[med-svn] [falconkit] 02/09: Merge tag 'upstream/0.4.2'
Afif Elghraoui
afif at moszumanska.debian.org
Wed Mar 9 07:38:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository falconkit.
commit 95df661dc26ef220d329f894f10350b25535bb5e
Merge: cff44ea 7e22b66
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Tue Mar 8 22:40:27 2016 -0800
Merge tag 'upstream/0.4.2'
Upstream version 0.4.2
.gitignore | 10 +
.gitmodules | 0
.travis.yml | 26 +
src/py_scripts/remove_dup_ctg.py => LICENSE | 41 +-
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(+), 1570 deletions(-)
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/falconkit.git
More information about the debian-med-commit
mailing list