[med-svn] [mira] 05/05: Imported Debian patch 4.0.2-1
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 2 15:37:46 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository mira.
commit 71892b1f1bdbcd714cd7065f83d3ad29e7dcbdf8
Merge: 15dab0f 2878605
Author: Thorsten Alteholz <debian at alteholz.de>
Date: Sat Apr 26 19:00:35 2014 +0200
Imported Debian patch 4.0.2-1
.tarball-version | 1 +
.version | 1 +
GETTING_STARTED | 13 +-
HELP_WANTED | 14 +-
INSTALL | 706 +-
Makefile.am | 65 +-
Makefile.in | 200 +-
README | 56 +-
README_build.html | 514 +
THANKS | 8 +-
aclocal.m4 | 8708 ++++++++-
build-aux/git-version-gen | 181 +
config.guess | 258 +-
config.sub | 209 +-
config/m4/ax_with_perl.m4 | 35 -
config/m4/ax_with_prog.m4 | 70 -
config/m4/libtool.m4 | 7377 --------
config/m4/ltoptions.m4 | 368 -
config/m4/ltsugar.m4 | 123 -
config/m4/ltversion.m4 | 23 -
config/m4/lt~obsolete.m4 | 92 -
configure | 10199 +++++-----
configure.in => configure.ac | 623 +-
debian/README.source | 27 -
debian/TODO | 3 -
debian/changelog | 124 +-
debian/compat | 2 +-
debian/control | 67 +-
debian/convert_project.1 | 302 +
debian/copyright | 110 +-
debian/fasta2frag.1 | 95 +
debian/fastaselect.1 | 47 +
debian/fastatool.1 | 49 +
debian/fastqselect.1 | 47 +
debian/fixACE4consed.1 | 32 +
debian/mira-assembler.install | 8 -
debian/mira-assembler.lintian-overrides | 2 +
debian/mira-assembler.manpages | 1 +
debian/mira-doc.README.Debian | 2 +-
debian/mira-doc.doc-base | 12 +
debian/mira.1 | 53 +
debian/miraSearchESTSNPs.1 | 43 +
debian/mirabait.1 | 131 +
debian/miradiff.1 | 36 +
debian/miramem.1 | 33 +
debian/miramer.1 | 36 +
debian/patches/add_shebang_lines | 27 -
debian/patches/boost-minimal.patch | 15 +
debian/patches/read_default_constructor.patch | 20 -
debian/patches/series | 4 +-
debian/patches/xsltproc_nonet_for_doc_build | 21 -
debian/rules | 75 +-
debian/scftool.1 | 50 +
debian/upstream | 15 +
debian/upstream-metadata.yaml | 18 -
debian/watch | 2 +-
distribution/Makefile | 171 +-
distribution/Makefile.am | 64 +-
distribution/Makefile.in | 119 +-
distribution/README | 84 +-
doc/Makefile | 110 +-
doc/Makefile.in | 58 +-
doc/docbook/Makefile | 180 +-
doc/docbook/Makefile.am | 45 +-
doc/docbook/Makefile.in | 128 +-
doc/docbook/attic/README.txt | 266 +
doc/docbook/{ => attic}/chap_454_part.xml | 433 +-
doc/docbook/{ => attic}/chap_iontor_part.xml | 712 +-
doc/docbook/attic/chap_pacbio_part.xml | 549 +
doc/docbook/{ => attic}/chap_sanger_part.xml | 74 +-
doc/docbook/attic/chap_solexa_part.xml | 1512 ++
doc/docbook/attic/pb_misc.xml | 839 +
doc/docbook/attic/solexa_lenski.xml | 499 +
doc/docbook/book.xsl | 7 +-
doc/docbook/book_3rdparty.xml | 28 +
doc/docbook/book_definitiveguide.xml | 87 +-
doc/docbook/bookfigures/ion_dh10bcovB13_12kb.png | Bin 28874 -> 0 bytes
doc/docbook/bookfigures/ion_dh10bcovB13_320kb.png | Bin 40689 -> 0 bytes
doc/docbook/bookfigures/results_mira2other.png | Bin 0 -> 80496 bytes
doc/docbook/bookfigures/results_miraconvert.png | Bin 0 -> 60664 bytes
doc/docbook/chap_3p_ghbambus_part.xml | 409 +
doc/docbook/chap_bitsandpieces_part.xml | 83 +
doc/docbook/chap_bonus_part.xml | 5 +-
doc/docbook/chap_bonus_part.xml~ | 349 -
doc/docbook/chap_dataprep_part.xml | 114 +
doc/docbook/chap_denovo_part.xml | 472 +
doc/docbook/chap_est_part.xml | 328 +-
