[med-svn] [falconkit] branch master updated (676072c -> be234b7)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Jun 22 14:27:49 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository falconkit.
from 676072c Set up test suite
new 04596f2 Remove README.Debian
new cf4e449 Add README.source explaining how to find releases
new 7621e55 Update email address and copyright year
new 0182114 Update source URL to current release series
new a091a1a Bump Standards-Version to 3.9.8
new e0f534b Rename source and binary package to match upstream name
new 95f7712 Imported Upstream version 0.7
new 96f1e69 Merge tag 'upstream/0.7'
new fb95bc7 Use DEB_SOURCE variable rather than hard-coding package name
new 957cb7e Globally use C.UTF-8 locale
new 87a37ce Add minimum dependency on networkx
new d6a9bed Revert "Rename source and binary package to match upstream name"
new ad9b257 Update shebang lines patch
new e6b22b6 Remove max version limit for networkx
new cbcd0f5 Don't install legacy py_scripts
new be5c0a2 Remove partial description from manpage - it still needs work
new 899dac9 Fix permissions on non-executable file
new be234b7 releasing package falconkit version 0.7-1
The 18 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:
README.md | 4 +-
debian/README.Debian | 8 -
debian/README.source | 13 +
debian/changelog | 11 +-
debian/control | 7 +-
debian/copyright | 4 +-
debian/falconkit.1 | 2 -
debian/patches/add-shebang-lines.patch | 8 +
debian/patches/networkx-version.patch | 17 +
debian/patches/pyscripts.patch | 14 +
debian/patches/series | 2 +
debian/rules | 21 +-
examples/fc_run_LG.cfg | 2 +-
examples/fc_run_arab.cfg | 2 +-
examples/fc_run_dmel.cfg | 2 +-
examples/fc_run_ecoli.cfg | 2 +-
examples/fc_run_ecoli_2.cfg | 2 +-
examples/logging.json | 35 ++
{src/py => falcon_kit}/FastaReader.py | 2 +-
{src/py => falcon_kit}/__init__.py | 0
falcon_kit/bash.py | 319 ++++++++++
{src/py => falcon_kit}/falcon_kit.py | 20 +-
{src/py => falcon_kit}/fc_asm_graph.py | 2 +-
falcon_kit/functional.py | 197 ++++++
{src/py => falcon_kit}/mains/__init__.py | 0
{src/py => falcon_kit}/mains/actg_coordinate.py | 2 +-
falcon_kit/mains/calc_cutoff.py | 36 ++
{src/py => falcon_kit}/mains/consensus.py | 116 ++--
{src/py => falcon_kit}/mains/contig_annotate.py | 2 +-
{src/py => falcon_kit}/mains/ctg_link_analysis.py | 13 +-
{src/py => falcon_kit}/mains/dedup_a_tigs.py | 3 +-
falcon_kit/mains/fasta2fasta.py | 239 +++++++
{src/py => falcon_kit}/mains/graph_to_contig.py | 4 +-
{src/py => falcon_kit}/mains/graph_to_utgs.py | 16 +-
{src/py => falcon_kit}/mains/ovlp_filter.py | 25 +-
{src/py => falcon_kit}/mains/ovlp_stats.py | 22 +-
{src/py => falcon_kit}/mains/ovlp_to_graph.py | 726 ++++++++++++----------
src/py/mains/run.py => falcon_kit/mains/run0.py | 533 ++++++++--------
falcon_kit/mains/run1.py | 542 ++++++++++++++++
{src/py => falcon_kit}/mains/tasks.py | 0
{src/py => falcon_kit}/multiproc.py | 0
falcon_kit/run_support.py | 472 ++++++++++++++
falcon_kit/stats_preassembly.py | 199 ++++++
{src/py => falcon_kit}/util/__init__.py | 0
