[med-svn] [mira] branch upstream updated (6722e03 -> 2878605)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 2 15:37:47 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository mira.
from 6722e03 Imported Upstream version 4.9.5
new 536f766 Imported Upstream version 3.4.0
new 2878605 Imported Upstream version 4.0.2
The 2 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 +-
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 +-
174 files changed, 19439 insertions(+), 31073 deletions(-)
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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