[med-svn] [abyss] branch master updated (af90083 -> 7697c42)
Charles Plessy
plessy at alioth.debian.org
Sun Sep 8 05:30:18 UTC 2013
This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch master
in repository abyss.
from af90083 releasing version 1.3.4-4
new 7edc28b Signal the use of git-buildpackage with this configuration file.
new 35fc6ca Initial upstream branch.
new 9587450 Imported 1.3.4 by hand.
new 9ec0c9c Connect the master and upstream branches with a merge.
new e05ee57 Imported Upstream version 1.3.5
new 55af673 Merge tag 'upstream/1.3.5'
new b391f1f Imported Upstream version 1.3.6
new c82f441 Merge tag 'upstream/1.3.6'
new 338dbbf Preparing the update to 1.3.6.
new a3beaac Normalised source package control file with config-model-edit.
new 02ab649 No new copyright nor license statement in the new upstream release.
new dd86394 Conforms with Policy version 3.9.4.
new 71d42ad Normalised VCS URLs.
new 7697c42 abyss (1.3.6-1) unstable; urgency=low
The 14 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:
ABYSS/Makefile.in | 224 +++++++++-----
AdjList/AdjList.cpp | 8 +-
AdjList/Makefile.in | 224 +++++++++-----
Align/Makefile.am | 17 +-
Align/Makefile.in | 371 ++++++++++++++--------
Align/Options.h | 11 +
Align/align.cc | 7 +-
Align/mergepairs.cc | 333 ++++++++++++++++++++
Align/smith_waterman.cpp | 24 +-
Assembly/Makefile.in | 291 ++++++++++-------
Assembly/Options.cpp | 4 +-
COPYRIGHT | 12 +-
ChangeLog | 97 ++++++
Common/BitUtil.h | 42 +--
Common/ContigProperties.h | 4 +
Common/Histogram.h | 45 ++-
Common/Makefile.in | 403 ++++++++++++++----------
Common/SAM.h | 21 ++
Common/SeqExt.h | 10 +-
Common/Sequence.cpp | 47 ++-
Common/Uncompress.cpp | 57 +++-
Consensus/Consensus.cpp | 7 +-
Consensus/Makefile.in | 224 +++++++++-----
DAssembler/DAssembler.cpp | 7 +-
DAssembler/Makefile.in | 248 +++++++++------
DataLayer/FastaReader.cpp | 33 +-
DataLayer/FastaReader.h | 5 +-
DataLayer/Makefile.in | 310 ++++++++++++-------
DataLayer/abyss-tofastq.cc | 4 +-
DataLayer/fac.cc | 49 ++-
DistanceEst/DistanceEst.cpp | 48 ++-
DistanceEst/MLE.cpp | 2 +-
DistanceEst/Makefile.in | 248 +++++++++------
FMIndex/Makefile.in | 255 +++++++++------
FMIndex/abyss-dawg.cc | 6 +-
FMIndex/count.cc | 6 +-
FilterGraph/FilterGraph.cpp | 46 ++-
FilterGraph/Makefile.in | 224 +++++++++-----
Graph/AdjIO.h | 12 +-
Graph/ContigGraphAlgorithms.h | 2 +-
Graph/GraphAlgorithms.h | 6 +-
Graph/Makefile.in | 294 +++++++++++-------
Graph/gc.cc | 4 +-
Graph/todot.cc | 4 +-
KAligner/KAligner.cpp | 6 +-
KAligner/Makefile.in | 248 +++++++++------
LICENSE | 2 +-
Layout/Makefile.am | 5 +
{SimpleGraph => Layout}/Makefile.in | 274 +++++++++-------
Layout/layout.cc | 319 +++++++++++++++++++
Makefile.am | 4 +-
Makefile.in | 296 +++++++++---------
Map/Makefile.in | 262 ++++++++++------
Map/index.cc | 6 +-
Map/map.cc | 59 +++-
Map/overlap.cc | 55 +++-
MergePaths/Makefile.in | 262 ++++++++++------
MergePaths/MergeContigs.cpp | 10 +-
MergePaths/MergePaths.cpp | 7 +-
MergePaths/PathConsensus.cpp | 6 +-
Misc/Makefile.am | 12 +
{ABYSS => Misc}/Makefile.in | 272 ++++++++--------
Misc/samtobreak.hs | 327 ++++++++++++++++++++
Overlap/Makefile.in | 224 +++++++++-----
Overlap/Overlap.cpp | 4 +-
Parallel/Makefile.in | 296 +++++++++++-------
Parallel/NetworkSequenceCollection.cpp | 13 +-
Parallel/parallelAbyss.cpp | 4 +
ParseAligns/Makefile.in | 259 ++++++++++------
ParseAligns/ParseAligns.cpp | 4 +-
ParseAligns/abyss-fixmate.cc | 134 +++++++-
PathOverlap/Makefile.in | 224 +++++++++-----
PathOverlap/PathOverlap.cpp | 7 +-
PopBubbles/Makefile.in | 224 +++++++++-----
PopBubbles/PopBubbles.cpp | 22 +-
README.html | 41 ++-
README.md | 29 +-
Scaffold/Makefile.in | 262 ++++++++++------
Scaffold/drawgraph.cc | 7 +-
Scaffold/junction.cc | 7 +-
Scaffold/scaffold.cc | 31 +-
SimpleGraph/Makefile.in | 224 +++++++++-----
SimpleGraph/SimpleGraph.cpp | 7 +-
aclocal.m4 | 485 +++++++++++++++++++----------
bin/Makefile.in | 110 ++++---
bin/abyss-pe | 31 +-
compile | 347 +++++++++++++++++++++
config.h.in | 9 +-
configure | 392 ++++++++++++++++++++---
configure.ac | 27 +-
debian/changelog | 12 +
debian/control | 28 +-
debian/copyright | 4 +-
debian/gbp.conf | 9 +
depcomp | 531 +++++++++++++++++++++-----------
dialign/Makefile.in | 192 ++++++++----
doc/ABYSS.1 | 12 +-
doc/Makefile.in | 124 +++++---
doc/abyss-pe.1 | 16 +-
doc/abyss-tofastq.1 | 4 +-
doc/flowchart.pdf | Bin 77904 -> 165274 bytes
doxygen.conf | 16 +-
install-sh | 35 ++-
kmerprint/Makefile.in | 195 +++++++-----
kmerprint/kmerprint.cc | 103 +++++--
missing | 461 +++++++++------------------
106 files changed, 8127 insertions(+), 3767 deletions(-)
create mode 100644 Align/Options.h
create mode 100644 Align/mergepairs.cc
create mode 100644 Layout/Makefile.am
copy {SimpleGraph => Layout}/Makefile.in (60%)
create mode 100644 Layout/layout.cc
create mode 100644 Misc/Makefile.am
copy {ABYSS => Misc}/Makefile.in (63%)
create mode 100644 Misc/samtobreak.hs
create mode 100755 compile
create mode 100644 debian/gbp.conf
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