This is an automated email from the git hooks/post-receive script.
plessy pushed a change to branch upstream
in repository last-align.
from 00a898d New upstream version 869
new 899a681 New upstream version 885
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 | 87 +++++++++++++++++++++++++++++++++++++++++++-
doc/last-dotplot.html | 17 +++++++--
doc/last-dotplot.txt | 15 ++++++--
doc/last-parallel.html | 4 +--
doc/last-parallel.txt | 4 +--
doc/last-train.html | 4 +++
doc/last-train.txt | 2 ++
doc/last-tuning.html | 7 ++--
doc/last-tuning.txt | 8 ++---
doc/last.html | 4 +--
doc/last.txt | 4 +--
doc/lastal.html | 13 ++++---
doc/lastal.txt | 9 +++--
doc/lastdb.html | 5 +--
doc/lastdb.txt | 5 +--
doc/maf-convert.html | 12 +++----
doc/maf-convert.txt | 18 +++++-----
scripts/fastq-interleave | 10 ++----
scripts/last-dotplot | 75 +++++++++++++++++++++++---------------
scripts/last-postmask | 23 +++++++-----
scripts/last-train | 79 ++++++++++++++++++++++++++--------------
scripts/maf-convert | 93 +++++++++++++++++++++++++++++++++++-------------
src/Alphabet.cc | 8 -----
src/Alphabet.hh | 3 --
src/LastEvaluer.cc | 2 +-
src/LastalArguments.cc | 33 ++++++++++++-----
src/MultiSequence.cc | 7 ----
src/MultiSequence.hh | 66 +++++++++++++++++++++++++++++++---
src/MultiSequenceQual.cc | 22 ++++--------
src/io.cc | 11 ++----
src/io.hh | 7 ++--
src/last-pair-probs.cc | 4 +--
src/lastal.cc | 32 ++---------------
src/lastdb.cc | 43 ++++++++++------------
src/makefile | 32 ++++++++---------
src/mcf_zstream.hh | 82 ++++++++++++++++++++++++++++++++++++++++++
src/version.hh | 2 +-
37 files changed, 569 insertions(+), 283 deletions(-)
create mode 100644 src/mcf_zstream.hh
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