[med-svn] [pbdagcon] branch master updated (90e5932 -> c232dbe)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Dec 21 09:26:48 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository pbdagcon.
from 90e5932 releasing package pbdagcon version 0~20160325+ds-1
new d191671 Add draft get-orig-source script
new b247711 Imported Upstream version 0.3+20161121+ds
new fb7c88b Merge tag 'upstream/0.3+20161121+ds'
new ee91433 get-orig-source: clean up after any exit
new 3f67734 d/copyright: Record copyright for DALIGNER/DAZZ_DB
new 6cb4709 Build with pbbam
new fecf616 Use pbseqlib metapackages as dependencies
new 77d4560 Build dazcon
new 4320327 Activate build-time tests
new 941ef56 Set environment variables so that the configure script can identify them
new 26c4858 Use debhelper compat 10
new c232dbe releasing package pbdagcon version 0.3+20161121+ds-1
The 12 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 | 11 -
.gitmodules | 9 -
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 +
DALIGNER/align.c | 5112 +++++++++++++++++++++++++++++++++++
DALIGNER/align.h | 335 +++
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 ++++++++++++
DAZZ_DB/DB.h | 415 +++
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 +++
configure.py | 6 +-
debian/TODO | 1 -
debian/changelog | 13 +
debian/compat | 2 +-
debian/control | 15 +-
debian/copyright | 27 +
debian/get-orig-source | 35 +
debian/install | 1 +
debian/patches/dazcon.patch | 16 -
debian/patches/series | 1 -
debian/rules | 21 +-
makefile | 2 +-
test/cpp/.gitignore | 2 -
71 files changed, 24240 insertions(+), 62 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
create mode 100644 DALIGNER/align.c
create mode 100644 DALIGNER/align.h
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
create mode 100644 DAZZ_DB/DB.h
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
delete mode 100644 debian/TODO
create mode 100755 debian/get-orig-source
delete mode 100644 debian/patches/dazcon.patch
delete mode 100644 test/cpp/.gitignore
--
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