[med-svn] [falcon] branch master updated (a2a0668 -> 583701b)
Afif Elghraoui
afif at moszumanska.debian.org
Sat Dec 16 08:03:28 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository falcon.
from a2a0668 Added references to registries.
new 7f1630a d/get-orig-source: make more robust
new 2082337 d/get-orig-source: use git clone --recursive to get submodules
new 698b47d d/get-orig-source: remove uscan-retrieved deficient tarball
new 6fa9904 New upstream version 1.8.8
new c2169c5 Merge tag 'upstream/1.8.8'
new 353e433 Update and refresh patches
new b64bf5b Incorporate changes from NMU (1.8.6-1.1)
new 8481d56 d/control: Exclude x32
new e907381 Update changelog
new 4f40b16 d/tests/control: s/ADTTMP/AUTOPKGTEST_TMP/
new c881a01 Update unit test invocation
new eacda7c Re-enable integration tests
new a61a633 Update copyright years
new 7633f80 Bump Standards-Version to 4.1.2
new 583701b releasing package falcon version 1.8.8-1
The 15 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:
DALIGNER/DBX.c | 85 ++
DALIGNER/DBX.h | 25 +
DALIGNER/GNUmakefile | 1 +
DALIGNER/LA4Falcon.c | 58 +-
DALIGNER/bamboo_build.sh | 28 +
DAZZ_DB/bamboo_build.sh | 23 +
FALCON-examples/git-sym.makefile | 6 +-
FALCON-examples/makefile | 2 +-
FALCON-examples/run/ecoli/fc_run.cfg | 8 +-
FALCON-examples/run/greg200k-sv2/fc_run.cfg | 13 +
FALCON-examples/run/greg200k-sv2/fc_unzip.cfg | 14 +-
FALCON-examples/run/greg200k-sv2/input.fofn | 4 +-
FALCON-examples/run/greg200k-sv2/input_bam.fofn | 2 +
.../run/synth0/{fc_run.cfg => fc_preads.cfg} | 26 +-
FALCON-examples/run/synth0/fc_run.cfg | 19 +-
FALCON-examples/run/synth0/makefile | 4 +-
FALCON-examples/run/synth0/preads.fofn | 2 +
FALCON/.travis.yml | 4 +-
FALCON/bamboo_build.sh | 28 +
FALCON/bamboo_test.sh | 14 +
FALCON/falcon_kit/FastaReader.py | 165 +--
FALCON/falcon_kit/__init__.py | 38 -
FALCON/falcon_kit/bash.py | 19 +-
FALCON/falcon_kit/falcon_kit.py | 47 +-
FALCON/falcon_kit/fc_asm_graph.py | 44 +-
FALCON/falcon_kit/functional.py | 22 +-
FALCON/falcon_kit/mains/actg_coordinate.py | 14 +-
FALCON/falcon_kit/mains/calc_cutoff.py | 20 +-
FALCON/falcon_kit/mains/dedup_a_tigs.py | 6 +-
FALCON/falcon_kit/mains/fetch_reads.py | 36 +-
FALCON/falcon_kit/mains/get_read_ctg_map.py | 3 +-
FALCON/falcon_kit/mains/graph_to_contig.py | 6 +-
FALCON/falcon_kit/mains/ovlp_filter.py | 8 +-
FALCON/falcon_kit/mains/ovlp_to_graph.py | 3 +-
FALCON/falcon_kit/mains/run1.py | 55 +-
FALCON/falcon_kit/pype_tasks.py | 4 +-
FALCON/falcon_kit/run_support.py | 49 +-
FALCON/falcon_kit/stats_preassembly.py | 17 +-
FALCON/falcon_kit/util/system.py | 9 +
FALCON/makefile | 65 ++
FALCON/mycoverage.cfg | 5 +
FALCON/mysitecustomize.py | 3 +
FALCON/setup.py | 1 +
FALCON/src/c/falcon.c | 13 +-
FALCON/src/py_scripts_v0.1/falcon_asm.py | 1154 ------------------
FALCON/src/py_scripts_v0.1/falcon_asm_s.py | 1220 --------------------
FALCON/src/py_scripts_v0.1/falcon_dedup.py | 119 --
FALCON/src/py_scripts_v0.1/falcon_fixasm.py | 213 ----
FALCON/src/py_scripts_v0.1/falcon_overlap.py | 328 ------
FALCON/src/py_scripts_v0.1/falcon_overlap2.py | 337 ------
FALCON/src/py_scripts_v0.1/falcon_qrm.py | 370 ------
FALCON/src/py_scripts_v0.1/falcon_qrm_0.py | 378 ------
FALCON/src/py_scripts_v0.1/falcon_sense.py | 248 ----
FALCON/src/py_scripts_v0.1/falcon_ucns_data.py | 120 --
