[med-svn] [pbdagcon] branch debian/jessie-backports updated (a431a2c -> 4f63805)
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 change to branch debian/jessie-backports
in repository pbdagcon.
from a431a2c pbdagcon (0~20151114+git1d12e13+ds-2~bpo8+1) jessie-backports; urgency=medium
adds 3e252a6 Bump Standards-Version to 3.9.8
adds a3aeb6d Update email address and bump copyright year
adds 3be8827 Use encrypted protocols for VCS URLs
adds 7c485db Do not use -isystem while building
adds 7aa546f releasing package pbdagcon version 0~20151114+git1d12e13+ds-3
adds 7b1ae4f Imported Upstream version 0~20160325+ds
adds 81a615b Merge tag 'upstream/0_20160325+ds'
adds f8f7818 Do not use rpath for pbseqlib
adds 31669ba Update patches
adds 3b309a6 d/rules: update for changes to build system and dependencies
adds 42116d3 Do not build dazcon for now (needs additional sources)
adds 892ceb9 d/copyright: Remove obsolete declarations
adds 90e5932 releasing package pbdagcon version 0~20160325+ds-1
adds d191671 Add draft get-orig-source script
adds b247711 Imported Upstream version 0.3+20161121+ds
adds fb7c88b Merge tag 'upstream/0.3+20161121+ds'
adds ee91433 get-orig-source: clean up after any exit
adds 3f67734 d/copyright: Record copyright for DALIGNER/DAZZ_DB
adds 6cb4709 Build with pbbam
adds fecf616 Use pbseqlib metapackages as dependencies
adds 77d4560 Build dazcon
adds 4320327 Activate build-time tests
adds 941ef56 Set environment variables so that the configure script can identify them
adds 26c4858 Use debhelper compat 10
adds c232dbe releasing package pbdagcon version 0.3+20161121+ds-1
new 47e4809 Merge tag 'debian/0.3+20161121+ds-1' into debian/jessie-backports
new ac596e2 Disable build-time tests requiring the unavailable googletest package.
new 4f63805 releasing package pbdagcon version 0.3+20161121+ds-1~bpo8+1
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
been added to this reference.
Summary of changes:
.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 | 42 +
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 | 26 +-
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, 21545 insertions(+), 3261 deletions(-)
delete mode 100644 .gitignore
delete mode 100644 .gitmodules
create mode 100644 DALIGNER/DB2Falcon.c
create mode 100644 DALIGNER/GNUmakefile
create mode 100644 DALIGNER/HPCdaligner.c
create mode 100644 DALIGNER/HPCmapper.c
create mode 100644 DALIGNER/LA4Falcon.c
create mode 100644 DALIGNER/LA4Ice.c
create mode 100644 DALIGNER/LAcat.c
create mode 100644 DALIGNER/LAcheck.c
create mode 100644 DALIGNER/LAdump.c
create mode 100644 DALIGNER/LAindex.c
create mode 100644 DALIGNER/LAmerge.c
create mode 100644 DALIGNER/LAshow.c
create mode 100644 DALIGNER/LAsort.c
create mode 100644 DALIGNER/LAsplit.c
create mode 100644 DALIGNER/LICENSE
create mode 100644 DALIGNER/Makefile
create mode 100644 DALIGNER/README
create mode 100644 DALIGNER/README_PB.md
rename {src/cpp => DALIGNER}/align.c (60%)
rename {src/cpp => DALIGNER}/align.h (75%)
create mode 100644 DALIGNER/daligner.c
create mode 100644 DALIGNER/daligner_p.c
create mode 100644 DALIGNER/filter.c
create mode 100644 DALIGNER/filter.h
create mode 100644 DALIGNER/filter_p.c
create mode 100644 DALIGNER/py_utils/DAPI.py
create mode 100644 DALIGNER/py_utils/DAPipe.py
create mode 100644 DALIGNER/py_utils/DBLA_to_falcon.py
create mode 100644 DALIGNER/py_utils/FALCON_ASM_NOTE
create mode 100644 DALIGNER/py_utils/LAPI.py
create mode 100644 DALIGNER/py_utils/LAPipe.py
create mode 100644 DAZZ_DB/Catrack.c
create mode 100644 DAZZ_DB/DAM2fasta.c
create mode 100644 DAZZ_DB/DB.c
rename {src/cpp => DAZZ_DB}/DB.h (69%)
create mode 100644 DAZZ_DB/DB2fasta.c
create mode 100644 DAZZ_DB/DB2quiva.c
create mode 100644 DAZZ_DB/DBdump.c
create mode 100644 DAZZ_DB/DBdust.c
create mode 100644 DAZZ_DB/DBrm.c
create mode 100644 DAZZ_DB/DBshow.c
create mode 100644 DAZZ_DB/DBsplit.c
create mode 100644 DAZZ_DB/DBstats.c
create mode 100644 DAZZ_DB/DBupgrade.Dec.31.2014.c
create mode 100644 DAZZ_DB/DBupgrade.Sep.25.2014.c
create mode 100644 DAZZ_DB/DUSTupgrade.Jan.1.2015.c
create mode 100644 DAZZ_DB/GNUmakefile
create mode 100644 DAZZ_DB/LICENSE
create mode 100644 DAZZ_DB/Makefile
create mode 100644 DAZZ_DB/QV.c
create mode 100644 DAZZ_DB/QV.h
create mode 100644 DAZZ_DB/README
create mode 100644 DAZZ_DB/fasta2DAM.c
create mode 100644 DAZZ_DB/fasta2DB.c
create mode 100644 DAZZ_DB/quiva2DB.c
create mode 100644 DAZZ_DB/simulator.c
copy src/cpp/pbdagcon_wf.sh => LICENSE (60%)
mode change 100755 => 100644
delete mode 100755 Makefile
create mode 100755 configure.py
create mode 100755 debian/get-orig-source
delete mode 100644 debian/lintian-overrides
delete mode 100644 debian/patches/disable-dazcon-tests.patch
delete mode 100644 debian/patches/external-libs.patch
delete mode 100644 debian/patches/gtest-directory.patch
create mode 100755 makefile
delete mode 100644 src/cpp/DB.c
delete mode 100644 src/cpp/Makefile
delete mode 100644 src/cpp/boost.mk
create mode 100644 src/cpp/makefile
delete mode 100644 src/cpp/pbi.mk
delete mode 100644 test/cpp/Makefile
delete mode 100644 test/cpp/gtest.mk
create mode 100644 test/cpp/makefile
create mode 100755 travis.sh
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