[med-svn] [pbdagcon] 01/03: Merge tag 'debian/0.3+20161121+ds-1' into debian/jessie-backports
Afif Elghraoui
afif at moszumanska.debian.org
Wed Apr 26 07:01:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch debian/jessie-backports
in repository pbdagcon.
commit 47e48092e143dca68afe4ee95de3af0ec6facf39
Merge: a431a2c c232dbe
Author: Afif Elghraoui <afif at debian.org>
Date: Wed Apr 26 01:43:14 2017 -0400
Merge tag 'debian/0.3+20161121+ds-1' into debian/jessie-backports
tagging package pbdagcon version debian/0.3+20161121+ds-1
Conflicts:
debian/changelog
.gitignore | 10 -
.gitmodules | 3 -
.travis.yml | 4 +-
DALIGNER/DB2Falcon.c | 133 ++
DALIGNER/GNUmakefile | 30 +
DALIGNER/HPCdaligner.c | 543 ++++++
DALIGNER/HPCmapper.c | 591 +++++++
DALIGNER/LA4Falcon.c | 802 +++++++++
DALIGNER/LA4Ice.c | 568 ++++++
DALIGNER/LAcat.c | 157 ++
DALIGNER/LAcheck.c | 310 ++++
DALIGNER/LAdump.c | 478 +++++
DALIGNER/LAindex.c | 201 +++
DALIGNER/LAmerge.c | 387 ++++
DALIGNER/LAshow.c | 594 +++++++
DALIGNER/LAsort.c | 252 +++
DALIGNER/LAsplit.c | 207 +++
DALIGNER/LICENSE | 34 +
DALIGNER/Makefile | 69 +
DALIGNER/README | 395 +++++
DALIGNER/README_PB.md | 8 +
{src/cpp => DALIGNER}/align.c | 2745 +++++++++++++++++++++--------
{src/cpp => DALIGNER}/align.h | 136 +-
DALIGNER/daligner.c | 726 ++++++++
DALIGNER/daligner_p.c | 1 +
DALIGNER/filter.c | 2266 ++++++++++++++++++++++++
DALIGNER/filter.h | 38 +
DALIGNER/filter_p.c | 2 +
DALIGNER/py_utils/DAPI.py | 72 +
DALIGNER/py_utils/DAPipe.py | 93 +
DALIGNER/py_utils/DBLA_to_falcon.py | 42 +
DALIGNER/py_utils/FALCON_ASM_NOTE | 27 +
DALIGNER/py_utils/LAPI.py | 110 ++
DALIGNER/py_utils/LAPipe.py | 177 ++
DAZZ_DB/Catrack.c | 259 +++
DAZZ_DB/DAM2fasta.c | 200 +++
DAZZ_DB/DB.c | 1690 ++++++++++++++++++
{src/cpp => DAZZ_DB}/DB.h | 200 ++-
DAZZ_DB/DB2fasta.c | 151 ++
DAZZ_DB/DB2quiva.c | 155 ++
DAZZ_DB/DBdump.c | 720 ++++++++
DAZZ_DB/DBdust.c | 471 +++++
DAZZ_DB/DBrm.c | 40 +
DAZZ_DB/DBshow.c | 577 ++++++
DAZZ_DB/DBsplit.c | 214 +++
DAZZ_DB/DBstats.c | 346 ++++
DAZZ_DB/DBupgrade.Dec.31.2014.c | 86 +
DAZZ_DB/DBupgrade.Sep.25.2014.c | 96 +
DAZZ_DB/DUSTupgrade.Jan.1.2015.c | 80 +
DAZZ_DB/GNUmakefile | 33 +
DAZZ_DB/LICENSE | 34 +
DAZZ_DB/Makefile | 70 +
DAZZ_DB/QV.c | 1369 ++++++++++++++
DAZZ_DB/QV.h | 90 +
DAZZ_DB/README | 459 +++++
DAZZ_DB/fasta2DAM.c | 412 +++++
DAZZ_DB/fasta2DB.c | 645 +++++++
DAZZ_DB/quiva2DB.c | 347 ++++
DAZZ_DB/simulator.c | 421 +++++
src/cpp/pbdagcon_wf.sh => LICENSE | 40 +-
Makefile | 48 -
README.md | 27 +-
configure.py | 320 ++++
debian/changelog | 34 +
debian/compat | 2 +-
debian/control | 24 +-
debian/copyright | 39 +-
debian/get-orig-source | 35 +
debian/install | 1 +
debian/lintian-overrides | 5 -
debian/patches/compiler-flags.patch | 30 +-
debian/patches/disable-dazcon-tests.patch | 16 -
