[med-svn] [crac] 03/07: Merge tag 'upstream/2.5.0+dfsg'
Andreas Tille
tille at debian.org
Mon Sep 12 13:45:58 UTC 2016
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tille pushed a commit to branch master
in repository crac.
commit 06b9e4219c1204cfa810b49648631b4cc8cf788f
Merge: 23f51de 4139840
Author: Andreas Tille <tille at debian.org>
Date: Mon Sep 12 14:39:43 2016 +0200
Merge tag 'upstream/2.5.0+dfsg'
Upstream version 2.5.0+dfsg
src/libGkArrays/AUTHORS | 19 -
src/libGkArrays/COPYING | 1047 -
src/libGkArrays/ChangeLog | 482 -
src/libGkArrays/INSTALL | 365 -
src/libGkArrays/Makefile.am | 191 -
src/libGkArrays/Makefile.in | 1072 -
src/libGkArrays/NEWS | 0
src/libGkArrays/README | 143 -
src/libGkArrays/aclocal.m4 | 1154 --
src/libGkArrays/config/compile | 347 -
src/libGkArrays/config/config.guess | 1530 --
src/libGkArrays/config/config.h.in | 145 -
src/libGkArrays/config/config.sub | 1773 --
src/libGkArrays/config/depcomp | 630 -
src/libGkArrays/config/install-sh | 520 -
src/libGkArrays/config/ltmain.sh | 9661 ---------
src/libGkArrays/config/m4/libtool.m4 | 7851 --------
src/libGkArrays/config/m4/ltoptions.m4 | 369 -
src/libGkArrays/config/m4/ltsugar.m4 | 123 -
src/libGkArrays/config/m4/ltversion.m4 | 23 -
src/libGkArrays/config/m4/lt~obsolete.m4 | 98 -
src/libGkArrays/config/missing | 376 -
src/libGkArrays/config/test-driver | 139 -
src/libGkArrays/config/texinfo.tex | 9291 ---------
src/libGkArrays/configure | 19364 -------------------
src/libGkArrays/configure.ac | 357 -
src/libGkArrays/control.in | 29 -
src/libGkArrays/doc/CeCILL-C.texi | 587 -
src/libGkArrays/doc/Makefile.am | 129 -
src/libGkArrays/doc/Makefile.in | 938 -
src/libGkArrays/doc/libGkArrays.3.in | 184 -
src/libGkArrays/doc/libGkArrays.info | 886 -
src/libGkArrays/doc/libGkArrays.texi | 400 -
src/libGkArrays/doc/package.texi.in | 2 -
src/libGkArrays/doc/texinfo.tex | 9291 ---------
src/libGkArrays/libGkArrays.pc.in | 10 -
src/libGkArrays/postinst.in | 108 -
src/libGkArrays/prerm.in | 108 -
src/libGkArrays/src/Makefile.am | 163 -
src/libGkArrays/src/Makefile.in | 1035 -
src/libGkArrays/src/basic.h | 64 -
src/libGkArrays/src/binvect.hxx | 119 -
src/libGkArrays/src/bitvector.cxx | 465 -
src/libGkArrays/src/bitvector.hxx | 159 -
src/libGkArrays/src/buildTables.cpp | 269 -
src/libGkArrays/src/const.h | 119 -
src/libGkArrays/src/gkArrays.cpp | 636 -
src/libGkArrays/src/gkArrays.h | 477 -
src/libGkArrays/src/gkArraysBuilder.cpp | 160 -
src/libGkArrays/src/gkArraysBuilder.h | 141 -
src/libGkArrays/src/gkArraysTypes.h | 139 -
src/libGkArrays/src/gkCFPSBuilder.cpp | 180 -
src/libGkArrays/src/gkCFPSBuilder.h | 146 -
src/libGkArrays/src/gkIFABuilder.cpp | 202 -
src/libGkArrays/src/gkIFABuilder.h | 154 -
src/libGkArrays/src/gkSABuilder.cpp | 487 -
src/libGkArrays/src/gkSABuilder.h | 242 -
src/libGkArrays/src/kseq/Makefile.am | 113 -
src/libGkArrays/src/kseq/Makefile.in | 675 -
src/libGkArrays/src/kseq/kseq.h | 229 -
src/libGkArrays/src/largebinvect.cxx | 1259 --
src/libGkArrays/src/largebinvect.hxx | 242 -
src/libGkArrays/src/libProgressBar-1.2.0/AUTHORS | 2 -
src/libGkArrays/src/libProgressBar-1.2.0/COPYING | 481 -
src/libGkArrays/src/libProgressBar-1.2.0/ChangeLog | 118 -
src/libGkArrays/src/libProgressBar-1.2.0/INSTALL | 365 -
.../src/libProgressBar-1.2.0/Makefile.am | 124 -
.../src/libProgressBar-1.2.0/Makefile.in | 989 -
src/libGkArrays/src/libProgressBar-1.2.0/NEWS | 0
src/libGkArrays/src/libProgressBar-1.2.0/README | 29 -
