[med-svn] [lagan] 06/08: Update upstream source from tag 'upstream/2.0'

[Andreas Tille]

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tille pushed a commit to branch master
in repository lagan.

commit db4716e2e2700cbaec0f838bc025f746168df425
Merge: 8e5c49f 1afdb83
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 9 18:31:27 2017 +0100

    Update upstream source from tag 'upstream/2.0'
    
    Update to upstream version '2.0'
    with Debian dir c8400d09c05418c2835313ad35a8a7e7ca83f398

 Makefile                      |    5 +
 Readmes/LICENSE               |  341 +++++++++
 Readmes/README.FIRST          |   80 ++
 Readmes/README.chaos          |  164 ++++
 Readmes/README.lagan          |   74 ++
 Readmes/README.mlagan         |   71 ++
 Readmes/README.shuffle        |   83 +++
 Readmes/README.tools          |  323 ++++++++
 Utils.pm                      |  553 ++++++++++++++
 anal_gloc.pl                  |  142 ++++
 blosum62.txt                  |   25 +
 blosum62s.txt                 |   25 +
 lagan.pl                      |  242 ++++++
 nucmatrix.txt                 |    9 +
 rechaos.pl                    |  375 ++++++++++
 sample.fasta                  |   25 +
 sample.params                 |   59 ++
 slagan-mfa.pl                 |   35 +
 slagan.pl                     |  153 ++++
 src/.gdb_history              |    2 +
 src/Makefile                  |   54 ++
 src/Utils.pm                  |  553 ++++++++++++++
 src/anal_gloc.pl              |  142 ++++
 src/anchors.c                 |  279 +++++++
 src/ancseq.cpp                |  720 ++++++++++++++++++
 src/ancseqrest.cpp            |  324 ++++++++
 src/cutmfa.cpp                |  148 ++++
 src/diagmatrix.c              |  344 +++++++++
 src/diagmatrix.h              |   54 ++
 src/faindex.cpp               |   56 ++
 src/fchaos.c                  | 1254 +++++++++++++++++++++++++++++++
 src/fchaos.h                  |   39 +
 src/filebuffer.c              |  199 +++++
 src/filebuffer.h              |   36 +
 src/global.c                  |  176 +++++
 src/global.h                  |   14 +
 src/glocal/Makefile           |   19 +
 src/glocal/default.score      |    5 +
 src/glocal/glocal.cpp         |  258 +++++++
 src/glocal/glocal.h           |   23 +
 src/glocal/io.cpp             |  293 ++++++++
 src/glocal/io.h               |   22 +
 src/glocal/leftinfluence.cpp  |  637 ++++++++++++++++
 src/glocal/leftinfluence.h    |  100 +++
 src/glocal/rightinfluence.cpp |  203 +++++
 src/glocal/rightinfluence.h   |   42 ++
 src/glocal/score.cpp          |  225 ++++++
 src/glocal/score.h            |   39 +
 src/glocal/structs.h          |   92 +++
 src/glocal/test.score         |    5 +
 src/lagan.pl                  |  242 ++++++
 src/lagan2mfa.cpp             |   95 +++
 src/makecons.cpp              |  220 ++++++
 src/mempage.c                 |   55 ++
 src/mempage.h                 |   34 +
 src/mlagan.c                  | 1095 +++++++++++++++++++++++++++
 src/multial.c                 | 1648 +++++++++++++++++++++++++++++++++++++++++
 src/multial.h                 |  125 ++++
 src/order.c                   |  842 +++++++++++++++++++++
 src/order.h                   |   29 +
 src/prolagan.c                | 1115 ++++++++++++++++++++++++++++
 src/rechaos.pl                |  375 ++++++++++
 src/skiplist.c                |  210 ++++++
 src/skiplist.h                |   29 +
 src/slagan-mfa.pl             |   35 +
 src/slagan.pl                 |  172 +++++
 src/sortlist.c                |   43 ++
 src/supermap.pl               | 1622 ++++++++++++++++++++++++++++++++++++++++
 src/thrtrie.c                 |  330 +++++++++
 src/thrtrie.h                 |   67 ++
 src/translate.c               |   78 ++
 src/translate.h               |    3 +
 src/util.cpp                  |   68 ++
 src/utils/Glue.cpp            |  493 ++++++++++++
 src/utils/MultiSequence.h     |  124 ++++
 src/utils/Output.h            |   20 +
 src/utils/SafeVector.h        |   44 ++
 src/utils/Sequence.h          |  229 ++++++
 src/utils/bin2bl.c            |  187 +++++
 src/utils/bin2mf.c            |   69 ++
 src/utils/cextract.c          |  113 +++
 src/utils/cmerge2.pl          |  207 ++++++
 src/utils/contigorder.c       |  350 +++++++++
 src/utils/cstat.c             |  252 +++++++
 src/utils/dotplot.cpp         |  107 +++
 src/utils/draft.pl            |  267 +++++++
 src/utils/fa2xfa.c            |  122 +++
 src/utils/getbounds.c         |   90 +++
 src/utils/getcontigpos.c      |   99 +++
 src/utils/getlength.c         |   47 ++
 src/utils/getoverlap.c        |   33 +
 src/utils/mextract.pl         |   88 +++
 src/utils/mf2bin.pl           |   93 +++
 src/utils/mpretty.pl          |  263 +++++++
 src/utils/mproject.pl         |   90 +++
 src/utils/mrun.pl             |  267 +++++++
 src/utils/mrunfile.pl         |  111 +++
 src/utils/mrunpairs.pl        |  267 +++++++
 src/utils/mviz.pl             |  222 ++++++
 src/utils/overlay.c           |  261 +++++++
 src/utils/rc.c                |   71 ++
 src/utils/scorealign.c        |  479 ++++++++++++
 src/utils/scorecontigs.c      |  410 ++++++++++
 src/utils/seqmerge.c          |   46 ++
 src/xmfa2mfa.pl               |   65 ++
 supermap.pl                   | 1622 ++++++++++++++++++++++++++++++++++++++++
 test.score                    |    5 +
 utils/Utils.pm                |  553 ++++++++++++++
 utils/cmerge2.pl              |  207 ++++++
 utils/draft.pl                |  267 +++++++
 utils/flipchaos.pl            |   13 +
 utils/mextract.pl             |   88 +++
 utils/mf2bin.pl               |   93 +++
 utils/mpretty.pl              |  263 +++++++
 utils/mproject.pl             |   90 +++
 utils/mrun.pl                 |  267 +++++++
 utils/mrunfile.pl             |  111 +++
 utils/mrunpairs.pl            |  267 +++++++
 utils/msplit.pl               |   90 +++
 utils/mviz.pl                 |  222 ++++++
 xmfa2mfa.pl                   |   65 ++
 121 files changed, 27482 insertions(+)

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