FALCON/src/py_scripts_v0.1/falcon_utgcns.py | 124 --
FALCON/src/py_scripts_v0.1/get_ovl.sh | 7 -
FALCON/src/py_scripts_v0.1/get_rdata.py | 207 ----
FALCON/src/py_scripts_v0.1/overlapper.py | 216 ----
FALCON/src/py_scripts_v0.1/ovlp_filter.sh | 6 -
FALCON/src/py_scripts_v0.1/redis_graph.py | 79 --
FALCON/src/py_scripts_v0.1/remove_dup_ctg.py | 75 --
FALCON/test/helpers.py | 4 +
FALCON/test/test_calc_cutoff.py | 43 +
FALCON/test/test_functional.py | 14 +
FALCON/test/test_stats_preassembly.py | 17 +-
FALCON/test_data/calc_cutoff/partial_capture.txt | 5 +
FALCON/travis.sh | 17 +-
bamboo_build_and_test.sh | 42 +
debian/changelog | 26 +-
debian/control | 5 +-
debian/copyright | 4 +-
debian/get-orig-source | 22 +-
debian/patches/build-system.patch | 2 +-
debian/patches/versioned-deps.patch | 2 +-
debian/rules | 2 +-
debian/tests/control | 15 +-
makefile | 6 +-
pypeFLOW/bamboo_build.sh | 29 +
pypeFLOW/makefile | 3 +
pypeFLOW/pwatcher/blocking.py | 4 +-
pypeFLOW/pwatcher/fs_based.py | 54 +-
pypeFLOW/pwatcher/mains/pypeflow_example.py | 14 +-
pypeFLOW/pwatcher/mains/query_server.py | 3 +-
pypeFLOW/pwatcher/network_based.py | 17 +-
pypeFLOW/pypeflow/do_task.py | 30 +-
pypeFLOW/pypeflow/simple_pwatcher_bridge.py | 2 +-
pypeFLOW/pypeflow/util.py | 7 +
travis.sh | 11 +-
88 files changed, 932 insertions(+), 5687 deletions(-)
create mode 100644 DALIGNER/DBX.c
create mode 100644 DALIGNER/DBX.h
create mode 100644 DALIGNER/bamboo_build.sh
create mode 100644 DAZZ_DB/bamboo_build.sh
create mode 100644 FALCON-examples/run/greg200k-sv2/input_bam.fofn
copy FALCON-examples/run/synth0/{fc_run.cfg => fc_preads.cfg} (71%)
create mode 100644 FALCON-examples/run/synth0/preads.fofn
create mode 100644 FALCON/bamboo_build.sh
create mode 100644 FALCON/bamboo_test.sh
create mode 100644 FALCON/makefile
create mode 100644 FALCON/mycoverage.cfg
create mode 100644 FALCON/mysitecustomize.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_asm.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_asm_s.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_dedup.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_fixasm.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_overlap.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_overlap2.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_qrm.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_qrm_0.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_sense.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_ucns_data.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_utgcns.py
delete mode 100644 FALCON/src/py_scripts_v0.1/get_ovl.sh
delete mode 100755 FALCON/src/py_scripts_v0.1/get_rdata.py
delete mode 100644 FALCON/src/py_scripts_v0.1/overlapper.py
delete mode 100644 FALCON/src/py_scripts_v0.1/ovlp_filter.sh
delete mode 100644 FALCON/src/py_scripts_v0.1/redis_graph.py
delete mode 100755 FALCON/src/py_scripts_v0.1/remove_dup_ctg.py
create mode 100644 FALCON/test/test_calc_cutoff.py
create mode 100644 FALCON/test_data/calc_cutoff/partial_capture.txt
create mode 100755 bamboo_build_and_test.sh
create mode 100644 pypeFLOW/bamboo_build.sh
create mode 100644 pypeFLOW/makefile
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/falcon.git
More information about the debian-med-commit
mailing list