[med-svn] [genometools] branch upstream updated (c743149 -> a131c3a)

Sascha Steinbiss sascha at steinbiss.name
Tue Mar 8 01:11:32 UTC 2016


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

sascha-guest pushed a change to branch upstream
in repository genometools.

      from  c743149   Imported Upstream version 1.5.8
       new  a131c3a   Imported Upstream version 1.5.8+ds

The 1 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:
 src/external/bzip2-1.0.6/CHANGES                   |    327 -
 src/external/bzip2-1.0.6/LICENSE                   |     42 -
 src/external/bzip2-1.0.6/Makefile                  |    217 -
 src/external/bzip2-1.0.6/Makefile-libbz2_so        |     59 -
 src/external/bzip2-1.0.6/README                    |    215 -
 .../bzip2-1.0.6/README.COMPILATION.PROBLEMS        |     58 -
 src/external/bzip2-1.0.6/README.XML.STUFF          |     45 -
 src/external/bzip2-1.0.6/blocksort.c               |   1094 -
 src/external/bzip2-1.0.6/bz-common.xsl             |     39 -
 src/external/bzip2-1.0.6/bz-fo.xsl                 |    276 -
 src/external/bzip2-1.0.6/bz-html.xsl               |     20 -
 src/external/bzip2-1.0.6/bzdiff                    |     76 -
 src/external/bzip2-1.0.6/bzdiff.1                  |     47 -
 src/external/bzip2-1.0.6/bzgrep                    |     75 -
 src/external/bzip2-1.0.6/bzgrep.1                  |     56 -
 src/external/bzip2-1.0.6/bzip.css                  |     74 -
 src/external/bzip2-1.0.6/bzip2.1                   |    454 -
 src/external/bzip2-1.0.6/bzip2.1.preformatted      |    399 -
 src/external/bzip2-1.0.6/bzip2.c                   |   2034 -
 src/external/bzip2-1.0.6/bzip2.txt                 |    391 -
 src/external/bzip2-1.0.6/bzip2recover.c            |    514 -
 src/external/bzip2-1.0.6/bzlib.c                   |   1572 -
 src/external/bzip2-1.0.6/bzlib.h                   |    282 -
 src/external/bzip2-1.0.6/bzlib_private.h           |    509 -
 src/external/bzip2-1.0.6/bzmore                    |     61 -
 src/external/bzip2-1.0.6/bzmore.1                  |    152 -
 src/external/bzip2-1.0.6/compress.c                |    672 -
 src/external/bzip2-1.0.6/crctable.c                |    104 -
 src/external/bzip2-1.0.6/decompress.c              |    646 -
 src/external/bzip2-1.0.6/dlltest.c                 |    175 -
 src/external/bzip2-1.0.6/dlltest.dsp               |     93 -
 src/external/bzip2-1.0.6/entities.xml              |      9 -
 src/external/bzip2-1.0.6/format.pl                 |     68 -
 src/external/bzip2-1.0.6/huffman.c                 |    205 -
 src/external/bzip2-1.0.6/libbz2.def                |     27 -
 src/external/bzip2-1.0.6/libbz2.dsp                |    130 -
 src/external/bzip2-1.0.6/makefile.msc              |     63 -
 src/external/bzip2-1.0.6/mk251.c                   |     31 -
 src/external/bzip2-1.0.6/randtable.c               |     84 -
 src/external/bzip2-1.0.6/spewG.c                   |     54 -
 src/external/bzip2-1.0.6/unzcrash.c                |    141 -
 src/external/bzip2-1.0.6/words0                    |      9 -
 src/external/bzip2-1.0.6/words1                    |      4 -
 src/external/bzip2-1.0.6/words2                    |      5 -
 src/external/bzip2-1.0.6/words3                    |     30 -
 src/external/bzip2-1.0.6/xmlproc.sh                |    114 -
 src/external/cgilua-5.1.3/Makefile                 |     21 -
 src/external/cgilua-5.1.3/Makefile.win             |     13 -
 src/external/cgilua-5.1.3/README                   |    119 -
 src/external/cgilua-5.1.3/doc/br/cgi-128.gif       |    Bin 4468 -> 0 bytes
 src/external/cgilua-5.1.3/doc/br/index.html        |    162 -
 src/external/cgilua-5.1.3/doc/br/libraries.html    |    143 -
 src/external/cgilua-5.1.3/doc/br/license.html      |    102 -
 src/external/cgilua-5.1.3/doc/br/manual.html       |    270 -
 src/external/cgilua-5.1.3/doc/br/reference.html    |    252 -
 src/external/cgilua-5.1.3/doc/br/sapi.html         |    152 -
 src/external/cgilua-5.1.3/doc/us/cgi-128.gif       |    Bin 4468 -> 0 bytes
 src/external/cgilua-5.1.3/doc/us/index.html        |    324 -
 src/external/cgilua-5.1.3/doc/us/libraries.html    |    255 -
 src/external/cgilua-5.1.3/doc/us/license.html      |    143 -
 src/external/cgilua-5.1.3/doc/us/manual.html       |    800 -
 src/external/cgilua-5.1.3/doc/us/reference.html    |    445 -
 src/external/cgilua-5.1.3/doc/us/sapi.html         |    236 -
 .../cgilua-5.1.3/examples/authentication_conf.lua  |    128 -
 src/external/cgilua-5.1.3/examples/check.lua       |     28 -
 src/external/cgilua-5.1.3/examples/login.lp        |     20 -
 .../cgilua-5.1.3/rockspec/cgilua-5.1.2-1.rockspec  |     33 -
 .../cgilua-5.1.3/rockspec/cgilua-5.1.2-2.rockspec  |     33 -
 .../rockspec/cgilua-5.1.2rc1-1.rockspec            |     33 -
 .../cgilua-5.1.3/rockspec/cgilua-5.1.3-1.rockspec  |     49 -
 .../cgilua-5.1.3/rockspec/cgilua-cvs-2.rockspec    |     29 -
 .../cgilua-5.1.3/rockspec/cgilua-cvs-3.rockspec    |     35 -
 .../cgilua-5.1.3/rockspec/cgilua-cvs-4.rockspec    |     51 -
 .../cgilua-5.1.3/src/cgilua/authentication.lua     |    219 -
 src/external/cgilua-5.1.3/src/cgilua/cgilua.lua    |    641 -
 src/external/cgilua-5.1.3/src/cgilua/cookies.lua   |    100 -
 .../cgilua-5.1.3/src/cgilua/dispatcher.lua         |     70 -
 src/external/cgilua-5.1.3/src/cgilua/loader.lua    |     91 -
 src/external/cgilua-5.1.3/src/cgilua/lp.lua        |    133 -
 src/external/cgilua-5.1.3/src/cgilua/mime.lua      |    174 -
 src/external/cgilua-5.1.3/src/cgilua/post.lua      |    293 -
 src/external/cgilua-5.1.3/src/cgilua/readuntil.lua |     44 -
 src/external/cgilua-5.1.3/src/cgilua/serialize.lua |    113 -
 src/external/cgilua-5.1.3/src/cgilua/session.lua   |    247 -
 src/external/cgilua-5.1.3/src/cgilua/urlcode.lua   |    100 -
 src/external/cgilua-5.1.3/tests/Makefile           |     18 -
 src/external/cgilua-5.1.3/tests/download.lua       |     75 -
 src/external/cgilua-5.1.3/tests/env.lua            |     26 -
 src/external/cgilua-5.1.3/tests/overview.lp        |     64 -
 src/external/cgilua-5.1.3/tests/prepara_sql2.lua   |     33 -
 src/external/cgilua-5.1.3/tests/tcgi1.lua          |     11 -
 src/external/cgilua-5.1.3/tests/test.html          |     78 -
 src/external/cgilua-5.1.3/tests/test_conc.lua      |     38 -
 src/external/cgilua-5.1.3/tests/test_cookies.lp    |     13 -
 src/external/cgilua-5.1.3/tests/test_cookies.lua   |     14 -
 src/external/cgilua-5.1.3/tests/test_err.lua       |      4 -
 src/external/cgilua-5.1.3/tests/test_fs.lua        |     23 -
 src/external/cgilua-5.1.3/tests/test_htk.lua       |     22 -
 src/external/cgilua-5.1.3/tests/test_lib.lua       |     31 -
 src/external/cgilua-5.1.3/tests/test_main.html     |    170 -
 src/external/cgilua-5.1.3/tests/test_main.lp       |     32 -
 src/external/cgilua-5.1.3/tests/test_main.lua      |     48 -
 src/external/cgilua-5.1.3/tests/test_session.lua   |     43 -
 src/external/cgilua-5.1.3/tests/test_sql.lua       |     13 -
 src/external/cgilua-5.1.3/tests/test_sql2.lua      |     24 -
 src/external/cgilua-5.1.3/tests/test_variables.lp  |     14 -
 src/external/cgilua-5.1.3/tests/tfcgi1.lua         |     10 -
 src/external/cgilua-5.1.3/tests/tmod1.lua          |     24 -
 src/external/expat-2.0.1/COPYING                   |     22 -
 src/external/expat-2.0.1/Changes                   |    169 -
 src/external/expat-2.0.1/MANIFEST                  |    128 -
