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satta pushed a change to branch master
in repository last-align.
from 34b894a Added references to RRID, OMICtools, bio.tools
new 00a898d New upstream version 869
new 0e7bcc0 Merge tag 'upstream/869'
new 116d814 new upstream release, bug fix
new 72682ad fix autopkgtest
The 4 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.txt | 198 +++++++++++++-
debian/changelog | 13 +-
debian/control | 4 +-
debian/tests/control | 2 +-
doc/last-dotplot.html | 126 ++++++++-
doc/last-dotplot.txt | 99 +++++--
doc/last-papers.html | 5 +
doc/last-papers.txt | 8 +
doc/last-train.html | 24 +-
doc/last-train.txt | 21 +-
doc/last-tutorial.html | 28 +-
doc/last-tutorial.txt | 27 +-
doc/lastal.html | 12 +-
doc/lastal.txt | 12 +-
doc/lastdb.html | 2 +-
doc/lastdb.txt | 2 +-
scripts/last-dotplot | 463 ++++++++++++++++++++++++---------
scripts/last-postmask | 8 +-
scripts/last-train | 129 ++++++---
scripts/maf-convert | 52 ++--
src/Alignment.cc | 25 +-
src/AlignmentWrite.cc | 5 +-
src/Centroid.cc | 52 ++--
src/Centroid.hh | 13 +-
src/LastEvaluer.cc | 17 +-
src/LastalArguments.cc | 25 +-
src/LastalArguments.hh | 1 +
src/LastdbArguments.cc | 18 +-
src/alp/sls_alignment_evaluer.cpp | 14 +-
src/alp/sls_alignment_evaluer.hpp | 4 +-
src/alp/sls_alp_data.cpp | 9 +-
src/alp/sls_alp_data.hpp | 4 +
src/alp/sls_basic.hpp | 8 +-
src/alp/sls_falp_alignment_evaluer.cpp | 10 -
src/alp/sls_fsa1_pvalues.cpp | 54 +---
src/alp/sls_fsa1_pvalues.hpp | 21 --
src/alp/sls_pvalues.cpp | 54 +---
src/alp/sls_pvalues.hpp | 20 --
src/getoptUtil.hh | 17 ++
src/lastal.cc | 13 +-
src/makefile | 4 +-
src/split/cbrc_split_aligner.hh | 2 +-
src/split/last-split.cc | 15 +-
src/version.hh | 2 +-
44 files changed, 1127 insertions(+), 515 deletions(-)
create mode 100644 src/getoptUtil.hh
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