[med-svn] [exonerate] branch master updated (0a5287b -> 6207500)
Andreas Tille
tille at debian.org
Sun Mar 20 11:46:07 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository exonerate.
from 0a5287b Moved packaging from SVN to Git
new d0bf543 Imported Upstream version 2.4.0
new 51e748d Merge tag 'upstream/2.4.0'
new 451184d New upstream version
new 622a997 Adapt patches
new 6207500 Better hardening, upload to unstable
The 5 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 | 27 +-
Makefile.in | 1 +
configure | 25 +-
configure.in | 21 +-
debian/changelog | 6 +-
debian/patches/fix_build-as-needed.patch | 25 +-
debian/patches/manpages.patch | 24 +-
debian/patches/manpagesyntax.patch | 8 +-
debian/patches/spelling.patch | 4 +-
debian/rules | 2 +
doc/Makefile.in | 1 +
doc/man/Makefile.in | 1 +
doc/man/man1/Makefile.in | 1 +
doc/man/man1/exonerate.1 | 63 +++-
src/Makefile.in | 1 +
src/bsdp/Makefile.am | 3 +-
src/bsdp/Makefile.in | 16 +-
src/bsdp/bsdp.c | 2 +-
src/bsdp/bsdp.h | 2 +-
src/bsdp/bsdp.test.c | 2 +-
src/bsdp/heuristic.c | 2 +-
src/bsdp/heuristic.h | 2 +-
src/bsdp/heuristic.test.c | 2 +-
src/bsdp/hpair.c | 2 +-
src/bsdp/hpair.h | 2 +-
src/bsdp/hpair.test.c | 2 +-
src/bsdp/sar.c | 2 +-
src/bsdp/sar.h | 2 +-
src/bsdp/sar.test.c | 2 +-
src/c4/Makefile.am | 9 +-
src/c4/Makefile.in | 17 +-
src/c4/alignment.c | 222 ++++++++++-
src/c4/alignment.h | 8 +-
src/c4/alignment.test.c | 2 +-
src/c4/c4.c | 8 +-
src/c4/c4.h | 5 +-
src/c4/c4.test.c | 2 +-
src/c4/cgutil.c | 2 +-
src/c4/cgutil.h | 2 +-
src/c4/cgutil.test.c | 2 +-
src/c4/codegen.c | 2 +-
src/c4/codegen.h | 2 +-
src/c4/codegen.test.c | 2 +-
src/c4/layout.c | 2 +-
src/c4/layout.h | 2 +-
src/c4/layout.test.c | 2 +-
src/c4/opair.c | 2 +-
src/c4/opair.h | 2 +-
src/c4/opair.test.c | 2 +-
src/c4/optimal.c | 2 +-
src/c4/optimal.h | 2 +-
src/c4/optimal.test.c | 2 +-
src/c4/region.c | 2 +-
src/c4/region.h | 2 +-
src/c4/region.test.c | 2 +-
src/c4/subopt.c | 2 +-
src/c4/subopt.h | 2 +-
src/c4/subopt.test.c | 2 +-
src/c4/viterbi.c | 2 +-
src/c4/viterbi.h | 2 +-
src/c4/viterbi.test.c | 2 +-
src/comparison/Makefile.am | 3 +
src/comparison/Makefile.in | 10 +-
src/comparison/comparison.c | 30 +-
src/comparison/comparison.h | 10 +-
src/comparison/comparison.test.c | 2 +-
src/comparison/hspset.c | 159 +++++---
src/comparison/hspset.h | 27 +-
src/comparison/hspset.test.c | 2 +-
src/comparison/match.c | 11 +-
src/comparison/match.h | 2 +-
src/comparison/match.test.c | 2 +-
src/comparison/pcr.c | 2 +-
src/comparison/pcr.h | 2 +-
src/comparison/pcr.test.c | 2 +-
src/comparison/seeder.c | 174 ++++++++-
src/comparison/seeder.h | 3 +-
src/comparison/seeder.test.c | 2 +-
src/comparison/wordhood.c | 2 +-
src/comparison/wordhood.h | 2 +-
src/comparison/wordhood.test.c | 2 +-
src/database/Makefile.am | 16 +-
src/database/Makefile.in | 18 +-
src/database/dataset.c | 27 +-
src/database/dataset.h | 3 +-
src/database/dataset.test.c | 2 +-
src/database/fastadb.c | 39 +-
src/database/fastadb.h | 6 +-
src/database/fastadb.test.c | 2 +-
src/database/fastapipe.c | 22 +-
src/database/fastapipe.h | 5 +-
src/database/fastapipe.test.c | 4 +-
src/database/index.c | 148 ++++++--
src/database/index.h | 10 +-