{src/py => falcon_kit}/util/io.py | 18 +-
falcon_kit/util/system.py | 32 +
setup.py | 26 +-
src/c/DW_banded.c | 36 +-
src/c/ext_falcon.c | 2 +-
src/c/falcon.c | 126 ++--
src/c/kmer_lookup.c | 46 +-
src/py/functional.py | 89 ---
src/py/run_support.py | 475 --------------
src/py_scripts/fc_run.py | 2 +-
src/py_scripts_v0.1/falcon_asm.py | 282 ++++-----
src/py_scripts_v0.1/falcon_asm_s.py | 278 ++++-----
src/py_scripts_v0.1/falcon_dedup.py | 12 +-
src/py_scripts_v0.1/falcon_fixasm.py | 16 +-
src/py_scripts_v0.1/falcon_overlap.py | 52 +-
src/py_scripts_v0.1/falcon_overlap2.py | 52 +-
src/py_scripts_v0.1/falcon_qrm.py | 48 +-
src/py_scripts_v0.1/falcon_qrm_0.py | 52 +-
src/py_scripts_v0.1/falcon_sense.py | 20 +-
src/py_scripts_v0.1/falcon_ucns_data.py | 10 +-
src/py_scripts_v0.1/falcon_utgcns.py | 20 +-
src/py_scripts_v0.1/get_rdata.py | 12 +-
src/py_scripts_v0.1/overlapper.py | 30 +-
src/py_scripts_v0.1/redis_graph.py | 2 +-
src/utils/fetch_preads.py | 4 +-
test/HPCdaligner_synth0.sh | 2 +-
test/helpers.py | 14 +
test/test_functional.py | 90 ++-
test/test_stats_preassembly.py | 53 ++
travis.sh | 4 +-
74 files changed, 3705 insertions(+), 1846 deletions(-)
delete mode 100644 debian/README.Debian
create mode 100644 debian/README.source
create mode 100644 debian/patches/networkx-version.patch
create mode 100644 debian/patches/pyscripts.patch
create mode 100644 examples/logging.json
rename {src/py => falcon_kit}/FastaReader.py (99%)
rename {src/py => falcon_kit}/__init__.py (100%)
create mode 100644 falcon_kit/bash.py
rename {src/py => falcon_kit}/falcon_kit.py (96%)
rename {src/py => falcon_kit}/fc_asm_graph.py (99%)
create mode 100644 falcon_kit/functional.py
rename {src/py => falcon_kit}/mains/__init__.py (100%)
rename {src/py => falcon_kit}/mains/actg_coordinate.py (94%)
create mode 100644 falcon_kit/mains/calc_cutoff.py
rename {src/py => falcon_kit}/mains/consensus.py (69%)
rename {src/py => falcon_kit}/mains/contig_annotate.py (95%)
rename {src/py => falcon_kit}/mains/ctg_link_analysis.py (87%)
rename {src/py => falcon_kit}/mains/dedup_a_tigs.py (93%)
create mode 100755 falcon_kit/mains/fasta2fasta.py
rename {src/py => falcon_kit}/mains/graph_to_contig.py (98%)
rename {src/py => falcon_kit}/mains/graph_to_utgs.py (98%)
rename {src/py => falcon_kit}/mains/ovlp_filter.py (94%)
rename {src/py => falcon_kit}/mains/ovlp_stats.py (79%)
rename {src/py => falcon_kit}/mains/ovlp_to_graph.py (83%)
rename src/py/mains/run.py => falcon_kit/mains/run0.py (52%)
create mode 100644 falcon_kit/mains/run1.py
rename {src/py => falcon_kit}/mains/tasks.py (100%)
rename {src/py => falcon_kit}/multiproc.py (100%)
create mode 100644 falcon_kit/run_support.py
create mode 100644 falcon_kit/stats_preassembly.py
rename {src/py => falcon_kit}/util/__init__.py (100%)
rename {src/py => falcon_kit}/util/io.py (93%)
create mode 100644 falcon_kit/util/system.py
delete mode 100644 src/py/functional.py
delete mode 100644 src/py/run_support.py
create mode 100644 test/helpers.py
create mode 100644 test/test_stats_preassembly.py
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