[med-svn] [cd-hit] branch master updated (fd43854 -> 37c773e)

[Sascha Steinbiss]

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

satta pushed a change to branch master
in repository cd-hit.

      from  fd43854   Preparing for new upstream version
       new  fd9a4d4   adjust patch to fix help2man
       new  08d8190   New upstream version 4.6.8
       new  ca5f9a9   Updated version 4.6.8 from 'upstream/4.6.8'
       new  4ef2c7b   new upstream version
       new  37c773e   enable correct man page generation for cd-hit-div

The 5 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:
 FET.pl                                             |  109 ++
 README                                             |    5 +-
 cdhit-common.c++                                   |  596 ++++++++--
 cdhit-common.h                                     |   38 +-
 cdhit-est-2d.c++                                   |   17 +-
 cdhit-est.c++                                      |   15 +-
 cdhit-utility.c++                                  |   63 +-
 clstr_list.pl                                      |   89 ++
 clstr_list_sort.pl                                 |   51 +
 debian/changelog                                   |    9 +
 debian/patches/enable_help2man.patch               |   22 +-
 debian/rules                                       |    5 +-
 doc/cd-hit-otu-miseq-Figure-1.png                  |  Bin 0 -> 119495 bytes
 doc/cdhit-user-guide.pdf                           |  Bin 898823 -> 421458 bytes
 doc/cdhit-user-guide.wiki                          |  432 +++++--
 ...psi-cd-hit-local.pl => psi-cd-hit-local-old.pl} |  245 +++-
 psi-cd-hit/psi-cd-hit-local.pl                     |  549 +++++++--
 psi-cd-hit/{psi-cd-hit.pl => psi-cd-hit-old.pl}    |   72 +-
 psi-cd-hit/psi-cd-hit.pl                           |   82 +-
 usecases/Miseq-16S/16S-ref-db-PE-splice.pl         |  458 ++++++++
 usecases/Miseq-16S/NG-Omics-Miseq-16S.pl           |  117 ++
 usecases/Miseq-16S/NG-Omics-WF.pl                  | 1189 ++++++++++++++++++++
 usecases/Miseq-16S/README                          |  200 ++++
 usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl          |  222 ++++
 usecases/Miseq-16S/clstr_2_OTU_table.pl            |   82 ++
 usecases/Miseq-16S/filter-chimeric-and-small.pl    |  237 ++++
 usecases/Miseq-16S/filter-chimeric-by-ref.pl       |  207 ++++
 usecases/Miseq-16S/filter-nontop-ref.pl            |   51 +
 usecases/Miseq-16S/filter-refonly-cluster.pl       |   34 +
 usecases/Miseq-16S/greengene-ann1.pl               |   75 ++
 usecases/Miseq-16S/pool_samples.pl                 |   78 ++
 31 files changed, 5011 insertions(+), 338 deletions(-)
 create mode 100755 FET.pl
 create mode 100755 clstr_list.pl
 create mode 100755 clstr_list_sort.pl
 create mode 100644 doc/cd-hit-otu-miseq-Figure-1.png
 copy psi-cd-hit/{psi-cd-hit-local.pl => psi-cd-hit-local-old.pl} (81%)
 copy psi-cd-hit/{psi-cd-hit.pl => psi-cd-hit-old.pl} (52%)
 create mode 100755 usecases/Miseq-16S/16S-ref-db-PE-splice.pl
 create mode 100644 usecases/Miseq-16S/NG-Omics-Miseq-16S.pl
 create mode 100755 usecases/Miseq-16S/NG-Omics-WF.pl
 create mode 100644 usecases/Miseq-16S/README
 create mode 100755 usecases/Miseq-16S/cd-hit-otu-miseq-PE.pl
 create mode 100755 usecases/Miseq-16S/clstr_2_OTU_table.pl
 create mode 100755 usecases/Miseq-16S/filter-chimeric-and-small.pl
 create mode 100755 usecases/Miseq-16S/filter-chimeric-by-ref.pl
 create mode 100755 usecases/Miseq-16S/filter-nontop-ref.pl
 create mode 100755 usecases/Miseq-16S/filter-refonly-cluster.pl
 create mode 100755 usecases/Miseq-16S/greengene-ann1.pl
 create mode 100755 usecases/Miseq-16S/pool_samples.pl

-- 
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