 src/external/expat-2.0.1/README                    |    137 -
 src/external/expat-2.0.1/examples/elements.c       |     65 -
 src/external/expat-2.0.1/examples/elements.dsp     |    103 -
 src/external/expat-2.0.1/examples/outline.c        |    106 -
 src/external/expat-2.0.1/examples/outline.dsp      |    103 -
 src/external/expat-2.0.1/lib/Makefile.MPW          |    206 -
 src/external/expat-2.0.1/lib/amigaconfig.h         |     32 -
 src/external/expat-2.0.1/lib/ascii.h               |     92 -
 src/external/expat-2.0.1/lib/asciitab.h            |     36 -
 src/external/expat-2.0.1/lib/expat.dsp             |    185 -
 src/external/expat-2.0.1/lib/expat.h               |   1014 -
 src/external/expat-2.0.1/lib/expat_external.h      |    115 -
 src/external/expat-2.0.1/lib/expat_static.dsp      |    162 -
 src/external/expat-2.0.1/lib/expatw.dsp            |    185 -
 src/external/expat-2.0.1/lib/expatw_static.dsp     |    162 -
 src/external/expat-2.0.1/lib/iasciitab.h           |     37 -
 src/external/expat-2.0.1/lib/internal.h            |     73 -
 src/external/expat-2.0.1/lib/latin1tab.h           |     36 -
 src/external/expat-2.0.1/lib/libexpat.def          |     73 -
 src/external/expat-2.0.1/lib/libexpatw.def         |     73 -
 src/external/expat-2.0.1/lib/macconfig.h           |     53 -
 src/external/expat-2.0.1/lib/nametab.h             |    150 -
 src/external/expat-2.0.1/lib/utf8tab.h             |     37 -
 src/external/expat-2.0.1/lib/winconfig.h           |     30 -
 src/external/expat-2.0.1/lib/xmlparse.c            |   6296 -
 src/external/expat-2.0.1/lib/xmlrole.c             |   1336 -
 src/external/expat-2.0.1/lib/xmlrole.h             |    114 -
 src/external/expat-2.0.1/lib/xmltok.c              |   1652 -
 src/external/expat-2.0.1/lib/xmltok.h              |    316 -
 src/external/expat-2.0.1/lib/xmltok_impl.c         |   1783 -
 src/external/expat-2.0.1/lib/xmltok_impl.h         |     46 -
 src/external/expat-2.0.1/lib/xmltok_ns.c           |    115 -
 src/external/lpeg-0.10.2/HISTORY                   |     77 -
 src/external/lpeg-0.10.2/lpeg-128.gif              |    Bin 4923 -> 0 bytes
 src/external/lpeg-0.10.2/lpeg.c                    |   2405 -
 src/external/lpeg-0.10.2/lpeg.h                    |     39 -
 src/external/lpeg-0.10.2/lpeg.html                 |   1423 -
 src/external/lpeg-0.10.2/makefile                  |     42 -
 src/external/lpeg-0.10.2/re.html                   |    486 -
 src/external/lpeg-0.10.2/re.lua                    |    248 -
 src/external/lpeg-0.10.2/test.lua                  |   1188 -
 src/external/lua-5.1.5/COPYRIGHT                   |     34 -
 src/external/lua-5.1.5/HISTORY                     |    183 -
 src/external/lua-5.1.5/INSTALL                     |     99 -
 src/external/lua-5.1.5/Makefile                    |    128 -
 src/external/lua-5.1.5/README                      |     37 -
 src/external/lua-5.1.5/doc/contents.html           |    497 -
 src/external/lua-5.1.5/doc/cover.png               |    Bin 3305 -> 0 bytes
 src/external/lua-5.1.5/doc/logo.gif                |    Bin 4232 -> 0 bytes
 src/external/lua-5.1.5/doc/lua.1                   |    163 -
 src/external/lua-5.1.5/doc/lua.css                 |     83 -
 src/external/lua-5.1.5/doc/lua.html                |    172 -
 src/external/lua-5.1.5/doc/luac.1                  |    136 -
 src/external/lua-5.1.5/doc/luac.html               |    145 -
 src/external/lua-5.1.5/doc/manual.css              |     24 -
 src/external/lua-5.1.5/doc/manual.html             |   8804 -
 src/external/lua-5.1.5/doc/readme.html             |     40 -
 src/external/lua-5.1.5/etc/Makefile                |     44 -
 src/external/lua-5.1.5/etc/README                  |     37 -
 src/external/lua-5.1.5/etc/all.c                   |     38 -
 src/external/lua-5.1.5/etc/lua.hpp                 |      9 -
 src/external/lua-5.1.5/etc/lua.ico                 |    Bin 1078 -> 0 bytes
 src/external/lua-5.1.5/etc/lua.pc                  |     31 -
 src/external/lua-5.1.5/etc/luavs.bat               |     28 -
 src/external/lua-5.1.5/etc/min.c                   |     39 -
 src/external/lua-5.1.5/etc/noparser.c              |     50 -
 src/external/lua-5.1.5/etc/strict.lua              |     41 -
 src/external/lua-5.1.5/src/Makefile                |    182 -
 src/external/lua-5.1.5/src/lapi.c                  |   1087 -
 src/external/lua-5.1.5/src/lapi.h                  |     16 -
 src/external/lua-5.1.5/src/lauxlib.c               |    653 -
 src/external/lua-5.1.5/src/lauxlib.h               |    174 -
 src/external/lua-5.1.5/src/lbaselib.c              |    653 -
 src/external/lua-5.1.5/src/lcode.c                 |    831 -
 src/external/lua-5.1.5/src/lcode.h                 |     76 -
 src/external/lua-5.1.5/src/ldblib.c                |    398 -
 src/external/lua-5.1.5/src/ldebug.c                |    638 -
 src/external/lua-5.1.5/src/ldebug.h                |     33 -
 src/external/lua-5.1.5/src/ldo.c                   |    519 -
 src/external/lua-5.1.5/src/ldo.h                   |     57 -
 src/external/lua-5.1.5/src/ldump.c                 |    164 -
 src/external/lua-5.1.5/src/lfunc.c                 |    174 -
 src/external/lua-5.1.5/src/lfunc.h                 |     34 -
 src/external/lua-5.1.5/src/lgc.c                   |    710 -
 src/external/lua-5.1.5/src/lgc.h                   |    110 -
 src/external/lua-5.1.5/src/linit.c                 |     38 -
 src/external/lua-5.1.5/src/liolib.c                |    556 -
 src/external/lua-5.1.5/src/llex.c                  |    463 -
 src/external/lua-5.1.5/src/llex.h                  |     81 -
 src/external/lua-5.1.5/src/llimits.h               |    128 -
 src/external/lua-5.1.5/src/lmathlib.c              |    263 -
 src/external/lua-5.1.5/src/lmem.c                  |     86 -
 src/external/lua-5.1.5/src/lmem.h                  |     49 -
 src/external/lua-5.1.5/src/loadlib.c               |    666 -
 src/external/lua-5.1.5/src/lobject.c               |    214 -
 src/external/lua-5.1.5/src/lobject.h               |    381 -
 src/external/lua-5.1.5/src/lopcodes.c              |    102 -
 src/external/lua-5.1.5/src/lopcodes.h              |    268 -
 src/external/lua-5.1.5/src/loslib.c                |    243 -
 src/external/lua-5.1.5/src/lparser.c               |   1339 -
 src/external/lua-5.1.5/src/lparser.h               |     82 -
 src/external/lua-5.1.5/src/lstate.c                |    214 -
 src/external/lua-5.1.5/src/lstate.h                |    169 -
 src/external/lua-5.1.5/src/lstring.c               |    111 -
 src/external/lua-5.1.5/src/lstring.h               |     31 -
 src/external/lua-5.1.5/src/lstrlib.c               |    871 -
 src/external/lua-5.1.5/src/ltable.c                |    588 -
 src/external/lua-5.1.5/src/ltable.h                |     40 -
 src/external/lua-5.1.5/src/ltablib.c               |    287 -
 src/external/lua-5.1.5/src/ltm.c                   |     75 -
 src/external/lua-5.1.5/src/ltm.h                   |     54 -
 src/external/lua-5.1.5/src/lua.c                   |    392 -
 src/external/lua-5.1.5/src/lua.h                   |    388 -
 src/external/lua-5.1.5/src/luac.c                  |    200 -
 src/external/lua-5.1.5/src/luaconf.h               |    763 -
 src/external/lua-5.1.5/src/lualib.h                |     53 -
 src/external/lua-5.1.5/src/lundump.c               |    227 -