src/database/index.test.c | 2 +-
src/general/Makefile.am | 15 +-
src/general/Makefile.in | 34 +-
src/general/argument.c | 11 +-
src/general/argument.h | 2 +-
src/general/argument.test.c | 2 +-
src/general/compoundfile.c | 50 ++-
src/general/compoundfile.h | 23 +-
src/general/compoundfile.test.c | 2 +-
src/general/jobqueue.c | 137 +++++++
src/general/jobqueue.h | 67 ++++
.../bitarray.test.c => general/jobqueue.test.c} | 33 +-
src/general/lineparse.c | 2 +-
src/general/lineparse.h | 2 +-
src/general/lineparse.test.c | 2 +-
src/general/socket.c | 52 ++-
src/general/socket.h | 5 +-
src/general/socket.test.c | 2 +-
src/general/threadref.c | 69 ++++
src/{hub/bsam.h => general/threadref.h} | 38 +-
src/{c4/c4.test.c => general/threadref.test.c} | 20 +-
src/hub/Makefile.am | 4 +
src/hub/Makefile.in | 18 +-
src/hub/analysis.c | 416 ++++++++++++++++++---
src/hub/analysis.h | 28 +-
src/hub/analysis.test.c | 2 +-
src/hub/bsam.c | 2 +-
src/hub/bsam.h | 2 +-
src/hub/bsam.test.c | 2 +-
src/hub/gam.c | 104 ++++--
src/hub/gam.h | 16 +-
src/hub/gam.test.c | 2 +-
src/model/Makefile.am | 1 +
src/model/Makefile.in | 51 ++-
src/model/affine.c | 2 +-
src/model/affine.h | 2 +-
src/model/affine.test.c | 2 +-
src/model/bootstrapper.c | 2 +-
src/model/cdna2genome.c | 2 +-
src/model/cdna2genome.h | 2 +-
src/model/cdna2genome.test.c | 4 +-
src/model/coding2coding.c | 2 +-
src/model/coding2coding.h | 2 +-
src/model/coding2coding.test.c | 2 +-
src/model/coding2genome.c | 2 +-
src/model/coding2genome.h | 2 +-
src/model/coding2genome.test.c | 2 +-
src/model/edit_distance.c | 2 +-
src/model/edit_distance.h | 2 +-
src/model/edit_distance.test.c | 2 +-
src/model/est2genome.c | 2 +-
src/model/est2genome.h | 2 +-
src/model/est2genome.test.c | 4 +-
src/model/frameshift.c | 2 +-
src/model/frameshift.h | 2 +-
src/model/frameshift.test.c | 2 +-
src/model/genome2genome.c | 2 +-
src/model/genome2genome.h | 2 +-
src/model/genome2genome.test.c | 2 +-
src/model/intron.c | 2 +-
src/model/intron.h | 2 +-
src/model/intron.test.c | 2 +-
src/model/modeltype.c | 2 +-
src/model/modeltype.h | 2 +-
src/model/modeltype.test.c | 2 +-
src/model/ner.c | 2 +-
src/model/ner.h | 2 +-
src/model/ner.test.c | 2 +-
src/model/phase.c | 2 +-
src/model/phase.h | 2 +-
src/model/phase.test.c | 2 +-
src/model/protein2dna.c | 2 +-
src/model/protein2dna.h | 2 +-
src/model/protein2dna.test.c | 2 +-
src/model/protein2genome.c | 2 +-
src/model/protein2genome.h | 2 +-
src/model/protein2genome.test.c | 6 +-
src/model/ungapped.c | 2 +-
src/model/ungapped.h | 2 +-
src/model/ungapped.test.c | 2 +-
src/program/Makefile.am | 6 +-
src/program/Makefile.in | 12 +-
src/program/exonerate-server.c | 77 +++-
src/program/exonerate.c | 8 +-
src/program/ipcress.c | 2 +-
src/sdp/Makefile.am | 1 +
src/sdp/Makefile.in | 12 +-
src/sdp/boundary.c | 2 +-
src/sdp/boundary.h | 2 +-
src/sdp/boundary.test.c | 2 +-
src/sdp/lookahead.c | 2 +-
src/sdp/lookahead.h | 2 +-
src/sdp/lookahead.test.c | 2 +-
src/sdp/scheduler.c | 2 +-
src/sdp/scheduler.h | 2 +-
src/sdp/scheduler.test.c | 2 +-
src/sdp/sdp.c | 8 +-
src/sdp/sdp.h | 5 +-
src/sdp/sdp.test.c | 2 +-
src/sdp/straceback.c | 2 +-
src/sdp/straceback.h | 2 +-
src/sdp/straceback.test.c | 2 +-
