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satta pushed a change to branch upstream
in repository last-align.
from 857fbc1 New upstream version 830
new 00a898d New upstream version 869
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.txt | 198 +++++++++++++-
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 +-
41 files changed, 1113 insertions(+), 510 deletions(-)
create mode 100644 src/getoptUtil.hh
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