[med-svn] [falconkit] branch master updated (cff44ea -> 18cf3d9)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Mar 9 07:38:39 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 cff44ea falconkit (0.1.3+20140820-1) unstable; urgency=low
new 7e22b66 Imported Upstream version 0.4.2
new 95df661 Merge tag 'upstream/0.4.2'
new c822ebd Prepare new revision
new f1512c2 Update Standards-Version to 3.9.7
new 0d09d3a Use encrypted protocols for VCS URLs
new 48fffcb Drop unneeded dependencies
new ed8a5e8 Drop incompatible patches and rules
new bb52cb6 Install test_data as doc rather than example
new 18cf3d9 Note the git revision where this release comes from
The 9 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:
.gitignore | 10 +
.gitmodules | 0
.travis.yml | 26 +
src/py/__init__.py => LICENSE | 5 +-
README.md | 156 +--
debian/changelog | 6 +
debian/control | 9 +-
debian/docs | 2 +-
debian/examples | 1 -
debian/patches/add-shebang-lines.patch | 12 -
debian/patches/python-multiarch.patch | 77 --
debian/patches/series | 2 -
debian/rules | 5 -
doc/README | 3 +
doc/falcon_icon.svg | 24 +
doc/falcon_icon2.png | Bin 0 -> 58715 bytes
doc/file_format_note.md | 113 --
examples/Dmel_asm.md | 250 ----
examples/HBAR.cfg | 72 -
examples/StarCluster.cfg | 24 -
examples/build_env.sh | 22 +
examples/build_env2.sh | 22 +
examples/ecoli_asm_graph_exploration.ipynb | 716 ++++++++++
examples/fc_run_LG.cfg | 36 +
examples/fc_run_arab.cfg | 36 +
examples/fc_run_dmel.cfg | 36 +
examples/fc_run_ecoli.cfg | 35 +
examples/fc_run_ecoli_2.cfg | 35 +
examples/install_note.sh | 84 --
examples/readme.md | 92 --
examples/run_asm.sh | 24 -
examples/run_ecoli_test.sh | 11 +
setup.py | 70 +-
src/c/DW_banded.c | 4 +-
src/c/Makefile | 2 +-
src/c/common.h | 5 +-
src/c/ext_falcon.c | 13 +
src/c/falcon.c | 622 ++++++---
src/c/kmer_lookup.c | 33 +-
src/py/FastaReader.py | 260 ++++
src/py/falcon_kit.py | 24 +-
src/py/fc_asm_graph.py | 212 +++
src/py/functional.py | 89 ++
src/py/mains/__init__.py | 0
src/py/mains/actg_coordinate.py | 27 +
.../falcon_sense.py => py/mains/consensus.py} | 144 +-
src/py/mains/contig_annotate.py | 29 +
src/py/mains/ctg_link_analysis.py | 80 ++
src/py/mains/dedup_a_tigs.py | 23 +
src/py/mains/graph_to_contig.py | 297 ++++
src/py/mains/graph_to_utgs.py | 160 +++
src/py/mains/ovlp_filter.py | 265 ++++
src/py/mains/ovlp_stats.py | 115 ++
src/py/mains/ovlp_to_graph.py | 1441 ++++++++++++++++++++
src/py/mains/run.py | 646 +++++++++
src/py/mains/tasks.py | 31 +
src/py/multiproc.py | 25 +
src/py/run_support.py | 475 +++++++
src/py/util/__init__.py | 0
src/py/util/io.py | 162 +++
src/py_scripts/fc_actg_coordinate.py | 5 +
src/py_scripts/fc_consensus.py | 5 +
src/py_scripts/fc_contig_annotate.py | 5 +
src/py_scripts/fc_ctg_link_analysis.py | 5 +
src/py_scripts/fc_dedup_a_tigs.py | 5 +
src/py_scripts/fc_graph_to_contig.py | 5 +
src/py_scripts/fc_graph_to_utgs.py | 5 +
src/py_scripts/fc_ovlp_filter.py | 5 +
src/py_scripts/fc_ovlp_stats.py | 5 +
src/py_scripts/fc_ovlp_to_graph.py | 5 +
src/py_scripts/fc_run.py | 5 +
src/{py_scripts => py_scripts_v0.1}/falcon_asm.py | 0
.../falcon_asm_s.py} | 869 +++++++-----
.../falcon_dedup.py | 0
.../falcon_fixasm.py | 4 +-
.../falcon_overlap.py | 0
.../falcon_overlap2.py | 0
src/{py_scripts => py_scripts_v0.1}/falcon_qrm.py | 0
.../falcon_qrm_0.py} | 132 +-
.../falcon_sense.py | 9 +-
.../falcon_ucns_data.py | 8 +-
.../falcon_utgcns.py | 0
src/py_scripts_v0.1/get_ovl.sh | 7 +
src/{py_scripts => py_scripts_v0.1}/get_rdata.py | 0
src/{py_scripts => py_scripts_v0.1}/overlapper.py | 0
src/py_scripts_v0.1/ovlp_filter.sh | 6 +
src/py_scripts_v0.1/redis_graph.py | 79 ++
.../remove_dup_ctg.py | 0
test/HPCdaligner_synth0.sh | 11 +
test/test_actg_coordinate.py | 9 +
test/test_consensus.py | 7 +
test/test_contig_annotate.py | 9 +
test/test_ctg_link_analysis.py | 9 +
test/test_functional.py | 31 +
test/test_graph_to_contig.py | 9 +
test/test_graph_to_utgs.py | 9 +
test/test_ovlp_filter.py | 65 +
test/test_ovlp_stats.py | 29 +
test/test_ovlp_to_graph.py | 7 +
test/test_run.py | 9 +
test/test_run_LG.py | 9 +
travis.sh | 18 +
102 files changed, 6962 insertions(+), 1638 deletions(-)
create mode 100644 .gitignore
create mode 100644 .gitmodules
create mode 100644 .travis.yml
