[med-svn] [falcon] 03/05: Merge tag 'upstream/1.8.4'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository falcon.

commit 542930b9136fc8a2963826fe4df0b54ebc376a4f
Merge: bd767ea 67b5061
Author: Afif Elghraoui <afif at debian.org>
Date:   Fri Dec 2 00:13:26 2016 -0800

    Merge tag 'upstream/1.8.4'
    
    Upstream version 1.8.4

 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 +-
 FALCON_unzip/LICENSE.txt                           |   32 +
 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/falcon_unzip/__init__.py              |   36 +
 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/falcon_unzip/phased_ovlp_to_graph.py  | 1545 ++++++++++++++++++++
 FALCON_unzip/falcon_unzip/phasing.py               |  569 +++++++
 FALCON_unzip/falcon_unzip/phasing_readmap.py       |   73 +
 FALCON_unzip/falcon_unzip/rr_hctg_track.py         |  201 +++
 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 +
 FALCON_unzip/src/py_scripts/fc_dedup_h_tigs.py     |    4 +
 .../src/py_scripts/fc_get_read_hctg_map.py         |    4 +
 FALCON_unzip/src/py_scripts/fc_graphs_to_h_tigs.py |    4 +
 .../src/py_scripts/fc_ovlp_filter_with_phase.py    |    6 +
 .../src/py_scripts/fc_phased_ovlp_to_graph.py      |    5 +
 FALCON_unzip/src/py_scripts/fc_phasing.py          |    5 +
 FALCON_unzip/src/py_scripts/fc_phasing_readmap.py  |    4 +
 FALCON_unzip/src/py_scripts/fc_quiver.py           |    4 +
 FALCON_unzip/src/py_scripts/fc_rr_hctg_track.py    |    4 +
 .../src/py_scripts/fc_select_reads_from_bam.py     |    4 +
 .../src/py_scripts/fc_track_reads_htigs0.py        |  398 +++++
 FALCON_unzip/src/py_scripts/fc_unzip.py            |    4 +
 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 +
 pypeFLOW/pwatcher/fs_based.py                      |    2 +-
 pypeFLOW/pwatcher/network_based.py                 |    2 +-
 pypeFLOW/pypeflow/simple_pwatcher_bridge.py        |   10 +-
 41 files changed, 5213 insertions(+), 57 deletions(-)

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