[med-svn] [falcon] 05/08: Merge tag 'upstream/1.7.5'
Afif Elghraoui
afif at moszumanska.debian.org
Sun Oct 23 12:18:48 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository falcon.
commit b828c5c7982e911a076c70ba67152191dc49973e
Merge: ffe1a23 8bf7774
Author: Afif Elghraoui <afif at debian.org>
Date: Sat Oct 22 22:29:46 2016 -0700
Merge tag 'upstream/1.7.5'
Upstream version 1.7.5
.gitignore | 10 -
.travis.yml | 24 +-
DALIGNER/DB2Falcon.c | 133 +
DALIGNER/GNUmakefile | 33 +
DALIGNER/HPC.daligner.c | 1585 ++
DALIGNER/LA4Falcon.c | 802 +
DALIGNER/LA4Ice.c | 568 +
DALIGNER/LAcat.c | 192 +
DALIGNER/LAcheck.c | 361 +
DALIGNER/LAdump.c | 487 +
DALIGNER/LAindex.c | 201 +
DALIGNER/LAmerge.c | 397 +
DALIGNER/LAshow.c | 618 +
DALIGNER/LAsort.c | 285 +
DALIGNER/LAsplit.c | 242 +
DALIGNER/LICENSE | 34 +
DALIGNER/Makefile | 53 +
DALIGNER/README | 521 +
DALIGNER/README_PB.md | 8 +
DALIGNER/align.c | 5157 +++++
DALIGNER/align.h | 354 +
DALIGNER/daligner.c | 731 +
DALIGNER/daligner_p.c | 1 +
DALIGNER/filter.c | 2306 +++
DALIGNER/filter.h | 35 +
DALIGNER/filter_p.c | 2 +
DALIGNER/py_utils/DAPI.py | 72 +
DALIGNER/py_utils/DAPipe.py | 93 +
DALIGNER/py_utils/DBLA_to_falcon.py | 42 +
DALIGNER/py_utils/FALCON_ASM_NOTE | 27 +
DALIGNER/py_utils/LAPI.py | 110 +
DALIGNER/py_utils/LAPipe.py | 177 +
DAMASKER/DB.c | 1736 ++
DAMASKER/DB.h | 420 +
DAMASKER/GNUmakefile | 25 +
DAMASKER/HPC.REPmask.c | 877 +
DAMASKER/HPC.TANmask.c | 530 +
DAMASKER/Makefile | 34 +
DAMASKER/QV.c | 1387 ++
DAMASKER/QV.h | 96 +
DAMASKER/README | 172 +
DAMASKER/REPmask.c | 636 +
DAMASKER/TANmask.c | 462 +
DAMASKER/align.c | 5157 +++++
DAMASKER/align.h | 354 +
DAMASKER/datander.c | 182 +
DAMASKER/tandem.c | 1364 ++
DAMASKER/tandem.h | 24 +
DAZZ_DB/Catrack.c | 259 +
DAZZ_DB/DAM2fasta.c | 213 +
DAZZ_DB/DB.c | 1742 ++
DAZZ_DB/DB.h | 420 +
DAZZ_DB/DB2fasta.c | 180 +
DAZZ_DB/DB2quiva.c | 189 +
DAZZ_DB/DBdump.c | 784 +
DAZZ_DB/DBdust.c | 471 +
DAZZ_DB/DBrm.c | 40 +
DAZZ_DB/DBshow.c | 579 +
DAZZ_DB/DBsplit.c | 216 +
DAZZ_DB/DBstats.c | 346 +
DAZZ_DB/DBupgrade.Dec.31.2014.c | 86 +
DAZZ_DB/DBupgrade.Sep.25.2014.c | 96 +
DAZZ_DB/DUSTupgrade.Jan.1.2015.c | 80 +
DAZZ_DB/GNUmakefile | 41 +
DAZZ_DB/LICENSE | 34 +
DAZZ_DB/Makefile | 75 +
DAZZ_DB/QV.c | 1387 ++
DAZZ_DB/QV.h | 96 +
DAZZ_DB/README | 502 +
DAZZ_DB/fasta2DAM.c | 687 +
DAZZ_DB/fasta2DB.c | 728 +
DAZZ_DB/quiva2DB.c | 510 +
DAZZ_DB/rangen.c | 182 +
DAZZ_DB/simulator.c | 573 +
FALCON-examples/LICENSE | 23 +
FALCON-examples/README.md | 24 +
FALCON-examples/data/git-sym.makefile | 30 +
FALCON-examples/data/makefile | 16 +
FALCON-examples/git-sym.makefile | 31 +
FALCON-examples/logging.ini | 46 +
FALCON-examples/makefile | 20 +
.../run/arab/fc_run.cfg | 9 +-
FALCON-examples/run/arab/input.fofn | 1 +
.../run/ecoli/fc_run.cfg | 8 +-
FALCON-examples/run/ecoli/input.fofn | 3 +
.../run/ecoli2/fc_run.cfg | 6 +-
