[med-svn] [mira] branch master updated (4aa59e0 -> 71892b1)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 2 15:37:39 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository mira.
from 4aa59e0 more spelling fixes
new 536f766 Imported Upstream version 3.4.0
new ff795a8 Imported Debian patch 3.4.0-2
new 15dab0f Imported Debian patch 3.4.0-3
new 2878605 Imported Upstream version 4.0.2
new 71892b1 Imported Debian patch 4.0.2-1
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:
.tarball-version | 2 +-
.version | 2 +-
Makefile.am | 2 +-
Makefile.in | 5 +-
README | 4 +-
README_build.html | 66 +-
aclocal.m4 | 3 +
configure | 1080 +--
configure.ac | 424 +-
debian/changelog | 32 -
debian/clean | 1 -
debian/control | 17 +-
debian/{mans => }/convert_project.1 | 0
debian/{mans => }/fasta2frag.1 | 0
debian/{mans => }/fastaselect.1 | 0
debian/{mans => }/fastatool.1 | 0
debian/{mans => }/fastqselect.1 | 0
debian/{mans => }/fixACE4consed.1 | 0
debian/mans/miraconvert.1 | 327 -
debian/mira-assembler.manpages | 2 +-
debian/mira-examples.lintian-overrides | 3 -
debian/{mans => }/mira.1 | 2 +-
debian/{mans => }/miraSearchESTSNPs.1 | 0
debian/{mans => }/mirabait.1 | 0
debian/{mans => }/miradiff.1 | 0
debian/{mans => }/miramem.1 | 0
debian/{mans => }/miramer.1 | 0
debian/patches/boost-minimal.patch | 15 +
debian/patches/fix_strange_link_issue.patch | 16 -
debian/patches/series | 3 +-
debian/patches/spelling.patch | 396 -
debian/rules | 5 +-
debian/{mans => }/scftool.1 | 0
debian/{upstream/metadata => upstream} | 0
depcomp | 563 +-
distribution/Makefile | 27 +-
distribution/Makefile.in | 3 +
distribution/README | 6 +-
doc/Makefile | 27 +-
doc/Makefile.in | 3 +
doc/docbook/Makefile | 27 +-
doc/docbook/Makefile.in | 3 +
doc/docbook/chap_dataprep_part.xml | 50 +-
doc/docbook/chap_denovo_part.xml | 5 +-
doc/docbook/chap_faq_part.xml | 10 +-
doc/docbook/chap_hard_part.xml | 52 +-
doc/docbook/chap_installation_part.xml | 71 +-
doc/docbook/chap_intro_part.xml | 9 +-
doc/docbook/chap_logfiles_part.xml | 8 +-
doc/docbook/chap_mirautils_part.xml | 551 +-
doc/docbook/chap_reference_part.xml | 2083 ++---
doc/docbook/chap_results_part.xml | 8 -
doc/docbook/chap_seqtechdesc_part.xml | 108 -
m4/ax_boost_base.m4 | 20 +-
m4/ax_cxx_have_std.m4 | 46 +
m4/ax_cxx_have_stl.m4 | 44 +
m4/ax_cxx_namespaces.m4 | 40 +
src/Makefile.am | 1 -
src/Makefile.in | 4 +-
src/caf/Makefile.in | 3 +
src/caf/caf.C | 361 +-
src/caf/caf.H | 59 +-
src/debuggersupport/Makefile.in | 3 +
src/errorhandling/Makefile.in | 3 +
src/errorhandling/errorhandling.C | 15 -
src/errorhandling/errorhandling.H | 7 -
src/io/Makefile.in | 3 +
src/io/annotationmappings.C | 12 +-
src/io/annotationmappings.H | 25 +-
src/io/exp.C | 2 -
src/io/fasta.C | 42 +-
src/io/fasta.H | 9 +-
src/io/scf.C | 4 -
src/memorc/Makefile.in | 3 +
src/memorc/memorc.C | 2 -
src/mira/CHANGES.txt | 138 -
src/mira/Makefile.am | 20 +-
src/mira/Makefile.in | 57 +-
src/mira/TODO | 122 +-
src/mira/ads.C | 100 +-