 src/external/lua-5.1.5/src/lundump.h               |     36 -
 src/external/lua-5.1.5/src/lvm.c                   |    767 -
 src/external/lua-5.1.5/src/lvm.h                   |     36 -
 src/external/lua-5.1.5/src/lzio.c                  |     82 -
 src/external/lua-5.1.5/src/lzio.h                  |     67 -
 src/external/lua-5.1.5/src/print.c                 |    227 -
 src/external/lua-5.1.5/test/README                 |     26 -
 src/external/lua-5.1.5/test/bisect.lua             |     27 -
 src/external/lua-5.1.5/test/cf.lua                 |     16 -
 src/external/lua-5.1.5/test/echo.lua               |      5 -
 src/external/lua-5.1.5/test/env.lua                |      7 -
 src/external/lua-5.1.5/test/factorial.lua          |     32 -
 src/external/lua-5.1.5/test/fib.lua                |     40 -
 src/external/lua-5.1.5/test/fibfor.lua             |     13 -
 src/external/lua-5.1.5/test/globals.lua            |     13 -
 src/external/lua-5.1.5/test/hello.lua              |      3 -
 src/external/lua-5.1.5/test/life.lua               |    111 -
 src/external/lua-5.1.5/test/luac.lua               |      7 -
 src/external/lua-5.1.5/test/printf.lua             |      7 -
 src/external/lua-5.1.5/test/readonly.lua           |     12 -
 src/external/lua-5.1.5/test/sieve.lua              |     29 -
 src/external/lua-5.1.5/test/sort.lua               |     66 -
 src/external/lua-5.1.5/test/table.lua              |     12 -
 src/external/lua-5.1.5/test/trace-calls.lua        |     32 -
 src/external/lua-5.1.5/test/trace-globals.lua      |     38 -
 src/external/lua-5.1.5/test/xd.lua                 |     14 -
 src/external/luafilesystem-1.5.0/Makefile          |     22 -
 src/external/luafilesystem-1.5.0/Makefile.win      |     25 -
 src/external/luafilesystem-1.5.0/README            |     66 -
 src/external/luafilesystem-1.5.0/config            |     24 -
 src/external/luafilesystem-1.5.0/config.win        |     19 -
 .../luafilesystem-1.5.0/doc/us/examples.html       |    103 -
 src/external/luafilesystem-1.5.0/doc/us/index.html |    192 -
 .../luafilesystem-1.5.0/doc/us/license.html        |    122 -
 .../luafilesystem-1.5.0/doc/us/luafilesystem.png   |    Bin 8535 -> 0 bytes
 .../luafilesystem-1.5.0/doc/us/manual.html         |    271 -
 .../rockspecs/luafilesystem-1.3.0-1.rockspec       |     27 -
 .../rockspecs/luafilesystem-1.4.0-1.rockspec       |     27 -
 .../rockspecs/luafilesystem-1.4.0-2.rockspec       |     43 -
 .../rockspecs/luafilesystem-1.4.1-1.rockspec       |     43 -
 .../rockspecs/luafilesystem-1.4.1rc1-1.rockspec    |     43 -
 .../rockspecs/luafilesystem-1.4.2-1.rockspec       |     26 -
 .../rockspecs/luafilesystem-1.5.0-1.rockspec       |     27 -
 .../rockspecs/luafilesystem-cvs-1.rockspec         |     44 -
 .../rockspecs/luafilesystem-cvs-2.rockspec         |     26 -
 src/external/luafilesystem-1.5.0/src/lfs.c         |    802 -
 src/external/luafilesystem-1.5.0/src/lfs.def       |      5 -
 src/external/luafilesystem-1.5.0/src/lfs.h         |     17 -
 src/external/luafilesystem-1.5.0/tests/test.lua    |    130 -
 src/external/luafilesystem-1.5.0/vc6/lfs.def       |      5 -
 .../luafilesystem-1.5.0/vc6/luafilesystem.dsw      |     33 -
 .../luafilesystem-1.5.0/vc6/luafilesystem_dll.dsp  |    127 -
 src/external/md5-1.1.2/Makefile                    |     37 -
 src/external/md5-1.1.2/Makefile.win                |     35 -
 src/external/md5-1.1.2/README                      |     32 -
 src/external/md5-1.1.2/config                      |     32 -
 src/external/md5-1.1.2/config.win                  |     23 -
 src/external/md5-1.1.2/configure                   |     27 -
 src/external/md5-1.1.2/doc/us/index.html           |    172 -
 src/external/md5-1.1.2/doc/us/license.html         |    122 -
 src/external/md5-1.1.2/doc/us/manual.html          |    229 -
 src/external/md5-1.1.2/doc/us/md5.png              |    Bin 4121 -> 0 bytes
 .../md5-1.1.2/rockspec/md5-1.1.1-1.rockspec        |     31 -
 .../md5-1.1.2/rockspec/md5-1.1.2-1.rockspec        |     39 -
 src/external/md5-1.1.2/rockspec/md5-cvs-1.rockspec |     39 -
 src/external/md5-1.1.2/src/des56.c                 |    548 -
 src/external/md5-1.1.2/src/des56.def               |      5 -
 src/external/md5-1.1.2/src/des56.h                 |     77 -
 src/external/md5-1.1.2/src/ldes56.c                |    152 -
 src/external/md5-1.1.2/src/ldes56.h                |      1 -
 src/external/md5-1.1.2/src/md5.c                   |    214 -
 src/external/md5-1.1.2/src/md5.def                 |      5 -
 src/external/md5-1.1.2/src/md5.h                   |     20 -
 src/external/md5-1.1.2/src/md5lib.c                |    203 -
 src/external/md5-1.1.2/tests/DES56/Makefile        |     30 -
 src/external/md5-1.1.2/tests/DES56/fdemo.c         |    178 -
 src/external/md5-1.1.2/tests/DES56/ftest.c         |    211 -
 src/external/md5-1.1.2/tests/test.lua              |    109 -
 src/external/md5-1.1.2/vc6/md5.def                 |      5 -
 src/external/md5-1.1.2/vc6/md5.dsw                 |     33 -
 src/external/md5-1.1.2/vc6/md5_dll.dsp             |    130 -
 src/external/samtools-0.1.18/AUTHORS               |     20 -
 src/external/samtools-0.1.18/COPYING               |     21 -
 src/external/samtools-0.1.18/ChangeLog             |   5948 -
 src/external/samtools-0.1.18/INSTALL               |     30 -
 src/external/samtools-0.1.18/Makefile              |     93 -
 src/external/samtools-0.1.18/Makefile.mingw        |     63 -
 src/external/samtools-0.1.18/NEWS                  |    806 -
 src/external/samtools-0.1.18/bam.c                 |    362 -
 src/external/samtools-0.1.18/bam.h                 |    767 -
 src/external/samtools-0.1.18/bam2bcf.c             |    351 -
 src/external/samtools-0.1.18/bam2bcf.h             |     57 -
 src/external/samtools-0.1.18/bam2bcf_indel.c       |    475 -
 src/external/samtools-0.1.18/bam2depth.c           |    112 -
 src/external/samtools-0.1.18/bam_aux.c             |    213 -
 src/external/samtools-0.1.18/bam_cat.c             |    184 -
 src/external/samtools-0.1.18/bam_color.c           |    127 -
 src/external/samtools-0.1.18/bam_endian.h          |     42 -
 src/external/samtools-0.1.18/bam_import.c          |    485 -
 src/external/samtools-0.1.18/bam_index.c           |    719 -
 src/external/samtools-0.1.18/bam_lpileup.c         |    198 -
 src/external/samtools-0.1.18/bam_mate.c            |     70 -
 src/external/samtools-0.1.18/bam_md.c              |    384 -
 src/external/samtools-0.1.18/bam_pileup.c          |    437 -
 src/external/samtools-0.1.18/bam_plcmd.c           |    546 -
 src/external/samtools-0.1.18/bam_reheader.c        |     61 -
 src/external/samtools-0.1.18/bam_rmdup.c           |    206 -
 src/external/samtools-0.1.18/bam_rmdupse.c         |    159 -
 src/external/samtools-0.1.18/bam_sort.c            |    438 -
 src/external/samtools-0.1.18/bam_stat.c            |     77 -
 src/external/samtools-0.1.18/bam_tview.c           |    440 -
 src/external/samtools-0.1.18/bamtk.c               |    109 -
 src/external/samtools-0.1.18/bcftools/Makefile     |     51 -
 src/external/samtools-0.1.18/bcftools/README       |     36 -
 src/external/samtools-0.1.18/bcftools/bcf.c        |    328 -
 src/external/samtools-0.1.18/bcftools/bcf.h        |    190 -
 src/external/samtools-0.1.18/bcftools/bcf.tex      |     77 -
 src/external/samtools-0.1.18/bcftools/bcf2qcall.c  |     91 -