FALCON-examples/run/ecoli2/input.fofn | 3 +
.../run/lambda-hgap/fc_run.cfg | 24 +-
FALCON-examples/run/lambda-hgap/input.fofn | 1 +
FALCON-examples/run/lambda-smb14/fc_run.cfg | 37 +
FALCON-examples/run/lambda-smb14/input.fofn | 1 +
FALCON-examples/run/lambda-smb14/logging.ini | 46 +
.../run/lambda/fc_run.cfg | 25 +-
FALCON-examples/run/lambda/input.fofn | 1 +
FALCON-examples/run/synth0/check.py | 38 +
FALCON-examples/run/synth0/data/ref.fasta | 2 +
FALCON-examples/run/synth0/data/synth0.fasta | 1750 ++
FALCON-examples/run/synth0/fc_run.cfg | 47 +
FALCON-examples/run/synth0/input.fofn | 1 +
FALCON-examples/run/synth0/logging.ini | 30 +
FALCON-examples/run/synth0/logging.json | 31 +
FALCON-examples/run/synth0/logging.many.ini | 66 +
FALCON-examples/run/synth0/makefile | 19 +
FALCON-examples/scripts/check.py | 44 +
FALCON-examples/scripts/circ-sim.py | 92 +
FALCON-examples/scripts/relabel_fasta.py | 30 +
FALCON-examples/scripts/synther.py | 140 +
LICENSE => FALCON-make/LICENSE | 0
FALCON-make/README.md | 84 +
FALCON-make/config-edit-user.sh | 18 +
FALCON-make/config-edit.sh | 17 +
FALCON-make/config-standard.sh | 19 +
FALCON-make/get-pip.py | 19177 +++++++++++++++++++
FALCON-make/makefile | 68 +
.travis.yml => FALCON/.travis.yml | 0
LICENSE => FALCON/LICENSE | 0
MANIFEST.in => FALCON/MANIFEST.in | 0
README.md => FALCON/README.md | 0
{doc => FALCON/doc}/README | 0
{doc => FALCON/doc}/falcon_icon.svg | 0
{doc => FALCON/doc}/falcon_icon2.png | Bin
{examples => FALCON/examples}/build_env.sh | 0
{examples => FALCON/examples}/build_env2.sh | 0
.../examples}/ecoli_asm_graph_exploration.ipynb | 0
{examples => FALCON/examples}/fc_run_LG.cfg | 0
{examples => FALCON/examples}/fc_run_arab.cfg | 0
{examples => FALCON/examples}/fc_run_dmel.cfg | 0
{examples => FALCON/examples}/fc_run_ecoli.cfg | 0
{examples => FALCON/examples}/fc_run_ecoli_2.cfg | 0
{examples => FALCON/examples}/logging.json | 0
{examples => FALCON/examples}/run_ecoli_test.sh | 0
{falcon_kit => FALCON/falcon_kit}/FastaReader.py | 0
{falcon_kit => FALCON/falcon_kit}/__init__.py | 0
{falcon_kit => FALCON/falcon_kit}/bash.py | 46 +-
{falcon_kit => FALCON/falcon_kit}/falcon_kit.py | 0
{falcon_kit => FALCON/falcon_kit}/fc_asm_graph.py | 0
{falcon_kit => FALCON/falcon_kit}/functional.py | 129 +-
.../falcon_kit}/mains/__init__.py | 0
.../falcon_kit}/mains/actg_coordinate.py | 0
.../falcon_kit}/mains/calc_cutoff.py | 0
.../falcon_kit}/mains/consensus.py | 0
.../falcon_kit}/mains/contig_annotate.py | 0
.../falcon_kit}/mains/ctg_link_analysis.py | 0
.../falcon_kit}/mains/dedup_a_tigs.py | 0
.../falcon_kit}/mains/fasta2fasta.py | 0
FALCON/falcon_kit/mains/fetch_reads.py | 133 +
FALCON/falcon_kit/mains/get_read_ctg_map.py | 129 +
.../falcon_kit}/mains/graph_to_contig.py | 0
.../falcon_kit}/mains/graph_to_utgs.py | 0
.../falcon_kit}/mains/ovlp_filter.py | 3 +-