debian/patches/external-libs.patch | 29 -
debian/patches/gtest-directory.patch | 91 -
debian/patches/series | 3 -
debian/rules | 24 +-
makefile | 45 +
src/cpp/Alignment.cpp | 123 +-
src/cpp/Alignment.hpp | 55 +-
src/cpp/AlnGraphBoost.cpp | 108 +-
src/cpp/AlnGraphBoost.hpp | 67 +-
src/cpp/AlnProvider.hpp | 47 +-
src/cpp/BlasrM5AlnProvider.cpp | 40 +-
src/cpp/BlasrM5AlnProvider.hpp | 55 +-
src/cpp/BoundedBuffer.hpp | 53 +-
src/cpp/DB.c | 1106 ------------
src/cpp/DazAlnProvider.cpp | 79 +-
src/cpp/DazAlnProvider.hpp | 62 +-
src/cpp/Makefile | 38 -
src/cpp/ProgramOpts.hpp | 5 +-
src/cpp/SimpleAligner.cpp | 40 +-
src/cpp/SimpleAligner.hpp | 42 +-
src/cpp/boost.mk | 18 -
src/cpp/dazcon.cpp | 78 +-
src/cpp/main.cpp | 88 +-
src/cpp/makefile | 76 +
src/cpp/pbdagcon_wf.sh | 39 -
src/cpp/pbi.mk | 22 -
src/q-sense.py | 39 -
test/cpp/AlignmentTest.cpp | 89 +-
test/cpp/AlnGraphBoostTest.cpp | 9 +-
test/cpp/Makefile | 77 -
test/cpp/TargetHitTest.cpp | 14 +-
test/cpp/TargetTest.cpp | 4 +-
test/cpp/gtest.mk | 10 -
test/cpp/makefile | 117 ++
travis.sh | 7 +
107 files changed, 21535 insertions(+), 3261 deletions(-)
diff --cc debian/changelog
index 98a2e8a,b028d26..41f6856
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,37 +1,43 @@@
+ pbdagcon (0.3+20161121+ds-1) unstable; urgency=medium
+
+ * New upstream revision (upstream git 87f393f)
+ * Include repository's submodules
+ * Base package versioning on program versions indicated in the source code
+ * Build with pbbam (Closes: #848755)
+ * Use pbseqlib metapackages as dependencies
+ * Build dazcon
+ * Activate build-time tests
+ * Use debhelper compat 10
+
+ -- Afif Elghraoui <afif at debian.org> Wed, 21 Dec 2016 01:18:19 -0800
+
+ pbdagcon (0~20160325+ds-1) unstable; urgency=medium
+
+ * Imported Upstream version 0~20160325+ds
+ (upstream git revision f19aed1)
+ * Do not use rpath for pbseqlib
+ * Update patches
+ * d/rules: update for changes to build system and dependencies
+ * Do not build dazcon for now (needs additional sources)
+ * d/copyright: Remove obsolete declarations
+
+ -- Afif Elghraoui <afif at debian.org> Sun, 23 Oct 2016 19:43:31 -0700
+
+ pbdagcon (0~20151114+git1d12e13+ds-3) unstable; urgency=low
+
+ * Bump Standards-Version to 3.9.8
+ * Update email address and bump copyright year
+ * Use encrypted protocols for VCS URLs
+ * Do not use -isystem while building (Closes: #831105)
+
+ -- Afif Elghraoui <afif at debian.org> Thu, 04 Aug 2016 00:42:55 -0700
+
+pbdagcon (0~20151114+git1d12e13+ds-2~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+
+ -- Afif Elghraoui <afif at ghraoui.name> Wed, 27 Jan 2016 22:22:37 -0800
+
pbdagcon (0~20151114+git1d12e13+ds-2) unstable; urgency=medium
* Adjust packaging for differences in pbseqlib organization.
--
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