 src/external/samtools-0.1.18/bcftools/bcfutils.c   |    390 -
 src/external/samtools-0.1.18/bcftools/call1.c      |    586 -
 src/external/samtools-0.1.18/bcftools/em.c         |    310 -
 src/external/samtools-0.1.18/bcftools/fet.c        |    112 -
 src/external/samtools-0.1.18/bcftools/index.c      |    335 -
 src/external/samtools-0.1.18/bcftools/kfunc.c      |    162 -
 src/external/samtools-0.1.18/bcftools/kmin.c       |    209 -
 src/external/samtools-0.1.18/bcftools/kmin.h       |     46 -
 src/external/samtools-0.1.18/bcftools/main.c       |    190 -
 src/external/samtools-0.1.18/bcftools/mut.c        |    127 -
 src/external/samtools-0.1.18/bcftools/prob1.c      |    554 -
 src/external/samtools-0.1.18/bcftools/prob1.h      |     42 -
 src/external/samtools-0.1.18/bcftools/vcf.c        |    244 -
 src/external/samtools-0.1.18/bcftools/vcfutils.pl  |    567 -
 src/external/samtools-0.1.18/bedidx.c              |    162 -
 src/external/samtools-0.1.18/bgzf.c                |    717 -
 src/external/samtools-0.1.18/bgzf.h                |    167 -
 src/external/samtools-0.1.18/bgzip.c               |    206 -
 src/external/samtools-0.1.18/cut_target.c          |    193 -
 src/external/samtools-0.1.18/errmod.c              |    130 -
 src/external/samtools-0.1.18/errmod.h              |     24 -
 src/external/samtools-0.1.18/examples/00README.txt |     23 -
 src/external/samtools-0.1.18/examples/Makefile     |     50 -
 src/external/samtools-0.1.18/examples/bam2bed.c    |     51 -
 src/external/samtools-0.1.18/examples/calDepth.c   |     62 -
 src/external/samtools-0.1.18/examples/ex1.fa       |     56 -
 src/external/samtools-0.1.18/examples/ex1.sam.gz   |    Bin 114565 -> 0 bytes
 src/external/samtools-0.1.18/examples/toy.fa       |      4 -
 src/external/samtools-0.1.18/examples/toy.sam      |     14 -
 src/external/samtools-0.1.18/faidx.c               |    432 -
 src/external/samtools-0.1.18/faidx.h               |    103 -
 src/external/samtools-0.1.18/kaln.c                |    486 -
 src/external/samtools-0.1.18/kaln.h                |     67 -
 src/external/samtools-0.1.18/khash.h               |    528 -
 src/external/samtools-0.1.18/klist.h               |     96 -
 src/external/samtools-0.1.18/knetfile.c            |    632 -
 src/external/samtools-0.1.18/knetfile.h            |     75 -
 src/external/samtools-0.1.18/kprobaln.c            |    278 -
 src/external/samtools-0.1.18/kprobaln.h            |     49 -
 src/external/samtools-0.1.18/kseq.h                |    224 -
 src/external/samtools-0.1.18/ksort.h               |    281 -
 src/external/samtools-0.1.18/kstring.c             |    212 -
 src/external/samtools-0.1.18/kstring.h             |    117 -
 src/external/samtools-0.1.18/misc/HmmGlocal.java   |    178 -
 src/external/samtools-0.1.18/misc/Makefile         |     63 -
 src/external/samtools-0.1.18/misc/blast2sam.pl     |     92 -
 src/external/samtools-0.1.18/misc/bowtie2sam.pl    |     92 -
 src/external/samtools-0.1.18/misc/export2sam.pl    |    545 -
 .../samtools-0.1.18/misc/interpolate_sam.pl        |    125 -
 src/external/samtools-0.1.18/misc/maq2sam.c        |    173 -
 src/external/samtools-0.1.18/misc/md5.c            |    296 -
 src/external/samtools-0.1.18/misc/md5.h            |     57 -
 src/external/samtools-0.1.18/misc/md5fa.c          |     58 -
 src/external/samtools-0.1.18/misc/novo2sam.pl      |    281 -
 src/external/samtools-0.1.18/misc/psl2sam.pl       |     65 -
 src/external/samtools-0.1.18/misc/sam2vcf.pl       |    270 -
 src/external/samtools-0.1.18/misc/samtools.pl      |    528 -
 src/external/samtools-0.1.18/misc/seqtk.c          |    783 -
 src/external/samtools-0.1.18/misc/soap2sam.pl      |    109 -
 src/external/samtools-0.1.18/misc/varfilter.py     |    205 -
 src/external/samtools-0.1.18/misc/wgsim.c          |    419 -
 src/external/samtools-0.1.18/misc/wgsim_eval.pl    |     91 -
 src/external/samtools-0.1.18/misc/zoom2sam.pl      |     97 -
 src/external/samtools-0.1.18/phase.c               |    687 -
 src/external/samtools-0.1.18/razf.c                |    853 -
 src/external/samtools-0.1.18/razf.h                |    134 -
 src/external/samtools-0.1.18/razip.c               |    141 -
 src/external/samtools-0.1.18/sam.c                 |    179 -
 src/external/samtools-0.1.18/sam.h                 |    100 -
 src/external/samtools-0.1.18/sam_header.c          |    736 -
 src/external/samtools-0.1.18/sam_header.h          |     24 -
 src/external/samtools-0.1.18/sam_view.c            |    406 -
 src/external/samtools-0.1.18/sample.c              |    107 -
 src/external/samtools-0.1.18/sample.h              |     17 -
 src/external/samtools-0.1.18/win32/xcurses.h       |   1377 -
 src/external/samtools-0.1.18/win32/zconf.h         |    332 -
 src/external/samtools-0.1.18/win32/zlib.h          |   1357 -
 src/external/sqlite-3.8.7.1/sqlite3.c              | 151638 ------------------
 src/external/sqlite-3.8.7.1/sqlite3.h              |   7543 -
 src/external/sqlite-3.8.7.1/sqlite3ext.h           |    517 -
 src/external/tre/.gitignore                        |     26 -
 src/external/tre/LICENSE                           |     29 -
 src/external/tre/README                            |    235 -
 src/external/tre/include/tre/tre-config.h          |    196 -
 src/external/tre/include/tre/tre.h                 |    276 -
 src/external/tre/lib/README                        |     69 -
 src/external/tre/lib/regcomp.c                     |    129 -
 src/external/tre/lib/regerror.c                    |     83 -
 src/external/tre/lib/regex.h                       |     38 -
 src/external/tre/lib/regexec.c                     |    348 -
 src/external/tre/lib/tre-ast.c                     |    226 -
 src/external/tre/lib/tre-ast.h                     |    129 -
 src/external/tre/lib/tre-compile.c                 |   2297 -
 src/external/tre/lib/tre-compile.h                 |     27 -
 src/external/tre/lib/tre-config.h.in               |     43 -
 src/external/tre/lib/tre-filter.c                  |     73 -
 src/external/tre/lib/tre-filter.h                  |     19 -
 src/external/tre/lib/tre-internal.h                |    287 -
 src/external/tre/lib/tre-match-backtrack.c         |    666 -
 src/external/tre/lib/tre-match-parallel.c          |    502 -
 src/external/tre/lib/tre-match-utils.h             |    215 -
 src/external/tre/lib/tre-mem.c                     |    156 -
 src/external/tre/lib/tre-mem.h                     |     66 -
 src/external/tre/lib/tre-parse.c                   |   1739 -
 src/external/tre/lib/tre-parse.h                   |     50 -
 src/external/tre/lib/tre-stack.c                   |    125 -
 src/external/tre/lib/tre-stack.h                   |     76 -
 src/external/tre/lib/tre.h                         |    276 -
 src/external/tre/lib/xmalloc.c                     |    352 -
 src/external/tre/lib/xmalloc.h                     |     77 -
 src/external/zlib-1.2.8/README                     |    115 -
 src/external/zlib-1.2.8/adler32.c                  |    179 -
 src/external/zlib-1.2.8/compress.c                 |     80 -
 src/external/zlib-1.2.8/crc32.c                    |    425 -
 src/external/zlib-1.2.8/crc32.h                    |    441 -
 src/external/zlib-1.2.8/deflate.c                  |   1967 -
 src/external/zlib-1.2.8/deflate.h                  |    346 -
 src/external/zlib-1.2.8/gzclose.c                  |     25 -
