[med-svn] [mira] branch master updated (241b54a -> 02778bc)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed May 4 22:22:51 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 241b54a Upload to unstable
new 2706801 Imported Upstream version 3.4.0
new 1765fee Imported Upstream version 4.0.2
new fb73716 Imported Upstream version 4.9.6
new 02778bc new upstream release
The 4 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 | 11 +-
Makefile.in | 14 +-
README | 2 +-
README_MAINTAINERS | 44 +
README_build.html | 272 +-
THANKS | 11 +-
aclocal.m4 | 5 +-
configure | 632 +-
configure.ac | 60 +-
debian/changelog | 19 +
debian/control | 62 +-
debian/mans/convert_project.1 | 302 -
debian/mans/fasta2frag.1 | 95 -
debian/mans/fastaselect.1 | 47 -
debian/mans/fastatool.1 | 49 -
debian/mans/fastqselect.1 | 47 -
debian/mans/fixACE4consed.1 | 32 -
debian/mans/miraSearchESTSNPs.1 | 43 -
debian/mans/mirabait.1 | 131 -
debian/mans/scftool.1 | 50 -
debian/mira-examples.examples | 2 +-
debian/mira-examples.lintian-overrides | 2 +-
debian/mira-rfam-12s-rrna.install | 3 +
debian/mira-rfam-12s-rrna.lintian-overrides | 2 +
debian/mira-rfam-12s-rrna.postinst | 10 +
debian/mira-rfam-12s-rrna.postrm | 7 +
debian/patches/fix_strange_link_issue.patch | 16 -
debian/patches/gcc-6.patch | 16 -
debian/patches/make-reproducible | 19 -
debian/patches/man-directory | 9 +
debian/patches/series | 5 +-
debian/patches/sls-rrna-fix | 19 +
debian/patches/spelling.patch | 390 +-
debian/rules | 78 +-
distribution/LICENCE | 2 +-
distribution/Makefile | 51 +-
distribution/Makefile.am | 36 +-
distribution/Makefile.in | 39 +-
distribution/README | 32 +-
doc/Makefile | 16 +-
doc/Makefile.am | 1 +
doc/Makefile.in | 4 +-
doc/README_documentation.txt | 10 +
doc/docbook/Makefile | 41 +-
doc/docbook/Makefile.am | 7 +
doc/docbook/Makefile.in | 29 +-
doc/docbook/book_definitiveguide.xml | 6 +-
doc/docbook/chap_bonus_part.xml | 8 +-
doc/docbook/chap_est_part.xml | 513 +-
doc/docbook/chap_installation_part.xml | 327 +-
doc/docbook/chap_intro_part.xml | 12 +-
doc/docbook/chap_mirautils_part.xml | 438 +-
doc/docbook/chap_preface_part.xml | 2 +-
doc/docbook/chap_reference_part.xml | 250 +-
doc/docbook/chap_seqtechdesc_part.xml | 2 +-
doc/docbook/chap_sra_part.xml | 2 +-
doc/docbook/copyrightfile | 2 +-
m4/ax_openmp.m4 | 119 +
man/Makefile.am | 3 +
{src/support => man}/Makefile.in | 47 +-
{debian/mans => man}/mira.1 | 42 +-
man/mirabait.1 | 193 +
{debian/mans => man}/miraconvert.1 | 37 +-
{debian/mans => man}/miradiff.1 | 15 +-
{debian/mans => man}/miramem.1 | 8 +-
{debian/mans => man}/miramer.1 | 15 +-
minidemo/README.txt | 183 -