.../falcon_kit}/mains/ovlp_stats.py | 0
.../falcon_kit}/mains/ovlp_to_graph.py | 0
FALCON/falcon_kit/mains/pr_ctg_track.py | 159 +
FALCON/falcon_kit/mains/report_pre_assembly.py | 46 +
FALCON/falcon_kit/mains/rr_ctg_track.py | 169 +
{falcon_kit => FALCON/falcon_kit}/mains/run0.py | 12 +-
{falcon_kit => FALCON/falcon_kit}/mains/run1.py | 136 +-
{falcon_kit => FALCON/falcon_kit}/mains/tasks.py | 0
{falcon_kit => FALCON/falcon_kit}/multiproc.py | 0
{falcon_kit => FALCON/falcon_kit}/run_support.py | 29 +-
.../falcon_kit}/stats_preassembly.py | 65 +-
{falcon_kit => FALCON/falcon_kit}/util/__init__.py | 0
{falcon_kit => FALCON/falcon_kit}/util/io.py | 12 +
{falcon_kit => FALCON/falcon_kit}/util/system.py | 0
setup.py => FALCON/setup.py | 6 +-
{src => FALCON/src}/c/DW_banded.c | 0
{src => FALCON/src}/c/Makefile | 0
{src => FALCON/src}/c/Makefile.osx | 0
{src => FALCON/src}/c/common.h | 0
{src => FALCON/src}/c/ext_falcon.c | 0
{src => FALCON/src}/c/falcon.c | 0
{src => FALCON/src}/c/kmer_lookup.c | 4 +-
.../src}/py_scripts/fc_actg_coordinate.py | 0
{src => FALCON/src}/py_scripts/fc_consensus.py | 0
.../src}/py_scripts/fc_contig_annotate.py | 0
.../src}/py_scripts/fc_ctg_link_analysis.py | 0
{src => FALCON/src}/py_scripts/fc_dedup_a_tigs.py | 0
.../src}/py_scripts/fc_graph_to_contig.py | 0
{src => FALCON/src}/py_scripts/fc_graph_to_utgs.py | 0
{src => FALCON/src}/py_scripts/fc_ovlp_filter.py | 0
{src => FALCON/src}/py_scripts/fc_ovlp_stats.py | 0
{src => FALCON/src}/py_scripts/fc_ovlp_to_graph.py | 0
{src => FALCON/src}/py_scripts/fc_run.py | 0
{src => FALCON/src}/py_scripts_v0.1/falcon_asm.py | 0
.../src}/py_scripts_v0.1/falcon_asm_s.py | 0
.../src}/py_scripts_v0.1/falcon_dedup.py | 0
.../src}/py_scripts_v0.1/falcon_fixasm.py | 0
.../src}/py_scripts_v0.1/falcon_overlap.py | 0
.../src}/py_scripts_v0.1/falcon_overlap2.py | 0
{src => FALCON/src}/py_scripts_v0.1/falcon_qrm.py | 0
.../src}/py_scripts_v0.1/falcon_qrm_0.py | 0
.../src}/py_scripts_v0.1/falcon_sense.py | 0
.../src}/py_scripts_v0.1/falcon_ucns_data.py | 0
.../src}/py_scripts_v0.1/falcon_utgcns.py | 0
{src => FALCON/src}/py_scripts_v0.1/get_ovl.sh | 0
{src => FALCON/src}/py_scripts_v0.1/get_rdata.py | 0
{src => FALCON/src}/py_scripts_v0.1/overlapper.py | 0
{src => FALCON/src}/py_scripts_v0.1/ovlp_filter.sh | 0
{src => FALCON/src}/py_scripts_v0.1/redis_graph.py | 0
.../src}/py_scripts_v0.1/remove_dup_ctg.py | 0
{src => FALCON/src}/utils/fetch_preads.py | 0
{test => FALCON/test}/HPCdaligner_synth0.sh | 0
FALCON/test/HPCdaligner_synth0_preads.sh | 9 +
{test => FALCON/test}/helpers.py | 0
{test => FALCON/test}/test_actg_coordinate.py | 0
{test => FALCON/test}/test_consensus.py | 0
{test => FALCON/test}/test_contig_annotate.py | 0
{test => FALCON/test}/test_ctg_link_analysis.py | 0
{test => FALCON/test}/test_functional.py | 82 +-
{test => FALCON/test}/test_graph_to_contig.py | 0