 src/external/zlib-1.2.8/gzguts.h                   |    209 -
 src/external/zlib-1.2.8/gzlib.c                    |    634 -
 src/external/zlib-1.2.8/gzread.c                   |    594 -
 src/external/zlib-1.2.8/gzwrite.c                  |    577 -
 src/external/zlib-1.2.8/infback.c                  |    640 -
 src/external/zlib-1.2.8/inffast.c                  |    340 -
 src/external/zlib-1.2.8/inffast.h                  |     11 -
 src/external/zlib-1.2.8/inffixed.h                 |     94 -
 src/external/zlib-1.2.8/inflate.c                  |   1512 -
 src/external/zlib-1.2.8/inflate.h                  |    122 -
 src/external/zlib-1.2.8/inftrees.c                 |    306 -
 src/external/zlib-1.2.8/inftrees.h                 |     62 -
 src/external/zlib-1.2.8/trees.c                    |   1226 -
 src/external/zlib-1.2.8/trees.h                    |    128 -
 src/external/zlib-1.2.8/uncompr.c                  |     59 -
 src/external/zlib-1.2.8/zconf.h                    |    513 -
 src/external/zlib-1.2.8/zlib.h                     |   1768 -
 src/external/zlib-1.2.8/zutil.c                    |    324 -
 src/external/zlib-1.2.8/zutil.h                    |    253 -
 483 files changed, 289898 deletions(-)
 delete mode 100644 src/external/bzip2-1.0.6/CHANGES
 delete mode 100644 src/external/bzip2-1.0.6/LICENSE
 delete mode 100644 src/external/bzip2-1.0.6/Makefile
 delete mode 100644 src/external/bzip2-1.0.6/Makefile-libbz2_so
 delete mode 100644 src/external/bzip2-1.0.6/README
 delete mode 100644 src/external/bzip2-1.0.6/README.COMPILATION.PROBLEMS
 delete mode 100644 src/external/bzip2-1.0.6/README.XML.STUFF
 delete mode 100644 src/external/bzip2-1.0.6/blocksort.c
 delete mode 100644 src/external/bzip2-1.0.6/bz-common.xsl
 delete mode 100644 src/external/bzip2-1.0.6/bz-fo.xsl
 delete mode 100644 src/external/bzip2-1.0.6/bz-html.xsl
 delete mode 100644 src/external/bzip2-1.0.6/bzdiff
 delete mode 100644 src/external/bzip2-1.0.6/bzdiff.1
 delete mode 100644 src/external/bzip2-1.0.6/bzgrep
 delete mode 100644 src/external/bzip2-1.0.6/bzgrep.1
 delete mode 100644 src/external/bzip2-1.0.6/bzip.css
 delete mode 100644 src/external/bzip2-1.0.6/bzip2.1
 delete mode 100644 src/external/bzip2-1.0.6/bzip2.1.preformatted
 delete mode 100644 src/external/bzip2-1.0.6/bzip2.c
 delete mode 100644 src/external/bzip2-1.0.6/bzip2.txt
 delete mode 100644 src/external/bzip2-1.0.6/bzip2recover.c
 delete mode 100644 src/external/bzip2-1.0.6/bzlib.c
 delete mode 100644 src/external/bzip2-1.0.6/bzlib.h
 delete mode 100644 src/external/bzip2-1.0.6/bzlib_private.h
 delete mode 100644 src/external/bzip2-1.0.6/bzmore
 delete mode 100644 src/external/bzip2-1.0.6/bzmore.1
 delete mode 100644 src/external/bzip2-1.0.6/compress.c
 delete mode 100644 src/external/bzip2-1.0.6/crctable.c
 delete mode 100644 src/external/bzip2-1.0.6/decompress.c
 delete mode 100644 src/external/bzip2-1.0.6/dlltest.c
 delete mode 100644 src/external/bzip2-1.0.6/dlltest.dsp
 delete mode 100644 src/external/bzip2-1.0.6/entities.xml
 delete mode 100755 src/external/bzip2-1.0.6/format.pl
 delete mode 100644 src/external/bzip2-1.0.6/huffman.c
 delete mode 100644 src/external/bzip2-1.0.6/libbz2.def
 delete mode 100644 src/external/bzip2-1.0.6/libbz2.dsp
 delete mode 100644 src/external/bzip2-1.0.6/makefile.msc
 delete mode 100644 src/external/bzip2-1.0.6/mk251.c
 delete mode 100644 src/external/bzip2-1.0.6/randtable.c
 delete mode 100644 src/external/bzip2-1.0.6/spewG.c
 delete mode 100644 src/external/bzip2-1.0.6/unzcrash.c
 delete mode 100644 src/external/bzip2-1.0.6/words0
 delete mode 100644 src/external/bzip2-1.0.6/words1
 delete mode 100644 src/external/bzip2-1.0.6/words2
 delete mode 100644 src/external/bzip2-1.0.6/words3
 delete mode 100755 src/external/bzip2-1.0.6/xmlproc.sh
 delete mode 100644 src/external/cgilua-5.1.3/Makefile
 delete mode 100644 src/external/cgilua-5.1.3/Makefile.win
 delete mode 100644 src/external/cgilua-5.1.3/README
 delete mode 100644 src/external/cgilua-5.1.3/doc/br/cgi-128.gif
 delete mode 100644 src/external/cgilua-5.1.3/doc/br/index.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/br/libraries.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/br/license.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/br/manual.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/br/reference.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/br/sapi.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/us/cgi-128.gif
 delete mode 100644 src/external/cgilua-5.1.3/doc/us/index.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/us/libraries.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/us/license.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/us/manual.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/us/reference.html
 delete mode 100644 src/external/cgilua-5.1.3/doc/us/sapi.html
 delete mode 100644 src/external/cgilua-5.1.3/examples/authentication_conf.lua
 delete mode 100644 src/external/cgilua-5.1.3/examples/check.lua
 delete mode 100644 src/external/cgilua-5.1.3/examples/login.lp
 delete mode 100644 src/external/cgilua-5.1.3/rockspec/cgilua-5.1.2-1.rockspec
 delete mode 100644 src/external/cgilua-5.1.3/rockspec/cgilua-5.1.2-2.rockspec
 delete mode 100644 src/external/cgilua-5.1.3/rockspec/cgilua-5.1.2rc1-1.rockspec
 delete mode 100644 src/external/cgilua-5.1.3/rockspec/cgilua-5.1.3-1.rockspec
 delete mode 100644 src/external/cgilua-5.1.3/rockspec/cgilua-cvs-2.rockspec
 delete mode 100644 src/external/cgilua-5.1.3/rockspec/cgilua-cvs-3.rockspec
 delete mode 100644 src/external/cgilua-5.1.3/rockspec/cgilua-cvs-4.rockspec
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/authentication.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/cgilua.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/cookies.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/dispatcher.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/loader.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/lp.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/mime.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/post.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/readuntil.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/serialize.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/session.lua
 delete mode 100644 src/external/cgilua-5.1.3/src/cgilua/urlcode.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/Makefile
 delete mode 100644 src/external/cgilua-5.1.3/tests/download.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/env.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/overview.lp
 delete mode 100644 src/external/cgilua-5.1.3/tests/prepara_sql2.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/tcgi1.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test.html
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_conc.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_cookies.lp
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_cookies.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_err.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_fs.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_htk.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_lib.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_main.html
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_main.lp