minidemo/bbdemo1/runme.sh | 31 -
minidemo/bbdemo2/parameters.par | 15 -
minidemo/bbdemo2/runme.sh | 61 -
.../bbdataset1/cjejuni_NCTC11168_first40kb.gbf | 1529 -
.../data/bbdataset1/cjejuni_demo_backbone_in.gbf | 1529 -
minidemo/data/bbdataset1/cjejuni_demo_in.fasta | 8755 --
.../data/bbdataset1/cjejuni_demo_in.fasta.qual | 16708 --
.../data/bbdataset1/cjejuni_demo_in.sanger.fasta | 8755 --
.../bbdataset1/cjejuni_demo_in.sanger.fasta.qual | 16708 --
.../data/bbdataset1/cjejuni_demo_straindata_in.txt | 545 -
.../cjejuni_demo_traceinfo_in.sanger.xml | 13891 --
.../data/bbdataset1/cjejuni_demo_traceinfo_in.xml | 13891 --
minidemo/data/exp_set1/122533a.t3.exp | 30 -
minidemo/data/exp_set1/122533a.t7.exp | 27 -
minidemo/data/exp_set1/122533b.t3.exp | 29 -
minidemo/data/exp_set1/122533b.t7.exp | 32 -
minidemo/data/exp_set1/122533c.t3.exp | 27 -
minidemo/data/exp_set1/122533c.t7.exp | 22 -
minidemo/data/exp_set1/230375a.t3.exp | 30 -
minidemo/data/exp_set1/230375a.t7.exp | 23 -
minidemo/data/exp_set1/230375b.t1.exp | 32 -
minidemo/data/exp_set1/230375b.t2.exp | 36 -
minidemo/data/exp_set1/230375b.t3.exp | 29 -
minidemo/data/exp_set1/230375b.t7.exp | 26 -
minidemo/data/exp_set1/230375c.t3.exp | 30 -
minidemo/data/exp_set1/230375c.t7.exp | 27 -
minidemo/data/exp_set1/U13a03c03.t1.exp | 29 -
minidemo/data/exp_set1/U13a03e10.p2.exp | 28 -
minidemo/data/exp_set1/U13a03e10.t1.exp | 24 -
minidemo/data/exp_set1/U13a03g02.t1.exp | 24 -
minidemo/data/exp_set1/U13a04c06.t1.exp | 26 -
minidemo/data/exp_set1/U13a05b10.t1.exp | 24 -
minidemo/data/exp_set1/U13a06d03.t1.exp | 26 -
minidemo/data/exp_set1/U13a08b04.t1.exp | 30 -
minidemo/data/exp_set1/U13a08f10.p2.exp | 27 -
minidemo/data/exp_set1/U13a08f11.t1.exp | 29 -
minidemo/data/exp_set1/U13e07d02.t2.exp | 27 -
minidemo/data/exp_set1/U13e07f02.t2.exp | 31 -
minidemo/data/exp_set1/fofn | 30 -
minidemo/data/fasta_estset1/README | 12 -
.../fasta_estset1/triphysaria_versicolor.fasta | 38234 -----
.../triphysaria_versicolor.fasta.qual | 124702 ---------------
.../triphysaria_versicolor.masked.fasta | 43967 ------
minidemo/data/fasta_estset1/tvc_mini.fasta | 94 -
minidemo/data/fasta_estset1/tvc_mini.fasta.qual | 178 -
minidemo/data/fasta_set1/U13small_m.fasta | 495 -
minidemo/data/fasta_set1/U13small_m.fasta.qual | 1405 -
minidemo/data/fasta_set1/U13small_nm.fasta | 495 -
minidemo/data/fasta_set1/U13small_nm.fasta.qual | 1405 -
minidemo/data/scf/122533a.t3.scf.gz | Bin 33171 -> 0 bytes
minidemo/data/scf/122533a.t7.scf.gz | Bin 27377 -> 0 bytes
minidemo/data/scf/122533b.t3.scf.gz | Bin 33291 -> 0 bytes
minidemo/data/scf/122533b.t7.scf.gz | Bin 31050 -> 0 bytes
