[med-svn] [kmer-tools] branch upstream updated (aa0e4a6 -> af8304a)

[Afif Elghraoui]

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

      from  aa0e4a6   Imported Upstream version 0~20141114+1994
       new  af8304a   Imported Upstream version 0~20150520+2004

The 1 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
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Summary of changes:
 README.atac                          |  100 +
 README.compiling                     |   34 +-
 README.meryl                         |  156 ++
 atac-driver/atac.pl                  |   40 +-
 configure.sh                         |    4 +-
 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 -
 40 files changed, 465 insertions(+), 11362 deletions(-)
 create mode 100644 README.atac
 create mode 100644 README.meryl
 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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