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_main.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_session.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_sql.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_sql2.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/test_variables.lp
 delete mode 100644 src/external/cgilua-5.1.3/tests/tfcgi1.lua
 delete mode 100644 src/external/cgilua-5.1.3/tests/tmod1.lua
 delete mode 100644 src/external/expat-2.0.1/COPYING
 delete mode 100644 src/external/expat-2.0.1/Changes
 delete mode 100644 src/external/expat-2.0.1/MANIFEST
 delete mode 100644 src/external/expat-2.0.1/README
 delete mode 100644 src/external/expat-2.0.1/examples/elements.c
 delete mode 100644 src/external/expat-2.0.1/examples/elements.dsp
 delete mode 100644 src/external/expat-2.0.1/examples/outline.c
 delete mode 100644 src/external/expat-2.0.1/examples/outline.dsp
 delete mode 100644 src/external/expat-2.0.1/lib/Makefile.MPW
 delete mode 100644 src/external/expat-2.0.1/lib/amigaconfig.h
 delete mode 100644 src/external/expat-2.0.1/lib/ascii.h
 delete mode 100644 src/external/expat-2.0.1/lib/asciitab.h
 delete mode 100644 src/external/expat-2.0.1/lib/expat.dsp
 delete mode 100644 src/external/expat-2.0.1/lib/expat.h
 delete mode 100644 src/external/expat-2.0.1/lib/expat_external.h
 delete mode 100644 src/external/expat-2.0.1/lib/expat_static.dsp
 delete mode 100644 src/external/expat-2.0.1/lib/expatw.dsp
 delete mode 100644 src/external/expat-2.0.1/lib/expatw_static.dsp
 delete mode 100644 src/external/expat-2.0.1/lib/iasciitab.h
 delete mode 100644 src/external/expat-2.0.1/lib/internal.h
 delete mode 100644 src/external/expat-2.0.1/lib/latin1tab.h
 delete mode 100644 src/external/expat-2.0.1/lib/libexpat.def
 delete mode 100644 src/external/expat-2.0.1/lib/libexpatw.def
 delete mode 100644 src/external/expat-2.0.1/lib/macconfig.h
 delete mode 100644 src/external/expat-2.0.1/lib/nametab.h
 delete mode 100644 src/external/expat-2.0.1/lib/utf8tab.h
 delete mode 100644 src/external/expat-2.0.1/lib/winconfig.h
 delete mode 100644 src/external/expat-2.0.1/lib/xmlparse.c
 delete mode 100644 src/external/expat-2.0.1/lib/xmlrole.c
 delete mode 100644 src/external/expat-2.0.1/lib/xmlrole.h
 delete mode 100644 src/external/expat-2.0.1/lib/xmltok.c
 delete mode 100644 src/external/expat-2.0.1/lib/xmltok.h
 delete mode 100644 src/external/expat-2.0.1/lib/xmltok_impl.c
 delete mode 100644 src/external/expat-2.0.1/lib/xmltok_impl.h
 delete mode 100644 src/external/expat-2.0.1/lib/xmltok_ns.c
 delete mode 100644 src/external/lpeg-0.10.2/HISTORY
 delete mode 100644 src/external/lpeg-0.10.2/lpeg-128.gif
 delete mode 100644 src/external/lpeg-0.10.2/lpeg.c
 delete mode 100644 src/external/lpeg-0.10.2/lpeg.h
 delete mode 100644 src/external/lpeg-0.10.2/lpeg.html
 delete mode 100644 src/external/lpeg-0.10.2/makefile
 delete mode 100644 src/external/lpeg-0.10.2/re.html
 delete mode 100644 src/external/lpeg-0.10.2/re.lua
 delete mode 100755 src/external/lpeg-0.10.2/test.lua
 delete mode 100644 src/external/lua-5.1.5/COPYRIGHT
 delete mode 100644 src/external/lua-5.1.5/HISTORY
 delete mode 100644 src/external/lua-5.1.5/INSTALL
 delete mode 100644 src/external/lua-5.1.5/Makefile
 delete mode 100644 src/external/lua-5.1.5/README
 delete mode 100644 src/external/lua-5.1.5/doc/contents.html
 delete mode 100644 src/external/lua-5.1.5/doc/cover.png
 delete mode 100644 src/external/lua-5.1.5/doc/logo.gif
 delete mode 100644 src/external/lua-5.1.5/doc/lua.1
 delete mode 100644 src/external/lua-5.1.5/doc/lua.css
 delete mode 100644 src/external/lua-5.1.5/doc/lua.html
 delete mode 100644 src/external/lua-5.1.5/doc/luac.1
 delete mode 100644 src/external/lua-5.1.5/doc/luac.html
 delete mode 100644 src/external/lua-5.1.5/doc/manual.css
 delete mode 100644 src/external/lua-5.1.5/doc/manual.html
 delete mode 100644 src/external/lua-5.1.5/doc/readme.html
 delete mode 100644 src/external/lua-5.1.5/etc/Makefile
 delete mode 100644 src/external/lua-5.1.5/etc/README
 delete mode 100644 src/external/lua-5.1.5/etc/all.c
 delete mode 100644 src/external/lua-5.1.5/etc/lua.hpp
 delete mode 100644 src/external/lua-5.1.5/etc/lua.ico
 delete mode 100644 src/external/lua-5.1.5/etc/lua.pc
 delete mode 100644 src/external/lua-5.1.5/etc/luavs.bat
 delete mode 100644 src/external/lua-5.1.5/etc/min.c
 delete mode 100644 src/external/lua-5.1.5/etc/noparser.c
 delete mode 100644 src/external/lua-5.1.5/etc/strict.lua
 delete mode 100644 src/external/lua-5.1.5/src/Makefile
 delete mode 100644 src/external/lua-5.1.5/src/lapi.c
 delete mode 100644 src/external/lua-5.1.5/src/lapi.h
 delete mode 100644 src/external/lua-5.1.5/src/lauxlib.c
 delete mode 100644 src/external/lua-5.1.5/src/lauxlib.h
 delete mode 100644 src/external/lua-5.1.5/src/lbaselib.c
 delete mode 100644 src/external/lua-5.1.5/src/lcode.c
 delete mode 100644 src/external/lua-5.1.5/src/lcode.h
 delete mode 100644 src/external/lua-5.1.5/src/ldblib.c
 delete mode 100644 src/external/lua-5.1.5/src/ldebug.c
 delete mode 100644 src/external/lua-5.1.5/src/ldebug.h
 delete mode 100644 src/external/lua-5.1.5/src/ldo.c
 delete mode 100644 src/external/lua-5.1.5/src/ldo.h
 delete mode 100644 src/external/lua-5.1.5/src/ldump.c
 delete mode 100644 src/external/lua-5.1.5/src/lfunc.c
 delete mode 100644 src/external/lua-5.1.5/src/lfunc.h
 delete mode 100644 src/external/lua-5.1.5/src/lgc.c
 delete mode 100644 src/external/lua-5.1.5/src/lgc.h
 delete mode 100644 src/external/lua-5.1.5/src/linit.c
 delete mode 100644 src/external/lua-5.1.5/src/liolib.c
 delete mode 100644 src/external/lua-5.1.5/src/llex.c
 delete mode 100644 src/external/lua-5.1.5/src/llex.h
 delete mode 100644 src/external/lua-5.1.5/src/llimits.h
 delete mode 100644 src/external/lua-5.1.5/src/lmathlib.c
 delete mode 100644 src/external/lua-5.1.5/src/lmem.c
 delete mode 100644 src/external/lua-5.1.5/src/lmem.h
 delete mode 100644 src/external/lua-5.1.5/src/loadlib.c
 delete mode 100644 src/external/lua-5.1.5/src/lobject.c
 delete mode 100644 src/external/lua-5.1.5/src/lobject.h
 delete mode 100644 src/external/lua-5.1.5/src/lopcodes.c
 delete mode 100644 src/external/lua-5.1.5/src/lopcodes.h
 delete mode 100644 src/external/lua-5.1.5/src/loslib.c
 delete mode 100644 src/external/lua-5.1.5/src/lparser.c
 delete mode 100644 src/external/lua-5.1.5/src/lparser.h
 delete mode 100644 src/external/lua-5.1.5/src/lstate.c
 delete mode 100644 src/external/lua-5.1.5/src/lstate.h
 delete mode 100644 src/external/lua-5.1.5/src/lstring.c
 delete mode 100644 src/external/lua-5.1.5/src/lstring.h
 delete mode 100644 src/external/lua-5.1.5/src/lstrlib.c
 delete mode 100644 src/external/lua-5.1.5/src/ltable.c
 delete mode 100644 src/external/lua-5.1.5/src/ltable.h
 delete mode 100644 src/external/lua-5.1.5/src/ltablib.c
 delete mode 100644 src/external/lua-5.1.5/src/ltm.c
 delete mode 100644 src/external/lua-5.1.5/src/ltm.h
 delete mode 100644 src/external/lua-5.1.5/src/lua.c
 delete mode 100644 src/external/lua-5.1.5/src/lua.h
 delete mode 100644 src/external/lua-5.1.5/src/luac.c
 delete mode 100644 src/external/lua-5.1.5/src/luaconf.h
 delete mode 100644 src/external/lua-5.1.5/src/lualib.h
 delete mode 100644 src/external/lua-5.1.5/src/lundump.c
 delete mode 100644 src/external/lua-5.1.5/src/lundump.h
 delete mode 100644 src/external/lua-5.1.5/src/lvm.c
 delete mode 100644 src/external/lua-5.1.5/src/lvm.h
 delete mode 100644 src/external/lua-5.1.5/src/lzio.c
 delete mode 100644 src/external/lua-5.1.5/src/lzio.h
