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commit 95df661dc26ef220d329f894f10350b25535bb5e Merge: cff44ea 7e22b66 Author: Afif Elghraoui <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
