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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit