[med-svn] [falcon] branch debian/jessie-backports updated (fb40a8a -> aaf8db6)
Afif Elghraoui
afif at moszumanska.debian.org
Tue Dec 13 08:28:53 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch debian/jessie-backports
in repository falcon.
from fb40a8a releasing package falcon version 1.8.3-1~bpo8+1
adds bd767ea d/upstream/metadata: quote authors list
adds 54d9a95 Imported Upstream version 1.8.4
adds 67b5061 Imported Upstream version 1.8.4
adds 542930b Merge tag 'upstream/1.8.4'
adds ee4fa9c Add license terms for new bundled module FALCON_unzip
adds 76e9ffb releasing package falcon version 1.8.4-1
new 349ce7a Merge tag 'debian/1.8.4-1' into debian/jessie-backports
new aaf8db6 releasing package falcon version 1.8.4-1~bpo8+1
The 2 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/LAmerge.c | 2 +-
DAZZ_DB/GNUmakefile | 2 +-
FALCON/falcon_kit/mains/get_read_ctg_map.py | 12 +-
FALCON/falcon_kit/mains/run1.py | 50 +-
pypeFLOW/LICENSE => FALCON_unzip/LICENSE.txt | 2 +-
FALCON_unzip/README.md | 1 +
FALCON_unzip/examples/fc_unzip.cfg | 17 +
FALCON_unzip/examples/unzip.sh | 2 +
FALCON_unzip/examples/unzip_obsoleted.sh | 33 +
.../falcon_unzip/__init__.py | 0
FALCON_unzip/falcon_unzip/dedup_h_tigs.py | 70 +++
FALCON_unzip/falcon_unzip/get_read_hctg_map.py | 110 ++++
FALCON_unzip/falcon_unzip/graphs_to_h_tigs.py | 678 +++++++++++++++++++++
.../falcon_unzip/ovlp_filter_with_phase.py | 354 +++++++++++
.../falcon_unzip/phased_ovlp_to_graph.py | 515 ++++++++--------
FALCON_unzip/falcon_unzip/phasing.py | 569 +++++++++++++++++
FALCON_unzip/falcon_unzip/phasing_readmap.py | 73 +++
.../falcon_unzip/rr_hctg_track.py | 66 +-
FALCON_unzip/falcon_unzip/run_quiver.py | 394 ++++++++++++
FALCON_unzip/falcon_unzip/select_reads_from_bam.py | 113 ++++
FALCON_unzip/falcon_unzip/unzip.py | 357 +++++++++++
FALCON_unzip/setup.py | 24 +
.../src/py_scripts/fc_dedup_h_tigs.py | 3 +-
.../src/py_scripts/fc_get_read_hctg_map.py | 3 +-
.../src/py_scripts/fc_graphs_to_h_tigs.py | 3 +-
.../src/py_scripts/fc_ovlp_filter_with_phase.py | 5 +-
.../src/py_scripts/fc_phased_ovlp_to_graph.py | 4 +-
.../src/py_scripts/fc_phasing.py | 4 +-
.../src/py_scripts/fc_phasing_readmap.py | 3 +-
.../src/py_scripts/fc_quiver.py | 3 +-
.../src/py_scripts/fc_rr_hctg_track.py | 3 +-
.../src/py_scripts/fc_select_reads_from_bam.py | 3 +-
.../src/py_scripts/fc_track_reads_htigs0.py | 398 ++++++++++++
.../src/py_scripts/fc_unzip.py | 3 +-
FALCON_unzip/src/py_utils/align.sh | 10 +
FALCON_unzip/src/py_utils/call_SV_from_mum.py | 85 +++
FALCON_unzip/src/py_utils/fetch_read.py | 12 +
FALCON_unzip/src/py_utils/split_bam.py | 28 +
debian/changelog | 14 +
debian/copyright | 5 +
debian/upstream/metadata | 2 +-
pypeFLOW/pwatcher/fs_based.py | 2 +-
pypeFLOW/pwatcher/network_based.py | 2 +-
pypeFLOW/pypeflow/simple_pwatcher_bridge.py | 10 +-
44 files changed, 3696 insertions(+), 353 deletions(-)
copy pypeFLOW/LICENSE => FALCON_unzip/LICENSE.txt (97%)
create mode 100644 FALCON_unzip/README.md
create mode 100644 FALCON_unzip/examples/fc_unzip.cfg
create mode 100644 FALCON_unzip/examples/unzip.sh
create mode 100644 FALCON_unzip/examples/unzip_obsoleted.sh
copy FALCON-make/LICENSE => FALCON_unzip/falcon_unzip/__init__.py (100%)
create mode 100644 FALCON_unzip/falcon_unzip/dedup_h_tigs.py
create mode 100644 FALCON_unzip/falcon_unzip/get_read_hctg_map.py
create mode 100644 FALCON_unzip/falcon_unzip/graphs_to_h_tigs.py
create mode 100644 FALCON_unzip/falcon_unzip/ovlp_filter_with_phase.py
copy FALCON/falcon_kit/mains/ovlp_to_graph.py => FALCON_unzip/falcon_unzip/phased_ovlp_to_graph.py (90%)
create mode 100644 FALCON_unzip/falcon_unzip/phasing.py
create mode 100644 FALCON_unzip/falcon_unzip/phasing_readmap.py
copy FALCON/falcon_kit/mains/rr_ctg_track.py => FALCON_unzip/falcon_unzip/rr_hctg_track.py (71%)
create mode 100644 FALCON_unzip/falcon_unzip/run_quiver.py
create mode 100644 FALCON_unzip/falcon_unzip/select_reads_from_bam.py
create mode 100644 FALCON_unzip/falcon_unzip/unzip.py
create mode 100755 FALCON_unzip/setup.py
copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_dedup_h_tigs.py (57%)
copy FALCON/src/py_scripts/fc_ovlp_stats.py => FALCON_unzip/src/py_scripts/fc_get_read_hctg_map.py (54%)
copy FALCON/src/py_scripts/fc_ovlp_stats.py => FALCON_unzip/src/py_scripts/fc_graphs_to_h_tigs.py (54%)
copy FALCON/src/py_scripts/fc_ctg_link_analysis.py => FALCON_unzip/src/py_scripts/fc_ovlp_filter_with_phase.py (51%)
copy FALCON/src/py_scripts/fc_dedup_a_tigs.py => FALCON_unzip/src/py_scripts/fc_phased_ovlp_to_graph.py (53%)
copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_phasing.py (59%)
copy FALCON/src/py_scripts/fc_ovlp_stats.py => FALCON_unzip/src/py_scripts/fc_phasing_readmap.py (55%)
copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_quiver.py (58%)
copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_rr_hctg_track.py (56%)
copy FALCON/src/py_scripts/fc_actg_coordinate.py => FALCON_unzip/src/py_scripts/fc_select_reads_from_bam.py (52%)
create mode 100644 FALCON_unzip/src/py_scripts/fc_track_reads_htigs0.py
copy FALCON/src/py_scripts/fc_run.py => FALCON_unzip/src/py_scripts/fc_unzip.py (58%)
create mode 100644 FALCON_unzip/src/py_utils/align.sh
create mode 100644 FALCON_unzip/src/py_utils/call_SV_from_mum.py
create mode 100644 FALCON_unzip/src/py_utils/fetch_read.py
create mode 100644 FALCON_unzip/src/py_utils/split_bam.py
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