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malex-guest pushed a change to branch upstream
in repository gmap.
from 536c54f Imported Upstream version 2014-07-04
new 4645328 Imported Upstream version 2014-07-28
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:
ChangeLog | 85 ++++
VERSION | 2 +-
configure | 24 +-
src/atoiindex.c | 18 +-
src/cmetindex.c | 18 +-
src/dynprog.h | 10 +-
src/dynprog_genome.c | 246 +++++-----
src/dynprog_simd.c | 271 +++++++++--
src/gmap.c | 5 +-
src/pair.c | 46 +-
src/pair.h | 7 +-
src/pairpool.c | 8 +-
src/stage1hr.c | 10 +-
src/stage2.c | 69 ++-
src/stage3.c | 529 ++++++++++++++-------
src/stage3.h | 3 +-
src/stage3hr.c | 1099 ++++++++++++-------------------------------
src/stage3hr.h | 10 +-
util/gff3_genes.pl.in | 47 +-
util/gff3_introns.pl.in | 30 +-
util/gff3_splicesites.pl.in | 34 +-
21 files changed, 1370 insertions(+), 1201 deletions(-)
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