minidemo/data/scf/122533c.t3.scf.gz | Bin 31614 -> 0 bytes
minidemo/data/scf/122533c.t7.scf.gz | Bin 24982 -> 0 bytes
minidemo/data/scf/230375a.t3.scf.gz | Bin 33316 -> 0 bytes
minidemo/data/scf/230375a.t7.scf.gz | Bin 24372 -> 0 bytes
minidemo/data/scf/230375b.t1.scf.gz | Bin 33659 -> 0 bytes
minidemo/data/scf/230375b.t2.scf.gz | Bin 38848 -> 0 bytes
minidemo/data/scf/230375b.t3.scf.gz | Bin 31433 -> 0 bytes
minidemo/data/scf/230375b.t7.scf.gz | Bin 29080 -> 0 bytes
minidemo/data/scf/230375c.t3.scf.gz | Bin 35285 -> 0 bytes
minidemo/data/scf/230375c.t7.scf.gz | Bin 32165 -> 0 bytes
minidemo/data/scf/U13a03c03.t1.scf.gz | Bin 35241 -> 0 bytes
minidemo/data/scf/U13a03e10.p2.scf.gz | Bin 34704 -> 0 bytes
minidemo/data/scf/U13a03e10.t1.scf.gz | Bin 32014 -> 0 bytes
minidemo/data/scf/U13a03g02.t1.scf.gz | Bin 28586 -> 0 bytes
minidemo/data/scf/U13a04c06.t1.scf.gz | Bin 33765 -> 0 bytes
minidemo/data/scf/U13a05b10.t1.scf.gz | Bin 33159 -> 0 bytes
minidemo/data/scf/U13a06d03.t1.scf.gz | Bin 29790 -> 0 bytes
minidemo/data/scf/U13a08b04.t1.scf.gz | Bin 37599 -> 0 bytes
minidemo/data/scf/U13a08f10.p2.scf.gz | Bin 34928 -> 0 bytes
minidemo/data/scf/U13a08f11.t1.scf.gz | Bin 34732 -> 0 bytes
minidemo/data/scf/U13e07d02.t2.scf.gz | Bin 33774 -> 0 bytes
minidemo/data/scf/U13e07f02.t2.scf.gz | Bin 43005 -> 0 bytes
.../data/screendata_454/msd_minimum454screen.fna | 12 -
minidemo/data/screendata_454/msd_primer454.fna | 8 -
minidemo/data/screendata_454/msd_testFrags454.fna | 26 -
minidemo/data/screendata_454/msd_uFrag1_454.fna | 2 -
minidemo/data/solexa_eco_art/ecoli_backbone_in.gbf | 251 -
minidemo/data/solexa_eco_art/ecoli_in.solexa.fasta | 10082 --
.../data/solexa_eco_art/ecoli_in.solexa.fasta.qual | 10082 --
.../data/solexa_eco_art/ecoli_straindata_in.txt | 5041 -
minidemo/data/spneu_t4_40k_454/spneu_t4_40k.gbf | 7579 -
.../spneu_t4_40k_454/spneu_t4_40k_in.454.fasta | 62664 --------
.../spneu_t4_40k_in.454.fasta.qual | 148418 ------------------
minidemo/demo1/runme.sh | 35 -
minidemo/demo2/runme.sh | 23 -
minidemo/demo3/demo3.par | 71 -
minidemo/demo3/runme.sh | 16 -
minidemo/demo4/runme.sh | 22 -
minidemo/demo5/runme.sh | 39 -
minidemo/estdemo1/README | 115 -
minidemo/estdemo1/runme.sh | 21 -
minidemo/estdemo2/README | 30 -
minidemo/estdemo2/runme.sh | 21 -
minidemo/estdemo2/step1_straindata_in.txt | 6 -
minidemo/estdemo2/tvc_straindata_in.txt | 6 -
minidemo/solexa1/README.txt | 24 -
minidemo/solexa1/runme.sh | 8 -
minidemo/solexa2/README.txt | 2 -
minidemo/solexa2/runme.sh | 8 -
minidemo/solexa3_lenski/1_fetchdata.sh | 12 -
minidemo/solexa3_lenski/2_prepdata.sh | 42 -
minidemo/solexa3_lenski/3_runassembly.sh | 18 -