 delete mode 100644 src/external/lua-5.1.5/src/print.c
 delete mode 100644 src/external/lua-5.1.5/test/README
 delete mode 100644 src/external/lua-5.1.5/test/bisect.lua
 delete mode 100644 src/external/lua-5.1.5/test/cf.lua
 delete mode 100644 src/external/lua-5.1.5/test/echo.lua
 delete mode 100644 src/external/lua-5.1.5/test/env.lua
 delete mode 100644 src/external/lua-5.1.5/test/factorial.lua
 delete mode 100644 src/external/lua-5.1.5/test/fib.lua
 delete mode 100644 src/external/lua-5.1.5/test/fibfor.lua
 delete mode 100644 src/external/lua-5.1.5/test/globals.lua
 delete mode 100644 src/external/lua-5.1.5/test/hello.lua
 delete mode 100644 src/external/lua-5.1.5/test/life.lua
 delete mode 100644 src/external/lua-5.1.5/test/luac.lua
 delete mode 100644 src/external/lua-5.1.5/test/printf.lua
 delete mode 100644 src/external/lua-5.1.5/test/readonly.lua
 delete mode 100644 src/external/lua-5.1.5/test/sieve.lua
 delete mode 100644 src/external/lua-5.1.5/test/sort.lua
 delete mode 100644 src/external/lua-5.1.5/test/table.lua
 delete mode 100644 src/external/lua-5.1.5/test/trace-calls.lua
 delete mode 100644 src/external/lua-5.1.5/test/trace-globals.lua
 delete mode 100644 src/external/lua-5.1.5/test/xd.lua
 delete mode 100644 src/external/luafilesystem-1.5.0/Makefile
 delete mode 100644 src/external/luafilesystem-1.5.0/Makefile.win
 delete mode 100644 src/external/luafilesystem-1.5.0/README
 delete mode 100644 src/external/luafilesystem-1.5.0/config
 delete mode 100644 src/external/luafilesystem-1.5.0/config.win
 delete mode 100644 src/external/luafilesystem-1.5.0/doc/us/examples.html
 delete mode 100644 src/external/luafilesystem-1.5.0/doc/us/index.html
 delete mode 100644 src/external/luafilesystem-1.5.0/doc/us/license.html
 delete mode 100644 src/external/luafilesystem-1.5.0/doc/us/luafilesystem.png
 delete mode 100644 src/external/luafilesystem-1.5.0/doc/us/manual.html
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.3.0-1.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.0-1.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.0-2.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.1-1.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.1rc1-1.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.4.2-1.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-1.5.0-1.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-cvs-1.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/rockspecs/luafilesystem-cvs-2.rockspec
 delete mode 100644 src/external/luafilesystem-1.5.0/src/lfs.c
 delete mode 100644 src/external/luafilesystem-1.5.0/src/lfs.def
 delete mode 100644 src/external/luafilesystem-1.5.0/src/lfs.h
 delete mode 100644 src/external/luafilesystem-1.5.0/tests/test.lua
 delete mode 100644 src/external/luafilesystem-1.5.0/vc6/lfs.def
 delete mode 100644 src/external/luafilesystem-1.5.0/vc6/luafilesystem.dsw
 delete mode 100644 src/external/luafilesystem-1.5.0/vc6/luafilesystem_dll.dsp
 delete mode 100644 src/external/md5-1.1.2/Makefile
 delete mode 100644 src/external/md5-1.1.2/Makefile.win
 delete mode 100644 src/external/md5-1.1.2/README
 delete mode 100644 src/external/md5-1.1.2/config
 delete mode 100644 src/external/md5-1.1.2/config.win
 delete mode 100755 src/external/md5-1.1.2/configure
 delete mode 100644 src/external/md5-1.1.2/doc/us/index.html
 delete mode 100644 src/external/md5-1.1.2/doc/us/license.html
 delete mode 100644 src/external/md5-1.1.2/doc/us/manual.html
 delete mode 100644 src/external/md5-1.1.2/doc/us/md5.png
 delete mode 100644 src/external/md5-1.1.2/rockspec/md5-1.1.1-1.rockspec
 delete mode 100644 src/external/md5-1.1.2/rockspec/md5-1.1.2-1.rockspec
 delete mode 100644 src/external/md5-1.1.2/rockspec/md5-cvs-1.rockspec
 delete mode 100644 src/external/md5-1.1.2/src/des56.c
 delete mode 100644 src/external/md5-1.1.2/src/des56.def
 delete mode 100644 src/external/md5-1.1.2/src/des56.h
 delete mode 100644 src/external/md5-1.1.2/src/ldes56.c
 delete mode 100644 src/external/md5-1.1.2/src/ldes56.h
 delete mode 100644 src/external/md5-1.1.2/src/md5.c
 delete mode 100644 src/external/md5-1.1.2/src/md5.def
 delete mode 100644 src/external/md5-1.1.2/src/md5.h
 delete mode 100644 src/external/md5-1.1.2/src/md5lib.c
 delete mode 100644 src/external/md5-1.1.2/tests/DES56/Makefile
 delete mode 100644 src/external/md5-1.1.2/tests/DES56/fdemo.c
 delete mode 100644 src/external/md5-1.1.2/tests/DES56/ftest.c
 delete mode 100644 src/external/md5-1.1.2/tests/test.lua
 delete mode 100644 src/external/md5-1.1.2/vc6/md5.def
 delete mode 100644 src/external/md5-1.1.2/vc6/md5.dsw
 delete mode 100644 src/external/md5-1.1.2/vc6/md5_dll.dsp
 delete mode 100644 src/external/samtools-0.1.18/AUTHORS
 delete mode 100644 src/external/samtools-0.1.18/COPYING
 delete mode 100644 src/external/samtools-0.1.18/ChangeLog
 delete mode 100644 src/external/samtools-0.1.18/INSTALL
 delete mode 100644 src/external/samtools-0.1.18/Makefile
 delete mode 100644 src/external/samtools-0.1.18/Makefile.mingw
 delete mode 100644 src/external/samtools-0.1.18/NEWS
 delete mode 100644 src/external/samtools-0.1.18/bam.c
 delete mode 100644 src/external/samtools-0.1.18/bam.h
 delete mode 100644 src/external/samtools-0.1.18/bam2bcf.c
 delete mode 100644 src/external/samtools-0.1.18/bam2bcf.h
 delete mode 100644 src/external/samtools-0.1.18/bam2bcf_indel.c
 delete mode 100644 src/external/samtools-0.1.18/bam2depth.c
 delete mode 100644 src/external/samtools-0.1.18/bam_aux.c
 delete mode 100644 src/external/samtools-0.1.18/bam_cat.c
 delete mode 100644 src/external/samtools-0.1.18/bam_color.c
 delete mode 100644 src/external/samtools-0.1.18/bam_endian.h
 delete mode 100644 src/external/samtools-0.1.18/bam_import.c
 delete mode 100644 src/external/samtools-0.1.18/bam_index.c
 delete mode 100644 src/external/samtools-0.1.18/bam_lpileup.c
 delete mode 100644 src/external/samtools-0.1.18/bam_mate.c
 delete mode 100644 src/external/samtools-0.1.18/bam_md.c
 delete mode 100644 src/external/samtools-0.1.18/bam_pileup.c
 delete mode 100644 src/external/samtools-0.1.18/bam_plcmd.c
 delete mode 100644 src/external/samtools-0.1.18/bam_reheader.c
 delete mode 100644 src/external/samtools-0.1.18/bam_rmdup.c
 delete mode 100644 src/external/samtools-0.1.18/bam_rmdupse.c
 delete mode 100644 src/external/samtools-0.1.18/bam_sort.c
 delete mode 100644 src/external/samtools-0.1.18/bam_stat.c
 delete mode 100644 src/external/samtools-0.1.18/bam_tview.c
 delete mode 100644 src/external/samtools-0.1.18/bamtk.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/Makefile
 delete mode 100644 src/external/samtools-0.1.18/bcftools/README
 delete mode 100644 src/external/samtools-0.1.18/bcftools/bcf.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/bcf.h
 delete mode 100644 src/external/samtools-0.1.18/bcftools/bcf.tex
 delete mode 100644 src/external/samtools-0.1.18/bcftools/bcf2qcall.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/bcfutils.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/call1.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/em.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/fet.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/index.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/kfunc.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/kmin.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/kmin.h
 delete mode 100644 src/external/samtools-0.1.18/bcftools/main.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/mut.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/prob1.c
