[med-svn] [falcon] 02/04: Merge tag 'upstream/1.8.6'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository falcon.

commit b665960c6d4332980149e895ec79409a9ec7d458
Merge: ccc50af 215b426
Author: Afif Elghraoui <afif at debian.org>
Date:   Tue Dec 27 23:42:14 2016 -0800

    Merge tag 'upstream/1.8.6'
    
    Upstream version 1.8.6

 FALCON/falcon_kit/bash.py                          |   36 +-
 FALCON/falcon_kit/functional.py                    |   14 +-
 FALCON/falcon_kit/mains/LAmerge.py                 |   51 +
 FALCON/falcon_kit/mains/LAsort.py                  |   46 +
 FALCON/falcon_kit/mains/run1.py                    |   14 +-
 FALCON/falcon_kit/pype_tasks.py                    |    8 +-
 FALCON/test/test_functional.py                     |    8 +
 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               |  570 --------
 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                      |   30 +-
 pypeFLOW/pypeflow/do_task.py                       |    4 +
 pypeFLOW/pypeflow/simple_pwatcher_bridge.py        |   59 +-
 44 files changed, 228 insertions(+), 5233 deletions(-)

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