minidemo/solexa3_lenski/README.txt | 10 -
src/Makefile.am | 30 +-
src/Makefile.in | 53 +-
src/caf/Makefile.in | 3 +-
src/caf/caf.C | 193 +-
src/caf/caf.H | 5 +-
src/caf/caf_flexer.cc | 134 +-
src/caf/caf_flexer.ll | 2 -
src/debuggersupport/Makefile.in | 3 +-
src/errorhandling/Makefile.in | 3 +-
src/errorhandling/errorhandling.C | 21 +-
src/errorhandling/errorhandling.H | 2 +-
src/io/Makefile.in | 3 +-
src/io/annotationmappings.C | 63 +-
src/io/exp.C | 63 +-
src/io/exp_flexer.cc | 159 +-
src/io/exp_flexer.ll | 3 -
src/io/fasta.C | 95 +-
src/io/fastq-mira.C | 32 +-
src/io/generalio.C | 8 +-
src/io/ncbiinfoxml.C | 23 +-
src/io/phd.C | 21 +-
src/io/scf.C | 38 +-
src/io/so.obo | 4 +-
src/memorc/Makefile.in | 3 +-
src/memorc/main.C | 18 +-
src/memorc/memorc.C | 9 +-
src/memorc/memorc.H | 2 +-
src/mira/CHANGES.txt | 83 +
src/mira/CHANGES_old.txt | 84 +-
src/mira/Makefile.am | 4 +-
src/mira/Makefile.in | 88 +-
src/mira/TODO | 34 +-
src/mira/adaptorsregex.solexa.xxd | 11 +
src/mira/ads.C | 49 +-
src/mira/adsfacts.C | 8 +-
src/mira/align.C | 26 +-
src/mira/assembly.C | 408 +-
src/mira/assembly.H | 10 +-
src/mira/assembly_buildcontigs.C | 276 +-
src/mira/assembly_info.C | 71 +-
src/mira/assembly_io.C | 346 +-
src/mira/assembly_misc.C | 201 +-
src/mira/assembly_output.C | 817 +-
src/mira/assembly_pbcorrect.C | 120 +-
src/mira/assembly_reduceskimhits.C | 1022 +-
src/mira/assembly_swalign.C | 248 +-
src/mira/contig.C | 515 +-
src/mira/contig.H | 26 +-
src/mira/contig_analysis.C | 335 +-
src/mira/contig_consensus.C | 215 +-
src/mira/contig_covanalysis.C | 50 +-
src/mira/contig_edit.C | 363 +-
src/mira/contig_featureinfo.C | 73 +-
src/mira/contig_output.C | 307 +-
src/mira/contig_pairconsistency.C | 27 +-
src/mira/dataprocessing.C | 366 +-
src/mira/dataprocessing.H | 13 +-
src/mira/demoparam.prm | 321 -
src/mira/dynamic.C | 46 +-
src/mira/estassembly.C | 13 +-
src/mira/gbf_parse.C | 176 +-
src/mira/gff_parse.C | 173 +-
src/mira/gff_save.C | 30 +-
src/mira/hashstats.C | 781 +-
src/mira/hashstats.H | 125 +-
src/mira/hashstats_sdbg.C | 106 +-
src/mira/maf_parse.C | 515 +-
src/mira/maf_parse.H | 5 +-
src/mira/manifest.C | 128 +-
src/mira/multitag.C | 52 +-
src/mira/multitag.H | 45 +-
src/mira/parameters.C | 544 +-
src/mira/parameters.H | 16 +-
src/mira/parameters_flexer.cc | 10659 +-
src/mira/parameters_flexer.ll | 22 +-
src/mira/parameters_tokens.h | 8 +-
src/mira/pcrcontainer.C | 70 +-
src/mira/ppathfinder.C | 101 +-
src/mira/preventinitfiasco.C | 46 +-
src/mira/read.C | 1472 +-
src/mira/read.H | 32 +-
src/mira/readgrouplib.C | 82 +-
src/mira/readgrouplib.H | 1 +
src/mira/readpool.C | 184 +-
