[med-svn] [mira] branch master updated (71892b1 -> 4aa59e0)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 2 15:44:39 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.
omits 71892b1 Imported Debian patch 4.0.2-1
omits 2878605 Imported Upstream version 4.0.2
omits 15dab0f Imported Debian patch 3.4.0-3
omits ff795a8 Imported Debian patch 3.4.0-2
omits 536f766 Imported Upstream version 3.4.0
This update removed existing revisions from the reference, leaving the
reference pointing at a previous point in the repository history.
* -- * -- N refs/heads/master (4aa59e0)
\
O -- O -- O (71892b1)
Any revisions marked "omits" are not gone; other references still
refer to them. Any revisions marked "discards" are gone forever.
No new revisions were added by this update.
Summary of changes:
.tarball-version | 2 +-
.version | 2 +-
Makefile.am | 2 +-
Makefile.in | 5 +-
README | 4 +-
README_build.html | 66 +-
aclocal.m4 | 3 -
configure | 1086 +--
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}/mira.1 | 2 +-
debian/{ => mans}/miraSearchESTSNPs.1 | 0
debian/{ => mans}/mirabait.1 | 0
debian/{convert_project.1 => mans/miraconvert.1} | 319 +-
debian/{ => mans}/miradiff.1 | 0
debian/{ => mans}/miramem.1 | 0
debian/{ => mans}/miramer.1 | 0
debian/{ => mans}/scftool.1 | 0
debian/mira-assembler.manpages | 2 +-
debian/mira-examples.lintian-overrides | 3 +
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/{upstream => upstream/metadata} | 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 | 2085 ++--
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 | 2888 ++----
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/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 | 3412 ++++---
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/{stdinc/template.H => mira/readlotstat.C} | 63 +-
src/{stdinc/template.H => mira/readlotstat.H} | 36 +-
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/{bloomfilter.C => simplebloomfilter.C} | 45 +-
src/mira/{bloomfilter.H => simplebloomfilter.H} | 114 +-
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_tagsnp.H => mod_diff.H} | 27 +-
src/modules/mod_mer.C | 524 +
src/modules/{mod_tagsnp.H => mod_mer.H} | 35 +-
src/modules/mod_mira.C | 59 +-
src/modules/mod_mira.H | 2 +
src/modules/mod_scaffold.C | 101 +
src/modules/{mod_memestim.H => mod_scaffold.H} | 25 +-
src/modules/mod_sigconex.C | 253 +
src/{mira/enums.H => modules/mod_sigconex.H} | 29 +-
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, 31478 insertions(+), 19674 deletions(-)
create mode 100644 debian/clean
copy 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%)
rename debian/{ => mans}/mira.1 (97%)
rename debian/{ => mans}/miraSearchESTSNPs.1 (100%)
rename debian/{ => mans}/mirabait.1 (100%)
rename debian/{convert_project.1 => mans/miraconvert.1} (51%)
rename debian/{ => mans}/miradiff.1 (100%)
rename debian/{ => mans}/miramem.1 (100%)
rename debian/{ => mans}/miramer.1 (100%)
rename debian/{ => mans}/scftool.1 (100%)
create mode 100644 debian/mira-examples.lintian-overrides
delete mode 100644 debian/patches/boost-minimal.patch
create mode 100644 debian/patches/fix_strange_link_issue.patch
create mode 100644 debian/patches/spelling.patch
rename debian/{upstream => upstream/metadata} (100%)
mode change 100644 => 100755 depcomp
delete mode 100644 m4/ax_cxx_have_std.m4
delete mode 100644 m4/ax_cxx_have_stl.m4
delete mode 100644 m4/ax_cxx_namespaces.m4
create mode 100644 src/mira/assembly_buildcontigs.C
create mode 100644 src/mira/assembly_pbcorrect.C
create mode 100644 src/mira/hashstats_sdbg.C
copy src/{stdinc/template.H => mira/readlotstat.C} (63%)
copy src/{stdinc/template.H => mira/readlotstat.H} (56%)
create mode 100644 src/mira/readpool_io.C
create mode 100644 src/mira/readpool_io.H
rename src/mira/{bloomfilter.C => simplebloomfilter.C} (54%)
rename src/mira/{bloomfilter.H => simplebloomfilter.H} (71%)
delete mode 100644 src/mira/skim_farc.C
create mode 100644 src/mira/vhash.H
create mode 100644 src/mira/vluint.H
create mode 100644 src/modules/mod_diff.C
copy src/modules/{mod_tagsnp.H => mod_diff.H} (71%)
create mode 100644 src/modules/mod_mer.C
copy src/modules/{mod_tagsnp.H => mod_mer.H} (58%)
create mode 100644 src/modules/mod_scaffold.C
copy src/modules/{mod_memestim.H => mod_scaffold.H} (74%)
create mode 100644 src/modules/mod_sigconex.C
copy src/{mira/enums.H => modules/mod_sigconex.H} (74%)
delete mode 100644 src/progs/miramer.C
create mode 100644 src/util/timer.H
--
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