 delete mode 100644 src/external/samtools-0.1.18/bcftools/prob1.h
 delete mode 100644 src/external/samtools-0.1.18/bcftools/vcf.c
 delete mode 100755 src/external/samtools-0.1.18/bcftools/vcfutils.pl
 delete mode 100644 src/external/samtools-0.1.18/bedidx.c
 delete mode 100644 src/external/samtools-0.1.18/bgzf.c
 delete mode 100644 src/external/samtools-0.1.18/bgzf.h
 delete mode 100644 src/external/samtools-0.1.18/bgzip.c
 delete mode 100644 src/external/samtools-0.1.18/cut_target.c
 delete mode 100644 src/external/samtools-0.1.18/errmod.c
 delete mode 100644 src/external/samtools-0.1.18/errmod.h
 delete mode 100644 src/external/samtools-0.1.18/examples/00README.txt
 delete mode 100644 src/external/samtools-0.1.18/examples/Makefile
 delete mode 100644 src/external/samtools-0.1.18/examples/bam2bed.c
 delete mode 100644 src/external/samtools-0.1.18/examples/calDepth.c
 delete mode 100644 src/external/samtools-0.1.18/examples/ex1.fa
 delete mode 100644 src/external/samtools-0.1.18/examples/ex1.sam.gz
 delete mode 100644 src/external/samtools-0.1.18/examples/toy.fa
 delete mode 100644 src/external/samtools-0.1.18/examples/toy.sam
 delete mode 100644 src/external/samtools-0.1.18/faidx.c
 delete mode 100644 src/external/samtools-0.1.18/faidx.h
 delete mode 100644 src/external/samtools-0.1.18/kaln.c
 delete mode 100644 src/external/samtools-0.1.18/kaln.h
 delete mode 100644 src/external/samtools-0.1.18/khash.h
 delete mode 100644 src/external/samtools-0.1.18/klist.h
 delete mode 100644 src/external/samtools-0.1.18/knetfile.c
 delete mode 100644 src/external/samtools-0.1.18/knetfile.h
 delete mode 100644 src/external/samtools-0.1.18/kprobaln.c
 delete mode 100644 src/external/samtools-0.1.18/kprobaln.h
 delete mode 100644 src/external/samtools-0.1.18/kseq.h
 delete mode 100644 src/external/samtools-0.1.18/ksort.h
 delete mode 100644 src/external/samtools-0.1.18/kstring.c
 delete mode 100644 src/external/samtools-0.1.18/kstring.h
 delete mode 100644 src/external/samtools-0.1.18/misc/HmmGlocal.java
 delete mode 100644 src/external/samtools-0.1.18/misc/Makefile
 delete mode 100755 src/external/samtools-0.1.18/misc/blast2sam.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/bowtie2sam.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/export2sam.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/interpolate_sam.pl
 delete mode 100644 src/external/samtools-0.1.18/misc/maq2sam.c
 delete mode 100644 src/external/samtools-0.1.18/misc/md5.c
 delete mode 100644 src/external/samtools-0.1.18/misc/md5.h
 delete mode 100644 src/external/samtools-0.1.18/misc/md5fa.c
 delete mode 100755 src/external/samtools-0.1.18/misc/novo2sam.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/psl2sam.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/sam2vcf.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/samtools.pl
 delete mode 100644 src/external/samtools-0.1.18/misc/seqtk.c
 delete mode 100755 src/external/samtools-0.1.18/misc/soap2sam.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/varfilter.py
 delete mode 100644 src/external/samtools-0.1.18/misc/wgsim.c
 delete mode 100755 src/external/samtools-0.1.18/misc/wgsim_eval.pl
 delete mode 100755 src/external/samtools-0.1.18/misc/zoom2sam.pl
 delete mode 100644 src/external/samtools-0.1.18/phase.c
 delete mode 100644 src/external/samtools-0.1.18/razf.c
 delete mode 100644 src/external/samtools-0.1.18/razf.h
 delete mode 100644 src/external/samtools-0.1.18/razip.c
 delete mode 100644 src/external/samtools-0.1.18/sam.c
 delete mode 100644 src/external/samtools-0.1.18/sam.h
 delete mode 100644 src/external/samtools-0.1.18/sam_header.c
 delete mode 100644 src/external/samtools-0.1.18/sam_header.h
 delete mode 100644 src/external/samtools-0.1.18/sam_view.c
 delete mode 100644 src/external/samtools-0.1.18/sample.c
 delete mode 100644 src/external/samtools-0.1.18/sample.h
 delete mode 100644 src/external/samtools-0.1.18/win32/xcurses.h
 delete mode 100644 src/external/samtools-0.1.18/win32/zconf.h
 delete mode 100644 src/external/samtools-0.1.18/win32/zlib.h
 delete mode 100644 src/external/sqlite-3.8.7.1/sqlite3.c
 delete mode 100644 src/external/sqlite-3.8.7.1/sqlite3.h
 delete mode 100644 src/external/sqlite-3.8.7.1/sqlite3ext.h
 delete mode 100644 src/external/tre/.gitignore
 delete mode 100644 src/external/tre/LICENSE
 delete mode 100644 src/external/tre/README
 delete mode 100644 src/external/tre/include/tre/tre-config.h
 delete mode 100644 src/external/tre/include/tre/tre.h
 delete mode 100644 src/external/tre/lib/README
 delete mode 100644 src/external/tre/lib/regcomp.c
 delete mode 100644 src/external/tre/lib/regerror.c
 delete mode 100644 src/external/tre/lib/regex.h
 delete mode 100644 src/external/tre/lib/regexec.c
 delete mode 100644 src/external/tre/lib/tre-ast.c
 delete mode 100644 src/external/tre/lib/tre-ast.h
 delete mode 100644 src/external/tre/lib/tre-compile.c
 delete mode 100644 src/external/tre/lib/tre-compile.h
 delete mode 100644 src/external/tre/lib/tre-config.h.in
 delete mode 100644 src/external/tre/lib/tre-filter.c
 delete mode 100644 src/external/tre/lib/tre-filter.h
 delete mode 100644 src/external/tre/lib/tre-internal.h
 delete mode 100644 src/external/tre/lib/tre-match-backtrack.c
 delete mode 100644 src/external/tre/lib/tre-match-parallel.c
 delete mode 100644 src/external/tre/lib/tre-match-utils.h
 delete mode 100644 src/external/tre/lib/tre-mem.c
 delete mode 100644 src/external/tre/lib/tre-mem.h
 delete mode 100644 src/external/tre/lib/tre-parse.c
 delete mode 100644 src/external/tre/lib/tre-parse.h
 delete mode 100644 src/external/tre/lib/tre-stack.c
 delete mode 100644 src/external/tre/lib/tre-stack.h
 delete mode 100644 src/external/tre/lib/tre.h
 delete mode 100644 src/external/tre/lib/xmalloc.c
 delete mode 100644 src/external/tre/lib/xmalloc.h
 delete mode 100644 src/external/zlib-1.2.8/README
 delete mode 100644 src/external/zlib-1.2.8/adler32.c
 delete mode 100644 src/external/zlib-1.2.8/compress.c
 delete mode 100644 src/external/zlib-1.2.8/crc32.c
 delete mode 100644 src/external/zlib-1.2.8/crc32.h
 delete mode 100644 src/external/zlib-1.2.8/deflate.c
 delete mode 100644 src/external/zlib-1.2.8/deflate.h
 delete mode 100644 src/external/zlib-1.2.8/gzclose.c
 delete mode 100644 src/external/zlib-1.2.8/gzguts.h
 delete mode 100644 src/external/zlib-1.2.8/gzlib.c
 delete mode 100644 src/external/zlib-1.2.8/gzread.c
 delete mode 100644 src/external/zlib-1.2.8/gzwrite.c
 delete mode 100644 src/external/zlib-1.2.8/infback.c
 delete mode 100644 src/external/zlib-1.2.8/inffast.c
 delete mode 100644 src/external/zlib-1.2.8/inffast.h
 delete mode 100644 src/external/zlib-1.2.8/inffixed.h
 delete mode 100644 src/external/zlib-1.2.8/inflate.c
 delete mode 100644 src/external/zlib-1.2.8/inflate.h
 delete mode 100644 src/external/zlib-1.2.8/inftrees.c
 delete mode 100644 src/external/zlib-1.2.8/inftrees.h
 delete mode 100644 src/external/zlib-1.2.8/trees.c
 delete mode 100644 src/external/zlib-1.2.8/trees.h
 delete mode 100644 src/external/zlib-1.2.8/uncompr.c
 delete mode 100644 src/external/zlib-1.2.8/zconf.h
 delete mode 100644 src/external/zlib-1.2.8/zlib.h
 delete mode 100644 src/external/zlib-1.2.8/zutil.c
 delete mode 100644 src/external/zlib-1.2.8/zutil.h

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/genometools.git



More information about the debian-med-commit mailing list