[med-svn] [mira] branch upstream updated (2878605 -> c96f53a)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue May 3 14:25:03 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 2878605 Imported Upstream version 4.0.2
new c96f53a Imported Upstream version 4.9.6
The 1 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 | 17 +-
README | 4 +-
README_MAINTAINERS | 44 +
README_build.html | 334 +-
THANKS | 11 +-
aclocal.m4 | 8 +-
configure | 1798 +-
configure.ac | 478 +-
depcomp | 563 +-
distribution/LICENCE | 2 +-
distribution/Makefile | 66 +-
distribution/Makefile.am | 36 +-
distribution/Makefile.in | 42 +-
distribution/README | 36 +-
doc/Makefile | 31 +-
doc/Makefile.am | 1 +
doc/Makefile.in | 7 +-
doc/README_documentation.txt | 10 +
doc/docbook/Makefile | 56 +-
doc/docbook/Makefile.am | 7 +
doc/docbook/Makefile.in | 32 +-
doc/docbook/book_definitiveguide.xml | 6 +-
doc/docbook/chap_bonus_part.xml | 8 +-
doc/docbook/chap_dataprep_part.xml | 50 +-
doc/docbook/chap_denovo_part.xml | 5 +-
doc/docbook/chap_est_part.xml | 513 +-
doc/docbook/chap_faq_part.xml | 10 +-
doc/docbook/chap_hard_part.xml | 52 +-
doc/docbook/chap_installation_part.xml | 396 +-
doc/docbook/chap_intro_part.xml | 21 +-
doc/docbook/chap_logfiles_part.xml | 8 +-
doc/docbook/chap_mirautils_part.xml | 755 +-
doc/docbook/chap_preface_part.xml | 2 +-
doc/docbook/chap_reference_part.xml | 2307 +-
doc/docbook/chap_results_part.xml | 8 +
doc/docbook/chap_seqtechdesc_part.xml | 108 +
doc/docbook/chap_sra_part.xml | 2 +-
doc/docbook/copyrightfile | 2 +-
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m4/ax_cxx_namespaces.m4 | 40 -
m4/ax_openmp.m4 | 119 +
man/Makefile.am | 3 +
{src/support => man}/Makefile.in | 50 +-
man/mira.1 | 69 +
man/mirabait.1 | 193 +
man/miraconvert.1 | 350 +
man/miradiff.1 | 33 +
man/miramem.1 | 33 +
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minidemo/bbdemo1/runme.sh | 31 -
minidemo/bbdemo2/parameters.par | 15 -
minidemo/bbdemo2/runme.sh | 61 -
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.../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 --
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.../cjejuni_demo_traceinfo_in.sanger.xml | 13891 --
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minidemo/data/exp_set1/122533a.t3.exp | 30 -
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minidemo/data/exp_set1/U13a03c03.t1.exp | 29 -
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minidemo/data/exp_set1/U13e07f02.t2.exp | 31 -
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minidemo/data/fasta_estset1/README | 12 -
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.../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 -
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.../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 | 29 +-
src/Makefile.in | 55 +-
src/caf/Makefile.in | 6 +-
src/caf/caf.C | 526 +-
src/caf/caf.H | 62 +-
src/caf/caf_flexer.cc | 134 +-
src/caf/caf_flexer.ll | 2 -
src/debuggersupport/Makefile.in | 6 +-
src/errorhandling/Makefile.in | 6 +-
src/errorhandling/errorhandling.C | 36 +-
src/errorhandling/errorhandling.H | 9 +-
src/io/Makefile.in | 6 +-
src/io/annotationmappings.C | 63 +-
src/io/annotationmappings.H | 25 +-
src/io/exp.C | 65 +-
src/io/exp_flexer.cc | 159 +-
src/io/exp_flexer.ll | 3 -
src/io/fasta.C | 125 +-
src/io/fasta.H | 9 +-
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 | 42 +-
src/io/so.obo | 4 +-
src/memorc/Makefile.in | 6 +-
src/memorc/main.C | 18 +-
src/memorc/memorc.C | 11 +-
src/memorc/memorc.H | 2 +-
src/mira/CHANGES.txt | 221 +
src/mira/CHANGES_old.txt | 84 +-
src/mira/Makefile.am | 24 +-
src/mira/Makefile.in | 145 +-
src/mira/TODO | 146 +-
src/mira/adaptorsregex.solexa.xxd | 11 +
src/mira/ads.C | 149 +-
src/mira/ads.H | 13 +-
src/mira/adsfacts.C | 8 +-
src/mira/adsfacts.H | 4 +-
src/mira/align.C | 466 +-
src/mira/align.H | 33 +-
src/mira/assembly.C | 3232 +-
src/mira/assembly.H | 423 +-
src/mira/assembly_buildcontigs.C | 2304 +
src/mira/assembly_info.C | 91 +-
src/mira/assembly_info.H | 1 -
src/mira/assembly_io.C | 713 +-
src/mira/assembly_misc.C | 1266 +-
src/mira/assembly_output.C | 1255 +-
src/mira/assembly_pbcorrect.C | 2128 +
src/mira/assembly_reduceskimhits.C | 1164 +-
src/mira/assembly_swalign.C | 535 +-
src/mira/contig.C | 774 +-
src/mira/contig.H | 673 +-
src/mira/contig_analysis.C | 588 +-
src/mira/contig_consensus.C | 1709 +-
src/mira/contig_covanalysis.C | 50 +-
src/mira/contig_edit.C | 404 +-
src/mira/contig_featureinfo.C | 100 +-
src/mira/contig_output.C | 632 +-
src/mira/contig_pairconsistency.C | 27 +-
src/mira/dataprocessing.C | 1005 +-
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src/mira/demoparam.prm | 321 -
src/mira/dynamic.C | 216 +-
src/mira/dynamic.H | 24 +-
src/mira/estassembly.C | 17 +-
src/mira/gbf_parse.C | 178 +-
src/mira/gbf_parse.H | 6 +-
src/mira/gff_parse.C | 181 +-
src/mira/gff_parse.H | 17 +-
src/mira/gff_save.C | 33 +-
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src/mira/hashstats_sdbg.C | 743 +
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src/mira/manifest.C | 139 +-
src/mira/multitag.C | 52 +-
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src/mira/preventinitfiasco.C | 96 +-
src/mira/read.C | 2148 +-
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src/mira/readgrouplib.C | 172 +-
src/mira/readgrouplib.H | 29 +
src/{stdinc/template.H => mira/readlotstat.C} | 63 +-
src/{stdinc/template.H => mira/readlotstat.H} | 36 +-
src/mira/readpool.C | 1210 +-
src/mira/readpool.H | 83 +-
src/mira/readpool_io.C | 1046 +
src/mira/readpool_io.H | 180 +
src/mira/readseqtypes.H | 36 +-
src/mira/sam_collect.C | 103 +-
src/mira/sam_collect.H | 3 -
src/mira/scaffolder.C | 167 +-
src/mira/scaffolder.H | 65 +-
src/mira/seqtohash.H | 6 +-
src/mira/{bloomfilter.C => simplebloomfilter.C} | 49 +-
src/mira/{bloomfilter.H => simplebloomfilter.H} | 114 +-
src/mira/skim.C | 1405 +-
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src/mira/skim_lowbph.C | 137 +-
src/mira/stringcontainer.H | 12 +-
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