.../src/libProgressBar-1.2.0/acinclude.m4 | 40 -
.../src/libProgressBar-1.2.0/aclocal.m4 | 1155 --
src/libGkArrays/src/libProgressBar-1.2.0/compile | 347 -
.../src/libProgressBar-1.2.0/config.guess | 1517 --
.../src/libProgressBar-1.2.0/config.sub | 1760 --
src/libGkArrays/src/libProgressBar-1.2.0/configure | 19343 ------------------
.../src/libProgressBar-1.2.0/configure.in | 101 -
.../src/libProgressBar-1.2.0/control.in | 18 -
src/libGkArrays/src/libProgressBar-1.2.0/depcomp | 630 -
.../src/libProgressBar-1.2.0/doc/Makefile.am | 47 -
.../src/libProgressBar-1.2.0/doc/Makefile.in | 849 -
.../src/libProgressBar-1.2.0/doc/lgpl.texinfo | 190 -
.../src/libProgressBar-1.2.0/doc/libProgressBar.3 | 94 -
.../libProgressBar-1.2.0/doc/libProgressBar.3.in | 94 -
.../libProgressBar-1.2.0/doc/libProgressBar.info | 294 -
.../doc/libProgressBar.texinfo | 165 -
.../src/libProgressBar-1.2.0/doc/texinfo.tex | 9291 ---------
.../src/libProgressBar-1.2.0/install-sh | 520 -
.../src/libProgressBar-1.2.0/libProgressBar.lsm.in | 24 -
.../src/libProgressBar-1.2.0/libProgressBar.pc.in | 10 -
.../libProgressBar-1.2.0/libProgressBar.spec.in | 107 -
.../libProgressBar/Makefile.am | 24 -
.../libProgressBar/Makefile.in | 788 -
.../libProgressBar/config.h.in | 129 -
.../libProgressBar/progressBar.cpp | 191 -
.../libProgressBar/progressBar.h | 269 -
.../libProgressBar-1.2.0/libProgressBar/testPB.cpp | 125 -
src/libGkArrays/src/libProgressBar-1.2.0/ltmain.sh | 9661 ---------
.../src/libProgressBar-1.2.0/m4/libtool.m4 | 7851 --------
.../src/libProgressBar-1.2.0/m4/ltoptions.m4 | 369 -
.../src/libProgressBar-1.2.0/m4/ltsugar.m4 | 123 -
.../src/libProgressBar-1.2.0/m4/ltversion.m4 | 23 -
.../src/libProgressBar-1.2.0/m4/lt~obsolete.m4 | 98 -
src/libGkArrays/src/libProgressBar-1.2.0/missing | 376 -
.../src/libProgressBar-1.2.0/mkinstalldirs | 162 -
.../src/libProgressBar-1.2.0/postinst.in | 4 -
src/libGkArrays/src/libProgressBar-1.2.0/prerm.in | 4 -
src/libGkArrays/src/readsReader.cpp | 405 -
src/libGkArrays/src/readsReader.h | 432 -
src/libGkArrays/src/solArray.cpp | 186 -
src/libGkArrays/src/solArray.h | 260 -
src/libGkArrays/src/sux/COPYING.LIB | 504 -
src/libGkArrays/src/sux/Makefile.am | 113 -
src/libGkArrays/src/sux/Makefile.in | 675 -
src/libGkArrays/src/sux/README | 74 -
src/libGkArrays/src/sux/macros.h | 26 -
src/libGkArrays/src/sux/popcount.h | 15 -
src/libGkArrays/src/sux/rank9b.cpp | 236 -
src/libGkArrays/src/sux/rank9b.h | 89 -
src/libGkArrays/src/utils.cpp | 214 -
src/libGkArrays/src/utils.h | 229 -
src/libGkArrays/tests/Makefile.am | 131 -
src/libGkArrays/tests/Makefile.in | 1150 --
src/libGkArrays/tests/checkConsistency.cpp | 332 -
src/libGkArrays/tests/checkConsistency.h | 139 -
src/libGkArrays/tests/checkPairedEnd.cpp | 146 -
src/libGkArrays/tests/checkPairedEnd.h | 107 -
src/libGkArrays/tests/compareVariableFixed.cpp | 190 -
src/libGkArrays/tests/compareVariableFixed.h | 121 -
src/libGkArrays/tests/dataset/data1.fa | 7 -
src/libGkArrays/tests/dataset/data2.fa | 7 -
src/libGkArrays/tests/dataset/variable.fa | 10 -
src/libGkArrays/tests/testConsistency.cpp | 141 -
src/libGkArrays/tests/testPairedEnd.cpp | 123 -
src/libGkArrays/tests/testVariable.h | 106 -
src/libGkArrays/tests/testVariableFixed.cpp | 118 -
src/libGkArrays/tests/testing.h | 65 -
src/libGkArrays/tests/variableAndFixedLength.cpp | 131 -
138 files changed, 143000 deletions(-)
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