[med-svn] [kmer] branch topic/atac-and-est updated (5ae2c5f -> 9c785c4)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Nov 30 10:22:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch topic/atac-and-est
in repository kmer.
discards 5ae2c5f Draft packaging for ATAC and ESTMapper
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
adds defa5e2 Fix source URL and debian/copyright
adds 5f20767 Prepare new revision
adds f97648f Rename source package to match primary binary package
adds 92700f5 Fix upstream name in d/copyright
adds 4846d3e Update my email address
adds 491095f Bump Standards-Version to 3.9.7
adds c34a91c Update VCS URLs
adds 3692fc0 Provide fake watch file to keep QA tools silent about no watch information
adds 045d6e5 debhelper 10
adds ce0895f cme fix dpkg-control
adds 98f5de7 upload to unstable
adds e1eaa56 Revert rename (f97648f1440752e246908af428a4b80e8bec7a28) for the moment since the only goal of this upload is to silence QA tools via fake watch file
adds 9109f28 Use Afif's debian.org address
adds c75f471 hardening=+all
new 8bb45fe new binary package: atac
new 9c785c4 (WIP) new binary package - estmapper
This update added new revisions after undoing existing revisions.
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branch are not in the new version. This situation occurs
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containing something like this:
* -- * -- B -- O -- O -- O (5ae2c5f)
\
N -- N -- N refs/heads/topic/atac-and-est (9c785c4)
You should already have received notification emails for all of the O
revisions, and so the following emails describe only the N revisions
from the common base, B.
Any revisions marked "omits" are not gone; other references still
refer to them. Any revisions marked "discards" are gone forever.
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:
debian/README.Debian | 10 ++
debian/README.source | 24 +++-
debian/atac.install | 70 ++++++++++--
debian/changelog | 36 +++++-
debian/compat | 2 +-
debian/control | 54 ++++-----
debian/copyright | 105 +++++++++++++++++-
debian/estmapper.install | 17 ++-
debian/leaff.manpages | 1 +
README.leaff => debian/man/leaff/leaff.1 | 104 +++++------------
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/patches/allow-freebsd-build.patch | 121 ++++++++++++++++++++
debian/patches/atac-helper-script-paths.patch | 38 ++++---
debian/patches/estmapper-helper-script-paths.patch | 75 +++++++++++++
debian/patches/series | 2 +
debian/rules | 9 +-
debian/sim4db.install | 46 +++++---
debian/sim4db.manpages | 1 +
debian/watch | 4 +
43 files changed, 772 insertions(+), 153 deletions(-)
create mode 100644 debian/README.Debian
create mode 100644 debian/leaff.manpages
copy README.leaff => debian/man/leaff/leaff.1 (74%)
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
create mode 100644 debian/patches/estmapper-helper-script-paths.patch
create mode 100644 debian/sim4db.manpages
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