[med-svn] [kmer-tools] 03/07: Merge tag 'upstream/0_20150520+2004'

[Afif Elghraoui]

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

commit 46147b695b26ae0641687337748b2aee41d02ab6
Merge: 8fb2f31 af8304a
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu May 21 19:40:02 2015 -0700

    Merge tag 'upstream/0_20150520+2004'
    
    Upstream version 0~20150520+2004

 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(-)

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