp] branch master updated (58408e0 -> 457e505)

[Sascha Steinbiss]

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sascha-guest pushed a change to branch master
in repository libtabixpp.

      from  58408e0   Stumbled upon this one at the end of the chain of dependencies of free-bayes; just fix the build for the moment
       new  8af1d9f   Imported Upstream version 0.0.20151117
       new  e17342b   Merge tag 'upstream/0.0.20151117'
       new  457e505   flesh out package a bit

The 3 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
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Summary of changes:
 .gitmodules                                   |   3 +
 ChangeLog                                     | 593 ---------------
 Makefile                                      |  90 +--
 NEWS                                          | 126 ----
 README                                        |   6 -
 README.md                                     |   5 +
 TabixReader.java                              | 395 ----------
 bam_endian.h                                  |  42 --
 bedidx.c                                      | 156 ----
 bgzf.c                                        | 714 ------------------
 bgzf.h                                        | 157 ----
 bgzip.c                                       | 206 ------
 debian/README.license                         |   3 +
 debian/changelog                              |   4 +-
 debian/control                                |  32 +-
 debian/libtabixpp-dev.links                   |   1 +
 debian/patches/build_with_debian_htslib.patch |  58 ++
 debian/patches/series                         |   1 +
 debian/rules                                  |  22 +-
 example.gtf.gz                                | Bin 3778 -> 0 bytes
 example.gtf.gz.tbi                            | Bin 259 -> 0 bytes
 index.c                                       | 998 --------------------------
 khash.h                                       | 486 -------------
 knetfile.c                                    | 632 ----------------
 knetfile.h                                    |  75 --
 kseq.h                                        | 227 ------
 ksort.h                                       | 271 -------
 kstring.c                                     | 165 -----
 kstring.h                                     |  68 --
 main.c                                        | 290 --------
 perl/MANIFEST                                 |   8 -
 perl/Makefile.PL                              |   8 -
 perl/Tabix.pm                                 |  76 --
 perl/Tabix.xs                                 |  71 --
 perl/TabixIterator.pm                         |  41 --
 perl/t/01local.t                              |  28 -
 perl/t/02remote.t                             |  28 -
 perl/typemap                                  |   3 -
 python/setup.py                               |  55 --
 python/tabixmodule.c                          | 408 -----------
 python/test.py                                |  91 ---
 tabix.1                                       | 132 ----
 tabix.cpp                                     |  85 ++-
 tabix.h                                       | 145 ----
 tabix.hpp                                     |  17 +-
 tabix.py                                      |  87 ---
 tabix.tex                                     | 121 ----
 47 files changed, 202 insertions(+), 7028 deletions(-)
 create mode 100644 .gitmodules
 delete mode 100644 ChangeLog
 delete mode 100644 NEWS
 delete mode 100644 README
 create mode 100644 README.md
 delete mode 100644 TabixReader.java
 delete mode 100644 bam_endian.h
 delete mode 100644 bedidx.c
 delete mode 100644 bgzf.c
 delete mode 100644 bgzf.h
 delete mode 100644 bgzip.c
 create mode 100644 debian/README.license
 create mode 100644 debian/libtabixpp-dev.links
 create mode 100644 debian/patches/build_with_debian_htslib.patch
 create mode 100644 debian/patches/series
 delete mode 100644 example.gtf.gz
 delete mode 100644 example.gtf.gz.tbi
 delete mode 100644 index.c
 delete mode 100644 khash.h
 delete mode 100644 knetfile.c
 delete mode 100644 knetfile.h
 delete mode 100644 kseq.h
 delete mode 100644 ksort.h
 delete mode 100644 kstring.c
 delete mode 100644 kstring.h
 delete mode 100644 main.c
 delete mode 100644 perl/MANIFEST
 delete mode 100644 perl/Makefile.PL
 delete mode 100644 perl/Tabix.pm
 delete mode 100644 perl/Tabix.xs
 delete mode 100644 perl/TabixIterator.pm
 delete mode 100644 perl/t/01local.t
 delete mode 100644 perl/t/02remote.t
 delete mode 100644 perl/typemap
 delete mode 100644 python/setup.py
 delete mode 100644 python/tabixmodule.c
 delete mode 100755 python/test.py
 delete mode 100644 tabix.1
 delete mode 100644 tabix.h
 delete mode 100755 tabix.py
 delete mode 100644 tabix.tex

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