[med-svn] [falconkit] branch upstream updated (0627e02 -> 7e22b66)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Mar 9 07:38:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository falconkit.
from 0627e02 Imported Upstream version 0.1.3+20140820
new 7e22b66 Imported Upstream version 0.4.2
The 1 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 +--
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 +
94 files changed, 6952 insertions(+), 1534 deletions(-)
create mode 100644 .gitignore
create mode 100644 .gitmodules
create mode 100644 .travis.yml
copy src/py/__init__.py => LICENSE (95%)
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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