[med-svn] [kmer-tools] branch master updated (b5faa3e -> 74cf124)

[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  b5faa3e   Add meryl to debian/control and make some associated changes
       new  8fb2f31   Upgrade svn revision
       new  af8304a   Imported Upstream version 0~20150520+2004
       new  46147b6   Merge tag 'upstream/0_20150520+2004'
       new  536e452   Update patches to apply cleanly to new upstream SVN "release"
       new  35f4f39   Update standards version (3.9.5->3.9.6)
       new  ba5dfe4   Add/update *.install files to appropriately place files
       new  74cf124   Remove the last of the template files

The 7 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:
 README.atac                          |  100 +
 README.compiling                     |   34 +-
 README.meryl                         |  156 ++
 atac-driver/atac.pl                  |   40 +-
 configure.sh                         |    4 +-
 debian/README.Debian                 |    6 -
 debian/changelog                     |    2 +-
 debian/control                       |    2 +-
 debian/kmer-tools.doc-base.EX        |   20 -
 debian/kmer.install                  |    7 +-
 debian/libkmer-dev.install           |   10 +-
 debian/libmeryl-dev.install          |    2 +
 debian/meryl.docs                    |    1 +
 debian/meryl.install                 |    1 +
 debian/patches/kazlib.patch          |    4 +-
 debian/patches/remove-kazlib.patch   |   17 +-
 libkmer/Make.include                 |    6 +-
 libkmer/percentCovered.C             |   66 -
 libseq/fastaFile.C                   |    4 +-
 libseq/fastqFile.C                   |    2 +
 libutil/intervalList.H               |    2 +-
 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/Make.include                   |   19 +-
 meryl/asmMerQC.C                     |  396 ----
 {libkmer => meryl}/kmer-mask.C       |    0
 meryl/m-heap.H                       |  152 --
 meryl/m.C                            |  118 -
 meryl/mapMers-depth.C                |  216 +-
 meryl/maskMers.C                     |    7 +
 meryl/testPositionBias.C             |  117 -
 51 files changed, 503 insertions(+), 11396 deletions(-)
 create mode 100644 README.atac
 create mode 100644 README.meryl
 delete mode 100644 debian/README.Debian
 delete mode 100644 debian/kmer-tools.doc-base.EX
 create mode 100644 debian/libmeryl-dev.install
 create mode 100644 debian/meryl.docs
 create mode 100644 debian/meryl.install
 delete mode 100644 libkmer/percentCovered.C
 delete mode 100644 libutil/kazlib/Make.include
 delete mode 100755 libutil/kazlib/blast.pl
 delete mode 100644 libutil/kazlib/dict.c
 delete mode 100644 libutil/kazlib/dict.h
 delete mode 100644 libutil/kazlib/docs/CHANGES
 delete mode 100644 libutil/kazlib/docs/MUST_READ
 delete mode 100644 libutil/kazlib/docs/README
 delete mode 100644 libutil/kazlib/docs/docs.ist
 delete mode 100644 libutil/kazlib/docs/docs.ltx
 delete mode 100644 libutil/kazlib/drivers/dict-main.c
 delete mode 100644 libutil/kazlib/drivers/except-main.c
 delete mode 100644 libutil/kazlib/drivers/hash-main.c
 delete mode 100644 libutil/kazlib/drivers/list-main.c
 delete mode 100644 libutil/kazlib/drivers/sfx-main.c
 delete mode 100644 libutil/kazlib/except.c
 delete mode 100644 libutil/kazlib/except.h
 delete mode 100644 libutil/kazlib/hash.c
 delete mode 100644 libutil/kazlib/hash.h
 delete mode 100644 libutil/kazlib/list.c
 delete mode 100644 libutil/kazlib/list.h
 delete mode 100644 libutil/kazlib/sfx.c
 delete mode 100644 libutil/kazlib/sfx.h
 delete mode 100644 meryl/asmMerQC.C
 rename {libkmer => meryl}/kmer-mask.C (100%)
 delete mode 100644 meryl/m-heap.H
 delete mode 100644 meryl/m.C
 delete mode 100644 meryl/testPositionBias.C

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