[med-svn] [falcon] branch upstream updated (215b426 -> 6fa9904)
Afif Elghraoui
afif at moszumanska.debian.org
Sat Dec 16 08:03:30 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository falcon.
from 215b426 Imported Upstream version 1.8.6
new 6fa9904 New upstream version 1.8.8
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:
DALIGNER/DBX.c | 85 ++
DALIGNER/DBX.h | 25 +
DALIGNER/GNUmakefile | 1 +
DALIGNER/LA4Falcon.c | 58 +-
DALIGNER/bamboo_build.sh | 28 +
DAZZ_DB/bamboo_build.sh | 23 +
FALCON-examples/git-sym.makefile | 6 +-
FALCON-examples/makefile | 2 +-
FALCON-examples/run/ecoli/fc_run.cfg | 8 +-
FALCON-examples/run/greg200k-sv2/fc_run.cfg | 13 +
FALCON-examples/run/greg200k-sv2/fc_unzip.cfg | 14 +-
FALCON-examples/run/greg200k-sv2/input.fofn | 4 +-
FALCON-examples/run/greg200k-sv2/input_bam.fofn | 2 +
.../run/synth0/{fc_run.cfg => fc_preads.cfg} | 26 +-
FALCON-examples/run/synth0/fc_run.cfg | 19 +-
FALCON-examples/run/synth0/makefile | 4 +-
FALCON-examples/run/synth0/preads.fofn | 2 +
FALCON/.travis.yml | 4 +-
FALCON/bamboo_build.sh | 28 +
FALCON/bamboo_test.sh | 14 +
FALCON/falcon_kit/FastaReader.py | 165 +--
FALCON/falcon_kit/__init__.py | 38 -
FALCON/falcon_kit/bash.py | 19 +-
FALCON/falcon_kit/falcon_kit.py | 47 +-
FALCON/falcon_kit/fc_asm_graph.py | 44 +-
FALCON/falcon_kit/functional.py | 22 +-
FALCON/falcon_kit/mains/actg_coordinate.py | 14 +-
FALCON/falcon_kit/mains/calc_cutoff.py | 20 +-
FALCON/falcon_kit/mains/dedup_a_tigs.py | 6 +-
FALCON/falcon_kit/mains/fetch_reads.py | 36 +-
FALCON/falcon_kit/mains/get_read_ctg_map.py | 3 +-
FALCON/falcon_kit/mains/graph_to_contig.py | 6 +-
FALCON/falcon_kit/mains/ovlp_filter.py | 8 +-
FALCON/falcon_kit/mains/ovlp_to_graph.py | 3 +-
FALCON/falcon_kit/mains/run1.py | 55 +-
FALCON/falcon_kit/pype_tasks.py | 4 +-
FALCON/falcon_kit/run_support.py | 49 +-
FALCON/falcon_kit/stats_preassembly.py | 17 +-
FALCON/falcon_kit/util/system.py | 9 +
FALCON/makefile | 65 ++
FALCON/mycoverage.cfg | 5 +
FALCON/mysitecustomize.py | 3 +
FALCON/setup.py | 1 +
FALCON/src/c/falcon.c | 13 +-
FALCON/src/py_scripts_v0.1/falcon_asm.py | 1154 ------------------
FALCON/src/py_scripts_v0.1/falcon_asm_s.py | 1220 --------------------
FALCON/src/py_scripts_v0.1/falcon_dedup.py | 119 --
FALCON/src/py_scripts_v0.1/falcon_fixasm.py | 213 ----
FALCON/src/py_scripts_v0.1/falcon_overlap.py | 328 ------
FALCON/src/py_scripts_v0.1/falcon_overlap2.py | 337 ------
FALCON/src/py_scripts_v0.1/falcon_qrm.py | 370 ------
FALCON/src/py_scripts_v0.1/falcon_qrm_0.py | 378 ------
FALCON/src/py_scripts_v0.1/falcon_sense.py | 248 ----
FALCON/src/py_scripts_v0.1/falcon_ucns_data.py | 120 --
FALCON/src/py_scripts_v0.1/falcon_utgcns.py | 124 --
FALCON/src/py_scripts_v0.1/get_ovl.sh | 7 -
FALCON/src/py_scripts_v0.1/get_rdata.py | 207 ----
FALCON/src/py_scripts_v0.1/overlapper.py | 216 ----
FALCON/src/py_scripts_v0.1/ovlp_filter.sh | 6 -
FALCON/src/py_scripts_v0.1/redis_graph.py | 79 --
FALCON/src/py_scripts_v0.1/remove_dup_ctg.py | 75 --
FALCON/test/helpers.py | 4 +
FALCON/test/test_calc_cutoff.py | 43 +
FALCON/test/test_functional.py | 14 +
FALCON/test/test_stats_preassembly.py | 17 +-
FALCON/test_data/calc_cutoff/partial_capture.txt | 5 +
FALCON/travis.sh | 17 +-
bamboo_build_and_test.sh | 42 +
makefile | 6 +-
pypeFLOW/bamboo_build.sh | 29 +
pypeFLOW/makefile | 3 +
pypeFLOW/pwatcher/blocking.py | 4 +-
pypeFLOW/pwatcher/fs_based.py | 54 +-
pypeFLOW/pwatcher/mains/pypeflow_example.py | 14 +-
pypeFLOW/pwatcher/mains/query_server.py | 3 +-
pypeFLOW/pwatcher/network_based.py | 17 +-
pypeFLOW/pypeflow/do_task.py | 30 +-
pypeFLOW/pypeflow/simple_pwatcher_bridge.py | 2 +-
pypeFLOW/pypeflow/util.py | 7 +
travis.sh | 11 +-
80 files changed, 873 insertions(+), 5668 deletions(-)
create mode 100644 DALIGNER/DBX.c
create mode 100644 DALIGNER/DBX.h
create mode 100644 DALIGNER/bamboo_build.sh
create mode 100644 DAZZ_DB/bamboo_build.sh
create mode 100644 FALCON-examples/run/greg200k-sv2/input_bam.fofn
copy FALCON-examples/run/synth0/{fc_run.cfg => fc_preads.cfg} (71%)
create mode 100644 FALCON-examples/run/synth0/preads.fofn
create mode 100644 FALCON/bamboo_build.sh
create mode 100644 FALCON/bamboo_test.sh
create mode 100644 FALCON/makefile
create mode 100644 FALCON/mycoverage.cfg
create mode 100644 FALCON/mysitecustomize.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_asm.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_asm_s.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_dedup.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_fixasm.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_overlap.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_overlap2.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_qrm.py
delete mode 100755 FALCON/src/py_scripts_v0.1/falcon_qrm_0.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_sense.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_ucns_data.py
delete mode 100644 FALCON/src/py_scripts_v0.1/falcon_utgcns.py
delete mode 100644 FALCON/src/py_scripts_v0.1/get_ovl.sh
delete mode 100755 FALCON/src/py_scripts_v0.1/get_rdata.py
delete mode 100644 FALCON/src/py_scripts_v0.1/overlapper.py
delete mode 100644 FALCON/src/py_scripts_v0.1/ovlp_filter.sh
delete mode 100644 FALCON/src/py_scripts_v0.1/redis_graph.py
delete mode 100755 FALCON/src/py_scripts_v0.1/remove_dup_ctg.py
create mode 100644 FALCON/test/test_calc_cutoff.py
create mode 100644 FALCON/test_data/calc_cutoff/partial_capture.txt
create mode 100755 bamboo_build_and_test.sh
create mode 100644 pypeFLOW/bamboo_build.sh
create mode 100644 pypeFLOW/makefile
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