src/mira/ads.H | 13 +-
src/mira/adsfacts.C | 4 +-
src/mira/adsfacts.H | 4 +-
src/mira/align.C | 446 +-
src/mira/align.H | 33 +-
src/mira/assembly.C | 2934 ++++--
src/mira/assembly.H | 415 +-
src/mira/assembly_buildcontigs.C | 2260 -----
src/mira/assembly_info.C | 20 +-
src/mira/assembly_info.H | 1 +
src/mira/assembly_io.C | 393 +-
src/mira/assembly_misc.C | 1125 +--
src/mira/assembly_output.C | 492 +-
src/mira/assembly_pbcorrect.C | 2126 -----
src/mira/assembly_reduceskimhits.C | 244 +-
src/mira/assembly_swalign.C | 313 +-
src/mira/{simplebloomfilter.C => bloomfilter.C} | 45 +-
src/mira/{simplebloomfilter.H => bloomfilter.H} | 114 +-
src/mira/contig.C | 351 +-
src/mira/contig.H | 649 +-
src/mira/contig_analysis.C | 261 +-
src/mira/contig_consensus.C | 1582 ++--
src/mira/contig_edit.C | 47 +-
src/mira/contig_featureinfo.C | 27 +-
src/mira/contig_output.C | 397 +-
src/mira/dataprocessing.C | 757 +-
src/mira/dataprocessing.H | 93 +-
src/mira/dynamic.C | 172 +-
src/mira/dynamic.H | 24 +-
src/mira/estassembly.C | 4 -
src/mira/gbf_parse.C | 2 -
src/mira/gbf_parse.H | 6 +-
src/mira/gff_parse.C | 8 +-
src/mira/gff_parse.H | 17 +-
src/mira/gff_save.C | 3 -
src/mira/gff_save.H | 5 +-
src/mira/hashstats.C | 3422 +++----
src/mira/hashstats.H | 799 +-
src/mira/hashstats_sdbg.C | 693 --
src/mira/hdeque.H | 2 +-
src/mira/maf_parse.C | 670 +-
src/mira/maf_parse.H | 120 +-
src/mira/manifest.C | 13 -
src/mira/overlapedges.H | 77 +-
src/mira/parameters.C | 905 +-
src/mira/parameters.H | 6 +-
src/mira/parameters_flexer.cc | 10562 +++++++++++-----------
src/mira/parameters_flexer.ll | 172 +-
src/mira/parameters_tokens.h | 33 +-
src/mira/pcrcontainer.H | 1 +
src/mira/ppathfinder.C | 677 +-
src/mira/ppathfinder.H | 49 +-
src/mira/preventinitfiasco.C | 56 +-
src/mira/read.C | 762 +-
src/mira/read.H | 49 +-
src/mira/readgrouplib.C | 100 +-
src/mira/readgrouplib.H | 28 -
src/mira/readlotstat.C | 51 -
src/mira/readlotstat.H | 64 -
src/mira/readpool.C | 1056 ++-
src/mira/readpool.H | 83 +-
src/mira/readpool_io.C | 1005 --
src/mira/readpool_io.H | 172 -
src/mira/readseqtypes.H | 35 +-
src/mira/sam_collect.C | 2 +-
src/mira/sam_collect.H | 3 +
src/mira/scaffolder.C | 163 +-
src/mira/scaffolder.H | 65 +-
src/mira/seqtohash.H | 6 +-
src/mira/skim.C | 994 +-
src/mira/skim.H | 111 +-
src/mira/skim_farc.C | 572 ++
src/mira/skim_lowbph.C | 49 +-
src/mira/structs.H | 61 +-
src/mira/types_basic.H | 2 +-
src/mira/vhash.H | 133 -
src/mira/vluint.H | 388 -
src/modules/Makefile.am | 4 +-
src/modules/Makefile.in | 20 +-
src/modules/misc.C | 9 +-
src/modules/misc.H | 4 +-
src/modules/mod_bait.C | 931 +-
src/modules/mod_bait.H | 96 +-
src/modules/mod_convert.C | 473 +-
src/modules/mod_convert.H | 13 +-
src/modules/mod_dbgreplay.C | 5 +-
src/modules/mod_diff.C | 305 -
src/modules/mod_diff.H | 55 -
src/modules/mod_mer.C | 524 --
src/modules/mod_mer.H | 67 -
src/modules/mod_mira.C | 59 +-
src/modules/mod_mira.H | 2 -
src/modules/mod_scaffold.C | 101 -
