[med-svn] [cd-hit] branch upstream updated (8a6f537 -> 08d8190)

[Sascha Steinbiss]

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

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

      from  8a6f537   Imported Upstream version 4.6.6
       new  08d8190   New upstream version 4.6.8

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
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 +
 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 ++
 28 files changed, 4980 insertions(+), 333 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

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/cd-hit.git