[med-svn] [kmer-tools] branch master updated (7ca1b47 -> f4c4fec)

[Afif Elghraoui]

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

afif-guest pushed a change to branch master
in repository kmer-tools.

      from  7ca1b47   Quote reference titles in d/upstream/metadata
       new  25696ff   Use cleaner nroff for one of my early man pages
       new  0b50551   Prepare new revision
       new  3b02fbc   Simplify get-orig-source script
       new  f2f4f95   Imported Upstream version 0~20150903+r2013
       new  ecfd489   Merge tag 'upstream/0_20150903+r2013'
       new  c13c8f8   Clean up source package: move meryl manpages to a subdirectory of debian/
       new  85bd00e   Add leaff and sim4db binary packages
       new  1705f78   Drop dependency on libbz2-dev
       new  33b46e1   Drop quilt patches
       new  3102ca3   Fix sim4db short description
       new  61d8913   Fix section/architecture of the kmer metapackage
       new  d3fdf8d   Set Vcs-Browser to point to cgit
       new  f4c4fec   Don't install other READMEs to metapackage docs

The 13 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:
 PACKAGING                                |  104 +
 configure.sh                             |    6 +-
 debian/changelog                         |    6 +
 debian/control                           |   58 +-
 debian/docs                              |    3 -
 debian/get-orig-source                   |   32 +-
 debian/leaff.docs                        |    1 +
 debian/leaff.install                     |    1 +
 debian/{ => man/meryl}/existDB.1         |   21 +-
 debian/{ => man/meryl}/kmer-mask.1       |    0
 debian/{ => man/meryl}/mapMers-depth.1   |    0
 debian/{ => man/meryl}/mapMers.1         |    0
 debian/{ => man/meryl}/meryl.1           |    0
 debian/{ => man/meryl}/positionDB.1      |    0
 debian/{ => man/meryl}/simple.1          |    0
 debian/meryl.manpages                    |    8 +-
 debian/patches/kazlib.patch              |   41 -
 debian/patches/remove-kazlib.patch       |   39 -
 debian/patches/series                    |    2 -
 debian/rules                             |   15 +-
 debian/sim4db.docs                       |    1 +
 debian/sim4db.install                    |   27 +
 libutil/kazlib/Make.include              |   27 +
 libutil/kazlib/blast.pl                  |   33 +
 libutil/kazlib/dict.c                    | 1238 +++++++++
 libutil/kazlib/dict.h                    |  142 +
 libutil/kazlib/docs/CHANGES              |  290 +++
 libutil/kazlib/docs/MUST_READ            |   25 +
 libutil/kazlib/docs/README               |   66 +
 libutil/kazlib/docs/docs.ist             |    4 +
 libutil/kazlib/docs/docs.ltx             | 4155 ++++++++++++++++++++++++++++++
 libutil/kazlib/drivers/dict-main.c       |  300 +++
 libutil/kazlib/drivers/except-main.c     |   57 +
 libutil/kazlib/drivers/hash-main.c       |  187 ++
 libutil/kazlib/drivers/list-main.c       |  152 ++
 libutil/kazlib/drivers/sfx-main.c        |   41 +
 libutil/kazlib/except.c                  |  347 +++
 libutil/kazlib/except.h                  |  147 ++
 libutil/kazlib/hash.c                    |  837 ++++++
 libutil/kazlib/hash.h                    |  238 ++
 libutil/kazlib/list.c                    |  766 ++++++
 libutil/kazlib/list.h                    |  152 ++
 libutil/kazlib/sfx.c                     | 1138 ++++++++
 libutil/kazlib/sfx.h                     |   46 +
 meryl/args.C                             |    2 +-
 meryl/build.C                            |   70 +-
 meryl/estimate.C                         |  136 +-
 meryl/kmer-mask.C                        |  344 ++-
 meryl/mapMers.C                          |   26 +-
 meryl/meryl.H                            |    7 +-
 sim4dbutils/reportAlignmentDifferences.C |    2 +-
 51 files changed, 10925 insertions(+), 415 deletions(-)
 create mode 100644 PACKAGING
 delete mode 100644 debian/docs
 create mode 100644 debian/leaff.docs
 create mode 100644 debian/leaff.install
 rename debian/{ => man/meryl}/existDB.1 (78%)
 rename debian/{ => man/meryl}/kmer-mask.1 (100%)
 rename debian/{ => man/meryl}/mapMers-depth.1 (100%)
 rename debian/{ => man/meryl}/mapMers.1 (100%)
 rename debian/{ => man/meryl}/meryl.1 (100%)
 rename debian/{ => man/meryl}/positionDB.1 (100%)
 rename debian/{ => man/meryl}/simple.1 (100%)
 delete mode 100644 debian/patches/kazlib.patch
 delete mode 100644 debian/patches/remove-kazlib.patch
 delete mode 100644 debian/patches/series
 create mode 100644 debian/sim4db.docs
 create mode 100644 debian/sim4db.install
 create mode 100644 libutil/kazlib/Make.include
 create mode 100755 libutil/kazlib/blast.pl
 create mode 100644 libutil/kazlib/dict.c
 create mode 100644 libutil/kazlib/dict.h
 create mode 100644 libutil/kazlib/docs/CHANGES
 create mode 100644 libutil/kazlib/docs/MUST_READ
 create mode 100644 libutil/kazlib/docs/README
 create mode 100644 libutil/kazlib/docs/docs.ist
 create mode 100644 libutil/kazlib/docs/docs.ltx
 create mode 100644 libutil/kazlib/drivers/dict-main.c
 create mode 100644 libutil/kazlib/drivers/except-main.c
 create mode 100644 libutil/kazlib/drivers/hash-main.c
 create mode 100644 libutil/kazlib/drivers/list-main.c
 create mode 100644 libutil/kazlib/drivers/sfx-main.c
 create mode 100644 libutil/kazlib/except.c
 create mode 100644 libutil/kazlib/except.h
 create mode 100644 libutil/kazlib/hash.c
 create mode 100644 libutil/kazlib/hash.h
 create mode 100644 libutil/kazlib/list.c
 create mode 100644 libutil/kazlib/list.h
 create mode 100644 libutil/kazlib/sfx.c
 create mode 100644 libutil/kazlib/sfx.h

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