src/modules/mod_scaffold.H | 50 -
src/modules/mod_sigconex.C | 253 -
src/modules/mod_sigconex.H | 51 -
src/modules/mod_tagsnp.C | 4 +-
src/progs/Makefile.am | 10 +-
src/progs/Makefile.in | 24 +-
src/progs/mira.C | 28 +-
src/progs/miramer.C | 494 +
src/progs/miratest.C | 517 +-
src/progs/quirks.C | 5 +-
src/scripts/Makefile.in | 3 +
src/stdinc/Makefile.in | 3 +
src/stdinc/defines.H | 2 +-
src/support/Makefile.in | 3 +
src/util/Makefile.am | 2 +-
src/util/Makefile.in | 5 +-
src/util/boostiostrutil.H | 4 +-
src/util/dptools.C | 55 +-
src/util/dptools.H | 29 +-
src/util/fileanddisk.C | 185 +-
src/util/fileanddisk.H | 28 +-
src/util/fmttext.H | 7 -
src/util/misc.C | 10 +-
src/util/progressindic.H | 14 +-
src/util/timer.H | 111 -
src/version.H | 2 +-
199 files changed, 19464 insertions(+), 31867 deletions(-)
delete mode 100644 debian/clean
rename debian/{mans => }/convert_project.1 (100%)
rename debian/{mans => }/fasta2frag.1 (100%)
rename debian/{mans => }/fastaselect.1 (100%)
rename debian/{mans => }/fastatool.1 (100%)
rename debian/{mans => }/fastqselect.1 (100%)
rename debian/{mans => }/fixACE4consed.1 (100%)
delete mode 100644 debian/mans/miraconvert.1
delete mode 100644 debian/mira-examples.lintian-overrides
rename debian/{mans => }/mira.1 (97%)
rename debian/{mans => }/miraSearchESTSNPs.1 (100%)
rename debian/{mans => }/mirabait.1 (100%)
rename debian/{mans => }/miradiff.1 (100%)
rename debian/{mans => }/miramem.1 (100%)
rename debian/{mans => }/miramer.1 (100%)
create mode 100644 debian/patches/boost-minimal.patch
delete mode 100644 debian/patches/fix_strange_link_issue.patch
delete mode 100644 debian/patches/spelling.patch
rename debian/{mans => }/scftool.1 (100%)
rename debian/{upstream/metadata => upstream} (100%)
mode change 100755 => 100644 depcomp
create mode 100644 m4/ax_cxx_have_std.m4
create mode 100644 m4/ax_cxx_have_stl.m4
create mode 100644 m4/ax_cxx_namespaces.m4
delete mode 100644 src/mira/assembly_buildcontigs.C
delete mode 100644 src/mira/assembly_pbcorrect.C
rename src/mira/{simplebloomfilter.C => bloomfilter.C} (54%)
rename src/mira/{simplebloomfilter.H => bloomfilter.H} (71%)
delete mode 100644 src/mira/hashstats_sdbg.C
delete mode 100644 src/mira/readlotstat.C
delete mode 100644 src/mira/readlotstat.H
delete mode 100644 src/mira/readpool_io.C
delete mode 100644 src/mira/readpool_io.H
create mode 100644 src/mira/skim_farc.C
delete mode 100644 src/mira/vhash.H
delete mode 100644 src/mira/vluint.H
delete mode 100644 src/modules/mod_diff.C
delete mode 100644 src/modules/mod_diff.H
delete mode 100644 src/modules/mod_mer.C
delete mode 100644 src/modules/mod_mer.H
delete mode 100644 src/modules/mod_scaffold.C
delete mode 100644 src/modules/mod_scaffold.H
delete mode 100644 src/modules/mod_sigconex.C
delete mode 100644 src/modules/mod_sigconex.H
create mode 100644 src/progs/miramer.C
delete mode 100644 src/util/timer.H
--
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