[med-svn] [kmer-tools] branch debian/jessie-backports updated (87104aa -> 1a4a6e6)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sat Jan 16 05:33:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch debian/jessie-backports
in repository kmer-tools.
from 87104aa Prepare first backport to jessie
adds 4c49e19 Add Suggests:gridengine-client
adds 7ca1b47 Quote reference titles in d/upstream/metadata
adds 25696ff Use cleaner nroff for one of my early man pages
adds 0b50551 Prepare new revision
adds 3b02fbc Simplify get-orig-source script
adds f2f4f95 Imported Upstream version 0~20150903+r2013
adds ecfd489 Merge tag 'upstream/0_20150903+r2013'
adds c13c8f8 Clean up source package: move meryl manpages to a subdirectory of debian/
adds 85bd00e Add leaff and sim4db binary packages
adds 1705f78 Drop dependency on libbz2-dev
adds 33b46e1 Drop quilt patches
adds 3102ca3 Fix sim4db short description
adds 61d8913 Fix section/architecture of the kmer metapackage
adds d3fdf8d Set Vcs-Browser to point to cgit
adds f4c4fec Don't install other READMEs to metapackage docs
adds b97d186 Annotate sim4db.install and exclude broken tools.
adds d4766ff Add manpages for sim4db
adds 4d0f828 Mention programs used internally by ESTMapper in manpage
adds b166596 Add manpage for leaff
adds 6ff49bf Update d/copyright
adds 3a1510f Update README.source to document situation with bundled kazlib
adds cc71a88 Make the build system more flexible
adds 2c5ae91 Add note in README.source regarding monolithic source package
adds 77c817f Add a heading to subsection in README.source
adds c53d318 Add README.Debian to let users know some components aren't yet packaged
adds e33b8d6 Add comment for why we can't use dh --parallel
adds 05de1bf kmer-tools (0~20150903+r2013-1) unstable; urgency=low
new 55c547e Merge tag 'debian/0_20150903+r2013-1' into debian/jessie-backports
new 1a4a6e6 kmer-tools (0~20150903+r2013-1~bpo8+1) jessie-backports; urgency=medium
The 2 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:
PACKAGING | 104 +
configure.sh | 6 +-
debian/README.Debian | 10 +
debian/README.source | 24 +-
debian/changelog | 29 +
debian/control | 59 +-
debian/copyright | 101 +-
debian/docs | 3 -
debian/get-orig-source | 32 +-
debian/leaff.docs | 1 +
debian/leaff.install | 1 +
debian/leaff.manpages | 1 +
README.leaff => debian/man/leaff/leaff.1 | 104 +-
debian/{ => man/meryl}/existDB.1 | 21 +-
debian/{ => man/meryl}/kmer-mask.1 | 0
debian/{ => man/meryl}/mapMers-depth.1 | 0
debian/{ => man/meryl}/mapMers.1 | 0
debian/{ => man/meryl}/meryl.1 | 0
debian/{ => man/meryl}/positionDB.1 | 0
debian/{ => man/meryl}/simple.1 | 0
debian/man/sim4db/cleanPolishes.1 | 1 +
debian/man/sim4db/comparePolishes.1 | 1 +
debian/man/sim4db/convertPolishes.1 | 1 +
debian/man/sim4db/convertToAtac.1 | 1 +
debian/man/sim4db/convertToExtent.1 | 1 +
debian/man/sim4db/depthOfPolishes.1 | 1 +
debian/man/sim4db/detectChimera.1 | 1 +
debian/man/sim4db/filterPolishes.1 | 1 +
debian/man/sim4db/fixPolishesIID.1 | 1 +
debian/man/sim4db/headPolishes.1 | 1 +
debian/man/sim4db/mappedCoverage.1 | 1 +
debian/man/sim4db/mergePolishes.1 | 1 +
debian/man/sim4db/parseSNP.1 | 1 +
debian/man/sim4db/pickBestPolish.1 | 1 +
debian/man/sim4db/pickUniquePolish.1 | 1 +
debian/man/sim4db/plotCoverageVsIdentity.1 | 1 +
debian/man/sim4db/realignPolishes.1 | 1 +
debian/man/sim4db/removeDuplicate.1 | 1 +
debian/man/sim4db/reportAlignmentDifferences.1 | 1 +
debian/man/sim4db/sim4db.1 | 123 +
debian/man/sim4db/sim4dbutils.1 | 60 +
debian/man/sim4db/sortPolishes.1 | 1 +
debian/man/sim4db/summarizePolishes.1 | 1 +
debian/man/sim4db/uniqPolishes.1 | 1 +
debian/man/sim4db/vennPolishes.1 | 1 +
debian/meryl.manpages | 8 +-
debian/patches/allow-freebsd-build.patch | 121 +
debian/patches/kazlib.patch | 41 -
debian/patches/remove-kazlib.patch | 39 -
debian/patches/series | 3 +-
debian/rules | 19 +-
debian/sim4db.docs | 1 +
debian/sim4db.install | 43 +
debian/sim4db.manpages | 1 +
debian/upstream/metadata | 4 +-
libutil/kazlib/Make.include | 27 +
libutil/kazlib/blast.pl | 33 +
libutil/kazlib/dict.c | 1238 +++++++
libutil/kazlib/dict.h | 142 +
libutil/kazlib/docs/CHANGES | 290 ++
libutil/kazlib/docs/MUST_READ | 25 +