copy src/py/__init__.py => LICENSE (95%)
delete mode 100644 debian/patches/add-shebang-lines.patch
delete mode 100644 debian/patches/python-multiarch.patch
create mode 100644 doc/README
create mode 100644 doc/falcon_icon.svg
create mode 100644 doc/falcon_icon2.png
delete mode 100644 doc/file_format_note.md
delete mode 100644 examples/Dmel_asm.md
delete mode 100755 examples/HBAR.cfg
delete mode 100644 examples/StarCluster.cfg
create mode 100644 examples/build_env.sh
create mode 100644 examples/build_env2.sh
create mode 100644 examples/ecoli_asm_graph_exploration.ipynb
create mode 100755 examples/fc_run_LG.cfg
create mode 100644 examples/fc_run_arab.cfg
create mode 100644 examples/fc_run_dmel.cfg
create mode 100644 examples/fc_run_ecoli.cfg
create mode 100644 examples/fc_run_ecoli_2.cfg
delete mode 100644 examples/install_note.sh
delete mode 100644 examples/readme.md
delete mode 100644 examples/run_asm.sh
create mode 100644 examples/run_ecoli_test.sh
create mode 100644 src/c/ext_falcon.c
create mode 100644 src/py/FastaReader.py
create mode 100644 src/py/fc_asm_graph.py
create mode 100644 src/py/functional.py
create mode 100644 src/py/mains/__init__.py
create mode 100644 src/py/mains/actg_coordinate.py
copy src/{py_scripts/falcon_sense.py => py/mains/consensus.py} (65%)
create mode 100644 src/py/mains/contig_annotate.py
create mode 100644 src/py/mains/ctg_link_analysis.py
create mode 100644 src/py/mains/dedup_a_tigs.py
create mode 100644 src/py/mains/graph_to_contig.py
create mode 100644 src/py/mains/graph_to_utgs.py
create mode 100644 src/py/mains/ovlp_filter.py
create mode 100644 src/py/mains/ovlp_stats.py
create mode 100644 src/py/mains/ovlp_to_graph.py
create mode 100644 src/py/mains/run.py
create mode 100644 src/py/mains/tasks.py
create mode 100644 src/py/multiproc.py
create mode 100644 src/py/run_support.py
create mode 100644 src/py/util/__init__.py
create mode 100644 src/py/util/io.py
create mode 100644 src/py_scripts/fc_actg_coordinate.py
create mode 100644 src/py_scripts/fc_consensus.py
create mode 100644 src/py_scripts/fc_contig_annotate.py
create mode 100644 src/py_scripts/fc_ctg_link_analysis.py
create mode 100644 src/py_scripts/fc_dedup_a_tigs.py
create mode 100644 src/py_scripts/fc_graph_to_contig.py
create mode 100644 src/py_scripts/fc_graph_to_utgs.py
create mode 100644 src/py_scripts/fc_ovlp_filter.py
create mode 100644 src/py_scripts/fc_ovlp_stats.py
create mode 100644 src/py_scripts/fc_ovlp_to_graph.py
create mode 100644 src/py_scripts/fc_run.py
rename src/{py_scripts => py_scripts_v0.1}/falcon_asm.py (100%)
rename src/{py_scripts/falcon_asm_dev.py => py_scripts_v0.1/falcon_asm_s.py} (55%)
rename src/{py_scripts => py_scripts_v0.1}/falcon_dedup.py (100%)
rename src/{py_scripts => py_scripts_v0.1}/falcon_fixasm.py (98%)
rename src/{py_scripts => py_scripts_v0.1}/falcon_overlap.py (100%)
rename src/{py_scripts => py_scripts_v0.1}/falcon_overlap2.py (100%)
copy src/{py_scripts => py_scripts_v0.1}/falcon_qrm.py (100%)
rename src/{py_scripts/falcon_qrm.py => py_scripts_v0.1/falcon_qrm_0.py} (80%)
rename src/{py_scripts => py_scripts_v0.1}/falcon_sense.py (95%)
rename src/{py_scripts => py_scripts_v0.1}/falcon_ucns_data.py (96%)
rename src/{py_scripts => py_scripts_v0.1}/falcon_utgcns.py (100%)
create mode 100644 src/py_scripts_v0.1/get_ovl.sh
rename src/{py_scripts => py_scripts_v0.1}/get_rdata.py (100%)
rename src/{py_scripts => py_scripts_v0.1}/overlapper.py (100%)
create mode 100644 src/py_scripts_v0.1/ovlp_filter.sh
create mode 100644 src/py_scripts_v0.1/redis_graph.py
rename src/{py_scripts => py_scripts_v0.1}/remove_dup_ctg.py (100%)
create mode 100644 test/HPCdaligner_synth0.sh
create mode 100644 test/test_actg_coordinate.py
create mode 100644 test/test_consensus.py
create mode 100644 test/test_contig_annotate.py
create mode 100644 test/test_ctg_link_analysis.py
create mode 100644 test/test_functional.py
create mode 100644 test/test_graph_to_contig.py
create mode 100644 test/test_graph_to_utgs.py
create mode 100644 test/test_ovlp_filter.py
create mode 100644 test/test_ovlp_stats.py
create mode 100644 test/test_ovlp_to_graph.py
create mode 100644 test/test_run.py
create mode 100644 test/test_run_LG.py
create mode 100755 travis.sh
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