src/sequence/Makefile.in | 1 +
src/sequence/alphabet.c | 44 ++-
src/sequence/alphabet.h | 9 +-
src/sequence/alphabet.test.c | 2 +-
src/sequence/codonsubmat.c | 2 +-
src/sequence/codonsubmat.h | 2 +-
src/sequence/codonsubmat.test.c | 2 +-
src/sequence/sequence.c | 105 +++++-
src/sequence/sequence.h | 11 +-
src/sequence/sequence.test.c | 2 +-
src/sequence/splice.c | 4 +-
src/sequence/splice.h | 2 +-
src/sequence/splice.test.c | 2 +-
src/sequence/submat.c | 4 +-
src/sequence/submat.h | 2 +-
src/sequence/submat.test.c | 2 +-
src/sequence/translate.c | 6 +-
src/sequence/translate.h | 2 +-
src/sequence/translate.test.c | 10 +-
src/struct/Makefile.am | 13 +-
src/struct/Makefile.in | 14 +-
src/struct/bitarray.c | 2 +-
src/struct/bitarray.h | 4 +-
src/struct/bitarray.test.c | 2 +-
src/struct/dejavu.c | 5 +-
src/struct/dejavu.h | 2 +-
src/struct/dejavu.test.c | 2 +-
src/struct/fsm.c | 4 +-
src/struct/fsm.h | 2 +-
src/struct/fsm.test.c | 2 +-
src/struct/matrix.c | 2 +-
src/struct/matrix.h | 2 +-
src/struct/matrix.test.c | 2 +-
src/struct/noitree.c | 2 +-
src/struct/noitree.h | 2 +-
src/struct/noitree.test.c | 2 +-
src/struct/pqueue.c | 2 +-
src/struct/pqueue.h | 2 +-
src/struct/pqueue.test.c | 2 +-
src/struct/rangetree.c | 2 +-
src/struct/rangetree.h | 2 +-
src/struct/rangetree.test.c | 2 +-
src/struct/recyclebin.c | 16 +-
src/struct/recyclebin.h | 2 +-
src/struct/recyclebin.test.c | 2 +-
src/struct/slist.c | 2 +-
src/struct/slist.h | 2 +-
src/struct/slist.test.c | 2 +-
src/struct/sparsecache.c | 2 +-
src/struct/sparsecache.h | 2 +-
src/struct/sparsecache.test.c | 2 +-
src/struct/splaytree.c | 2 +-
src/struct/splaytree.h | 2 +-
src/struct/splaytree.test.c | 2 +-
src/struct/vfsm.c | 2 +-
src/struct/vfsm.h | 6 +-
src/struct/vfsm.test.c | 2 +-
src/util/Makefile.am | 1 +
src/util/Makefile.in | 10 +-
src/util/esd2esi.c | 16 +-
src/util/fasta2esd.c | 2 +-
src/util/fastaannotatecdna.c | 2 +-
src/util/fastachecksum.c | 2 +-
src/util/fastaclean.c | 2 +-
src/util/fastaclip.c | 2 +-
src/util/fastacomposition.c | 2 +-
src/util/fastadiff.c | 2 +-
src/util/fastaexplode.c | 2 +-
src/util/fastafetch.c | 6 +-
src/util/fastahardmask.c | 2 +-
src/util/fastaindex.c | 2 +-
src/util/fastalength.c | 2 +-
src/util/fastanrdb.c | 2 +-
src/util/fastaoverlap.c | 2 +-
src/util/fastareformat.c | 2 +-
src/util/fastaremove.c | 2 +-
src/util/fastarevcomp.c | 2 +-
src/util/fastasoftmask.c | 2 +-
src/util/fastasort.c | 2 +-
src/util/fastasplit.c | 2 +-
src/util/fastasubseq.c | 2 +-
src/util/fastatranslate.c | 8 +-
src/util/fastavalidcds.c | 2 +-
test/Makefile.in | 1 +
test/data/Makefile.in | 1 +
test/data/cdna/Makefile.in | 1 +
test/data/protein/Makefile.in | 1 +
test/exonerate/Makefile.in | 1 +
test/ipcress/Makefile.in | 1 +
test/util/Makefile.in | 1 +
286 files changed, 2540 insertions(+), 688 deletions(-)
create mode 100644 src/general/jobqueue.c
create mode 100644 src/general/jobqueue.h
copy src/{struct/bitarray.test.c => general/jobqueue.test.c} (50%)
create mode 100644 src/general/threadref.c
copy src/{hub/bsam.h => general/threadref.h} (57%)
copy src/{c4/c4.test.c => general/threadref.test.c} (70%)
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