libutil/kazlib/docs/README | 66 +
libutil/kazlib/docs/docs.ist | 4 +
libutil/kazlib/docs/docs.ltx | 4155 ++++++++++++++++++++++++
libutil/kazlib/drivers/dict-main.c | 300 ++
libutil/kazlib/drivers/except-main.c | 57 +
libutil/kazlib/drivers/hash-main.c | 187 ++
libutil/kazlib/drivers/list-main.c | 152 +
libutil/kazlib/drivers/sfx-main.c | 41 +
libutil/kazlib/except.c | 347 ++
libutil/kazlib/except.h | 147 +
libutil/kazlib/hash.c | 837 +++++
libutil/kazlib/hash.h | 238 ++
libutil/kazlib/list.c | 766 +++++
libutil/kazlib/list.h | 152 +
libutil/kazlib/sfx.c | 1138 +++++++
libutil/kazlib/sfx.h | 46 +
meryl/args.C | 2 +-
meryl/build.C | 70 +-
meryl/estimate.C | 136 +-
meryl/kmer-mask.C | 344 +-
meryl/mapMers.C | 26 +-
meryl/meryl.H | 7 +-
sim4dbutils/reportAlignmentDifferences.C | 2 +-
84 files changed, 11461 insertions(+), 496 deletions(-)
create mode 100644 PACKAGING
create mode 100644 debian/README.Debian
delete mode 100644 debian/docs
create mode 100644 debian/leaff.docs
create mode 100644 debian/leaff.install
create mode 100644 debian/leaff.manpages
copy README.leaff => debian/man/leaff/leaff.1 (74%)
rename debian/{ => man/meryl}/existDB.1 (78%)
rename debian/{ => man/meryl}/kmer-mask.1 (100%)
rename debian/{ => man/meryl}/mapMers-depth.1 (100%)
rename debian/{ => man/meryl}/mapMers.1 (100%)
rename debian/{ => man/meryl}/meryl.1 (100%)
rename debian/{ => man/meryl}/positionDB.1 (100%)
rename debian/{ => man/meryl}/simple.1 (100%)
create mode 120000 debian/man/sim4db/cleanPolishes.1
create mode 120000 debian/man/sim4db/comparePolishes.1
create mode 120000 debian/man/sim4db/convertPolishes.1
create mode 120000 debian/man/sim4db/convertToAtac.1
create mode 120000 debian/man/sim4db/convertToExtent.1
create mode 120000 debian/man/sim4db/depthOfPolishes.1
create mode 120000 debian/man/sim4db/detectChimera.1
create mode 120000 debian/man/sim4db/filterPolishes.1
create mode 120000 debian/man/sim4db/fixPolishesIID.1
create mode 120000 debian/man/sim4db/headPolishes.1
create mode 120000 debian/man/sim4db/mappedCoverage.1
create mode 120000 debian/man/sim4db/mergePolishes.1
create mode 120000 debian/man/sim4db/parseSNP.1
create mode 120000 debian/man/sim4db/pickBestPolish.1
create mode 120000 debian/man/sim4db/pickUniquePolish.1
create mode 120000 debian/man/sim4db/plotCoverageVsIdentity.1
create mode 120000 debian/man/sim4db/realignPolishes.1
create mode 120000 debian/man/sim4db/removeDuplicate.1
create mode 120000 debian/man/sim4db/reportAlignmentDifferences.1
create mode 100644 debian/man/sim4db/sim4db.1
create mode 100644 debian/man/sim4db/sim4dbutils.1
create mode 120000 debian/man/sim4db/sortPolishes.1
create mode 120000 debian/man/sim4db/summarizePolishes.1
create mode 120000 debian/man/sim4db/uniqPolishes.1
create mode 120000 debian/man/sim4db/vennPolishes.1
create mode 100644 debian/patches/allow-freebsd-build.patch
delete mode 100644 debian/patches/kazlib.patch
delete mode 100644 debian/patches/remove-kazlib.patch
create mode 100644 debian/sim4db.docs
create mode 100644 debian/sim4db.install
create mode 100644 debian/sim4db.manpages
create mode 100644 libutil/kazlib/Make.include
create mode 100755 libutil/kazlib/blast.pl
create mode 100644 libutil/kazlib/dict.c
create mode 100644 libutil/kazlib/dict.h
create mode 100644 libutil/kazlib/docs/CHANGES
create mode 100644 libutil/kazlib/docs/MUST_READ
create mode 100644 libutil/kazlib/docs/README
create mode 100644 libutil/kazlib/docs/docs.ist
create mode 100644 libutil/kazlib/docs/docs.ltx
create mode 100644 libutil/kazlib/drivers/dict-main.c
create mode 100644 libutil/kazlib/drivers/except-main.c
create mode 100644 libutil/kazlib/drivers/hash-main.c
create mode 100644 libutil/kazlib/drivers/list-main.c
create mode 100644 libutil/kazlib/drivers/sfx-main.c
create mode 100644 libutil/kazlib/except.c
create mode 100644 libutil/kazlib/except.h
create mode 100644 libutil/kazlib/hash.c
create mode 100644 libutil/kazlib/hash.h
create mode 100644 libutil/kazlib/list.c
create mode 100644 libutil/kazlib/list.h
create mode 100644 libutil/kazlib/sfx.c
create mode 100644 libutil/kazlib/sfx.h
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