[med-svn] [vsearch] branch upstream updated (c46e44d -> 38304cc)

[Andreas Tille]

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

tille pushed a change to branch upstream
in repository vsearch.

      from  c46e44d   New upstream version 2.3.4
       new  38304cc   New upstream version 2.4.3

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:
 .gitignore           |   2 +
 LICENSE.txt          |   2 +-
 README.md            |  62 ++--
 configure.ac         |  12 +-
 man/vsearch.1        |  64 ++--
 src/Makefile.am      |  36 +-
 src/abundance.cc     |  20 +-
 src/abundance.h      |   6 +-
 src/align.cc         | 100 +++---
 src/align.h          |  42 +--
 src/align_simd.cc    | 963 ++++++++++++++++++++++++++++++++++++++-------------
 src/align_simd.h     |   2 +-
 src/allpairs.cc      |  91 ++---
 src/allpairs.h       |   2 +-
 src/arch.cc          | 158 ++++++++-
 src/arch.h           |  13 +-
 src/bitmap.cc        |   6 +-
 src/bitmap.h         |   2 +-
 src/chimera.cc       | 110 +++---
 src/chimera.h        |   2 +-
 src/cluster.cc       |  96 ++---
 src/cluster.h        |   2 +-
 src/cpu.cc           |  49 ++-
 src/cpu.h            |   8 +-
 src/db.cc            |  60 ++--
 src/db.h             |  24 +-
 src/dbhash.cc        |  42 +--
 src/dbhash.h         |  24 +-
 src/dbindex.cc       |  24 +-
 src/dbindex.h        |   6 +-
 src/derep.cc         | 136 ++++----
 src/derep.h          |   2 +-
 src/dynlibs.cc       |  73 +++-
 src/dynlibs.h        |  10 +-
 src/eestats.cc       |  82 ++---
 src/eestats.h        |   2 +-
 src/fasta.cc         |  54 +--
 src/fasta.h          |  34 +-
 src/fastq.cc         |  66 ++--
 src/fastq.h          |  20 +-
 src/fastqops.cc      | 216 ++++++------
 src/fastqops.h       |   2 +-
 src/fastx.cc         |  40 ++-
 src/fastx.h          |  43 +--
 src/linmemalign.cc   | 156 ++++-----
 src/linmemalign.h    | 100 +++---
 src/maps.cc          |   2 +-
 src/maps.h           |   2 +-
 src/mask.cc          |  10 +-
 src/mask.h           |   2 +-
 src/mergepairs.cc    | 177 +++++-----
 src/mergepairs.h     |   2 +-
 src/minheap.cc       |   8 +-
 src/minheap.h        |   3 +-
 src/msa.cc           |  26 +-
 src/msa.h            |   4 +-
 src/otutable.cc      |  48 ++-
 src/otutable.h       |   4 +-
 src/rerep.cc         |  14 +-
 src/rerep.h          |   2 +-
 src/results.cc       |  83 ++---
 src/results.h        |  14 +-
 src/search.cc        |  71 ++--
 src/search.h         |   2 +-
 src/searchcore.cc    |  42 ++-
 src/searchcore.h     |   2 +-
 src/searchexact.cc   |  79 +++--
 src/searchexact.h    |   2 +-
 src/showalign.cc     |  64 ++--
 src/showalign.h      |  12 +-
 src/shuffle.cc       |   6 +-
 src/shuffle.h        |   2 +-
 src/sortbylength.cc  |   4 +-
 src/sortbylength.h   |   2 +-
 src/sortbysize.cc    |   6 +-
 src/sortbysize.h     |   2 +-
 src/subsample.cc     |  26 +-
 src/subsample.h      |   2 +-
 src/unique.cc        |  40 +--
 src/unique.h         |   2 +-
 src/userfields.cc    |   6 +-
 src/userfields.h     |   2 +-
 src/util.cc          | 134 +++----
 src/util.h           |  20 +-
 src/vsearch.cc       | 203 ++++++-----
 src/vsearch.h        | 218 +++++++-----
 src/xstring.h        |   2 +-
 test/unclassified.sh |  70 ++++
 88 files changed, 2688 insertions(+), 1800 deletions(-)

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