{test => FALCON/test}/test_graph_to_utgs.py | 0
{test => FALCON/test}/test_ovlp_filter.py | 0
{test => FALCON/test}/test_ovlp_stats.py | 0
{test => FALCON/test}/test_ovlp_to_graph.py | 0
{test => FALCON/test}/test_run.py | 0
{test => FALCON/test}/test_run_LG.py | 0
{test => FALCON/test}/test_stats_preassembly.py | 23 +-
{test_data => FALCON/test_data}/t1.fa | 0
{test_data => FALCON/test_data}/t1.fofn | 0
{test_data => FALCON/test_data}/t2.fa | 0
{test_data => FALCON/test_data}/t2.fofn | 0
travis.sh => FALCON/travis.sh | 0
README.md | 62 +-
default-env.sh | 11 +
env.sh | 11 +
makefile | 25 +
.travis.yml => pypeFLOW/.travis.yml | 7 +-
pypeFLOW/License.txt | 20 +
pypeFLOW/README.rst | 71 +
pypeFLOW/doc/Example1.png | Bin 0 -> 19144 bytes
pypeFLOW/doc/Example2.png | Bin 0 -> 182447 bytes
pypeFLOW/doc/Makefile | 153 +
pypeFLOW/doc/concurrent_execution.rst | 15 +
pypeFLOW/doc/conf.py | 242 +
pypeFLOW/doc/examples.rst | 175 +
pypeFLOW/doc/index.rst | 28 +
pypeFLOW/doc/introduction.rst | 62 +
pypeFLOW/doc/modules.rst | 7 +
pypeFLOW/doc/pypeflow.rst | 35 +
pypeFLOW/doc/rdf_resprentation.rst | 134 +
pypeFLOW/example/PypeTest.py | 268 +
pypeFLOW/example/README.txt | 10 +
pypeFLOW/example/test_shutdown.py | 72 +
.../example/testdata/.placeholder | 0
pypeFLOW/examples-pwatcher/README.md | 60 +
pypeFLOW/examples-pwatcher/ab/delete.json | 1 +
pypeFLOW/examples-pwatcher/ab/jobs/b | 3 +
pypeFLOW/examples-pwatcher/ab/jobs/c | 3 +
.../examples-pwatcher/ab/logging-cfg.json | 28 +-
pypeFLOW/examples-pwatcher/ab/makefile | 10 +
pypeFLOW/examples-pwatcher/ab/query-ab.json | 5 +
pypeFLOW/examples-pwatcher/ab/run.json | 12 +
.../escher--unbelievable-527581_1024_768.jpg | Bin 0 -> 202550 bytes
pypeFLOW/presentation/pipelines.png | Bin 0 -> 617718 bytes
pypeFLOW/presentation/pypeFLOW_tutorial.html | 2412 +++
pypeFLOW/presentation/pypeFLOW_tutorial.rst | 505 +
.../mains => pypeFLOW/pwatcher}/__init__.py | 0
pypeFLOW/pwatcher/fs_based.py | 797 +
.../pwatcher}/mains/__init__.py | 0
pypeFLOW/pwatcher/mains/fs_heartbeat.py | 149 +
pypeFLOW/pwatcher/mains/pwatcher.py | 12 +
pypeFLOW/pwatcher/mains/pypeflow_example.py | 133 +
.../mains => pypeFLOW/pypeflow}/__init__.py | 0
pypeFLOW/pypeflow/common.py | 149 +
pypeFLOW/pypeflow/controller.py | 875 +
pypeFLOW/pypeflow/data.py | 315 +
pypeFLOW/pypeflow/pwatcher_bridge.py | 370 +
pypeFLOW/pypeflow/task.py | 892 +
pypeFLOW/readme.slurm.md | 112 +
pypeFLOW/setup.py | 27 +
{falcon_kit/mains => pypeFLOW/src}/__init__.py | 0
pypeFLOW/src/tests/test_pypeflow_common.py | 23 +
pypeFLOW/src/tests/test_pypeflow_controller.py | 497 +
pypeFLOW/src/tests/test_pypeflow_data.py | 202 +
pypeFLOW/src/tests/test_pypeflow_task.py | 326 +
pypeFLOW/travis.sh | 11 +
travis.sh | 22 +-
277 files changed, 71973 insertions(+), 239 deletions(-)
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