src/mira/readpool.H | 2 -
src/mira/readpool_io.C | 189 +-
src/mira/readpool_io.H | 28 +-
src/mira/readseqtypes.H | 1 +
src/mira/sam_collect.C | 101 +-
src/mira/scaffolder.C | 10 +-
src/mira/simplebloomfilter.C | 4 +-
src/mira/skim.C | 525 +-
src/mira/skim.H | 7 +-
src/mira/skim_lowbph.C | 94 +-
src/mira/stringcontainer.H | 12 +-
src/mira/structs.H | 7 +-
src/mira/vluint.H | 5 +
src/mira/warnings.C | 16 +-
src/modules/Makefile.in | 3 +-
src/modules/misc.C | 24 +-
src/modules/mod_bait.C | 544 +-
src/modules/mod_bait.H | 29 +-
src/modules/mod_convert.C | 451 +-
src/modules/mod_diff.C | 16 +-
src/modules/mod_memestim.C | 52 +-
src/modules/mod_mer.C | 283 +-
src/modules/mod_mer.H | 13 +-
src/modules/mod_mira.C | 360 +-
src/modules/mod_sigconex.C | 8 +-
src/modules/mod_tagsnp.C | 87 +-
src/other/Makefile.am | 3 +
{doc => src/other}/Makefile.in | 13 +-
src/other/sls/Makefile.am | 18 +
{doc => src/other/sls}/Makefile.in | 50 +-
src/other/sls/README.txt | 15 +
src/other/sls/mira-createsls/Makefile.am | 3 +
{doc => src/other/sls/mira-createsls}/Makefile.in | 13 +-
src/other/sls/mira-createsls/bin/Makefile.am | 2 +
.../sls/mira-createsls/bin}/Makefile.in | 44 +-
src/other/sls/mira-createsls/bin/dedup.pl | 47 +
.../sls/mira-createsls/bin/mask_potential_rrna.pl | 107 +
.../sls/mira-createsls/bin/mira-create_sls.pl | 449 +
src/other/sls/mira-install-sls-rrna.sh | 104 +
src/other/sls/rfam_rrna-21-12.sls.gz | Bin 0 -> 10421035 bytes
src/progs/Makefile.am | 77 +-
src/progs/Makefile.in | 88 +-
src/progs/compileinfo.itxt.xxd.C | 17 +
src/progs/mira.C | 59 +-
src/progs/miratest.C | 16 +
src/scripts/Makefile.am | 25 +-
src/scripts/Makefile.in | 50 +-
src/scripts/fasta2frag.tcl | 583 -
src/scripts/fixACE4consed.tcl | 64 -
src/stdinc/Makefile.in | 3 +-
src/stdinc/defines.H | 2 +
src/stdinc/stlincludes.H | 6 +-
src/stdinc/types.H | 4 +-
src/support/Makefile.in | 3 +-
src/util/Makefile.in | 3 +-
src/util/dptools.C | 38 +-
src/util/fileanddisk.C | 222 +-
src/util/fileanddisk.H | 15 +-
src/util/fmttext.C | 12 +-
src/util/machineinfo.C | 26 +-
src/util/misc.C | 40 +-
src/util/stlimprove.H | 149 +-
src/version.H | 18 +-
src/version/Makefile.am | 29 +
src/{memorc => version}/Makefile.in | 103 +-
src/version/mversion.C | 3 +
src/{version.stub => version/mversion.H} | 3 +
src/{version.stub => version/mversion.stub} | 0
327 files changed, 16548 insertions(+), 555647 deletions(-)
create mode 100644 README_MAINTAINERS
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copy {src/support => man}/Makefile.in (89%)
rename {debian/mans => man}/mira.1 (53%)
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