[med-svn] [falcon] 05/15: Merge tag 'upstream/1.8.8'

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository falcon.

commit c2169c5844e46324f2dbd7410ebcfce45118d488
Merge: 698b47d 6fa9904
Author: Afif Elghraoui <afif at debian.org>
Date:   Sat Dec 16 01:24:21 2017 -0500

    Merge tag 'upstream/1.8.8'
    
    Upstream version 1.8.8

 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(-)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/falcon.git