[med-svn] [pbdagcon] 03/12: Merge tag 'upstream/0.3+20161121+ds'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository pbdagcon.

commit fb7c88b9786bad7dc51c1b85ec00293fb1d926c4
Merge: d191671 b247711
Author: Afif Elghraoui <afif at debian.org>
Date:   Tue Dec 20 21:58:58 2016 -0800

    Merge tag 'upstream/0.3+20161121+ds'
    
    Upstream version 0.3+20161121+ds

 .gitignore                          |   11 -
 .gitmodules                         |    9 -
 DALIGNER/DB2Falcon.c                |  133 +
 DALIGNER/GNUmakefile                |   30 +
 DALIGNER/HPCdaligner.c              |  543 ++++
 DALIGNER/HPCmapper.c                |  591 ++++
 DALIGNER/LA4Falcon.c                |  802 ++++++
 DALIGNER/LA4Ice.c                   |  568 ++++
 DALIGNER/LAcat.c                    |  157 ++
 DALIGNER/LAcheck.c                  |  310 +++
 DALIGNER/LAdump.c                   |  478 ++++
 DALIGNER/LAindex.c                  |  201 ++
 DALIGNER/LAmerge.c                  |  387 +++
 DALIGNER/LAshow.c                   |  594 ++++
 DALIGNER/LAsort.c                   |  252 ++
 DALIGNER/LAsplit.c                  |  207 ++
 DALIGNER/LICENSE                    |   34 +
 DALIGNER/Makefile                   |   69 +
 DALIGNER/README                     |  395 +++
 DALIGNER/README_PB.md               |    8 +
 DALIGNER/align.c                    | 5112 +++++++++++++++++++++++++++++++++++
 DALIGNER/align.h                    |  335 +++
 DALIGNER/daligner.c                 |  726 +++++
 DALIGNER/daligner_p.c               |    1 +
 DALIGNER/filter.c                   | 2266 ++++++++++++++++
 DALIGNER/filter.h                   |   38 +
 DALIGNER/filter_p.c                 |    2 +
 DALIGNER/py_utils/DAPI.py           |   72 +
 DALIGNER/py_utils/DAPipe.py         |   93 +
 DALIGNER/py_utils/DBLA_to_falcon.py |   42 +
 DALIGNER/py_utils/FALCON_ASM_NOTE   |   27 +
 DALIGNER/py_utils/LAPI.py           |  110 +
 DALIGNER/py_utils/LAPipe.py         |  177 ++
 DAZZ_DB/Catrack.c                   |  259 ++
 DAZZ_DB/DAM2fasta.c                 |  200 ++
 DAZZ_DB/DB.c                        | 1690 ++++++++++++
 DAZZ_DB/DB.h                        |  415 +++
 DAZZ_DB/DB2fasta.c                  |  151 ++
 DAZZ_DB/DB2quiva.c                  |  155 ++
 DAZZ_DB/DBdump.c                    |  720 +++++
 DAZZ_DB/DBdust.c                    |  471 ++++
 DAZZ_DB/DBrm.c                      |   40 +
 DAZZ_DB/DBshow.c                    |  577 ++++
 DAZZ_DB/DBsplit.c                   |  214 ++
 DAZZ_DB/DBstats.c                   |  346 +++
 DAZZ_DB/DBupgrade.Dec.31.2014.c     |   86 +
 DAZZ_DB/DBupgrade.Sep.25.2014.c     |   96 +
 DAZZ_DB/DUSTupgrade.Jan.1.2015.c    |   80 +
 DAZZ_DB/GNUmakefile                 |   33 +
 DAZZ_DB/LICENSE                     |   34 +
 DAZZ_DB/Makefile                    |   70 +
 DAZZ_DB/QV.c                        | 1369 ++++++++++
 DAZZ_DB/QV.h                        |   90 +
 DAZZ_DB/README                      |  459 ++++
 DAZZ_DB/fasta2DAM.c                 |  412 +++
 DAZZ_DB/fasta2DB.c                  |  645 +++++
 DAZZ_DB/quiva2DB.c                  |  347 +++
 DAZZ_DB/simulator.c                 |  421 +++
 configure.py                        |    6 +-
 makefile                            |    2 +-
 test/cpp/.gitignore                 |    2 -
 61 files changed, 24144 insertions(+), 26 deletions(-)

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