[med-svn] [falcon] branch upstream updated (d74e7a3 -> 215b426)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository falcon.

      from  d74e7a3   Imported Upstream version 1.8.5
       new  215b426   Imported Upstream version 1.8.6

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:
 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(-)
 create mode 100644 FALCON/falcon_kit/mains/LAmerge.py
 create mode 100644 FALCON/falcon_kit/mains/LAsort.py
 delete mode 100644 FALCON_unzip/LICENSE.txt
 delete mode 100644 FALCON_unzip/README.md
 delete mode 100644 FALCON_unzip/examples/fc_unzip.cfg
 delete mode 100644 FALCON_unzip/examples/unzip.sh
 delete mode 100644 FALCON_unzip/examples/unzip_obsoleted.sh
 delete mode 100644 FALCON_unzip/falcon_unzip/__init__.py
 delete mode 100644 FALCON_unzip/falcon_unzip/dedup_h_tigs.py
 delete mode 100644 FALCON_unzip/falcon_unzip/get_read_hctg_map.py
 delete mode 100644 FALCON_unzip/falcon_unzip/graphs_to_h_tigs.py
 delete mode 100644 FALCON_unzip/falcon_unzip/ovlp_filter_with_phase.py
 delete mode 100644 FALCON_unzip/falcon_unzip/phased_ovlp_to_graph.py
 delete mode 100644 FALCON_unzip/falcon_unzip/phasing.py
 delete mode 100644 FALCON_unzip/falcon_unzip/phasing_readmap.py
 delete mode 100644 FALCON_unzip/falcon_unzip/rr_hctg_track.py
 delete mode 100644 FALCON_unzip/falcon_unzip/run_quiver.py
 delete mode 100644 FALCON_unzip/falcon_unzip/select_reads_from_bam.py
 delete mode 100644 FALCON_unzip/falcon_unzip/unzip.py
 delete mode 100755 FALCON_unzip/setup.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_dedup_h_tigs.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_get_read_hctg_map.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_graphs_to_h_tigs.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_ovlp_filter_with_phase.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_phased_ovlp_to_graph.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_phasing.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_phasing_readmap.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_quiver.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_rr_hctg_track.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_select_reads_from_bam.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_track_reads_htigs0.py
 delete mode 100644 FALCON_unzip/src/py_scripts/fc_unzip.py
 delete mode 100644 FALCON_unzip/src/py_utils/align.sh
 delete mode 100644 FALCON_unzip/src/py_utils/call_SV_from_mum.py
 delete mode 100644 FALCON_unzip/src/py_utils/fetch_read.py
 delete mode 100644 FALCON_unzip/src/py_utils/split_bam.py

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