doc/docbook/chap_faq_part.xml | 135 +-
doc/docbook/chap_hard_part.xml | 99 +-
doc/docbook/chap_installation_part.xml | 675 +-
doc/docbook/chap_intro_part.xml | 170 +-
doc/docbook/chap_logfiles_part.xml | 24 +-
doc/docbook/chap_maf_part.xml | 55 +-
doc/docbook/chap_mapping_part.xml | 776 +
doc/docbook/chap_mirautils_part.xml | 218 +-
doc/docbook/chap_pacbio_part.xml | 1786 --
doc/docbook/chap_preface_part.xml | 21 +-
doc/docbook/chap_preface_part.xml~ | 135 -
doc/docbook/chap_reference_part.xml | 5090 ++---
doc/docbook/chap_results_part.xml | 852 +-
doc/docbook/chap_seqadvice_part.xml | 820 +-
doc/docbook/chap_seqtechdesc_part.xml | 783 +
doc/docbook/chap_solexa_part.xml | 1995 --
doc/docbook/chap_specialparams_part.xml | 79 +
doc/docbook/chap_sra_part.xml | 145 +
doc/docbook/{versionfile => copyrightfile} | 3 +-
doc/docbook/doccss/miradocstyle.css | 10 +-
doc/docbook/replace_all.sh | 9 +
doc/docbook/{versionfile => version.stub} | 1 -
doc/docbook/warning_frontofchapter.xml | 12 +
{doc/docbook/doccss => doccss}/miradocstyle.css | 10 +-
ltmain.sh | 4016 ++--
{config/m4 => m4}/ax_boost_base.m4 | 9 +-
m4/ax_boost_filesystem.m4 | 118 +
m4/ax_boost_iostreams.m4 | 116 +
{config/m4 => m4}/ax_boost_regex.m4 | 19 +-
m4/ax_boost_system.m4 | 120 +
{config/m4 => m4}/ax_boost_thread.m4 | 33 +-
{config/m4 => m4}/ax_check_zlib.m4 | 13 +-
{config/m4 => m4}/ax_cxx_have_std.m4 | 0
{config/m4 => m4}/ax_cxx_have_stl.m4 | 0
{config/m4 => m4}/ax_cxx_namespaces.m4 | 0
{config/m4 => m4}/ax_lib_expat.m4 | 18 +-
minidemo/bbdemo2/runme.sh | 14 +-
minidemo/estdemo2/README | 6 +-
minidemo/solexa1/runme.sh | 3 +-
minidemo/solexa2/runme.sh | 3 +-
missing | 53 +-
src/EdIt/Makefile.am | 10 -
src/EdIt/Makefile.in | 549 -
src/EdIt/faultRegion.C | 1222 --
src/EdIt/hypothesen.C | 2305 ---
src/EdIt/hypothesen.H | 281 -
src/EdIt/parameters.C | 563 -
src/EdIt/parameters.H | 307 -
src/EdIt/parameters_flexer.cc | 2106 ---
src/EdIt/parameters_flexer.ll | 160 -
src/EdIt/parameters_tokens.h | 74 -
src/Makefile.am | 37 +-
src/Makefile.in | 116 +-
src/caf/Makefile.am | 7 +-
src/caf/Makefile.in | 98 +-
src/caf/caf.C | 677 +-
src/caf/caf.H | 100 +-
src/caf/caf_flexer.cc | 2250 ++-
src/caf/caf_flexer.ll | 55 +-
src/debuggersupport/Makefile.am | 5 +
src/{examine => debuggersupport}/Makefile.in | 104 +-
src/debuggersupport/dbgsupport.C | 59 +
.../dbgsupport.H} | 27 +-
src/errorhandling/Makefile.am | 3 +-
src/errorhandling/Makefile.in | 62 +-
src/errorhandling/errorhandling.C | 92 +-
src/errorhandling/errorhandling.H | 42 +-
src/examine/Makefile.am | 7 -
src/examine/afh_info.C | 541 -
src/examine/buffer.C | 296 -
src/examine/buffer.H | 84 -
src/examine/calc.C | 754 -
src/examine/cfh.C | 420 -
src/examine/globals.H | 239 -
src/examine/misc.C | 398 -
src/examine/misc.H | 76 -
src/examine/prescan.C | 261 -
src/examine/prescan.H | 102 -
src/examine/ranges.C | 591 -
src/examine/scf_look.C | 2655 ---
src/examine/scf_look.H | 406 -
src/examine/scfbuffer.H | 70 -
src/examples_programming/Makefile.am | 25 -
src/examples_programming/Makefile.in | 532 -
src/examples_programming/README | 6 -
src/examples_programming/mira_101.C | 114 -
src/examples_programming/read_101.C | 155 -
src/examples_programming/readpool_101.C | 142 -
src/io/Makefile.am | 49 +-
src/io/Makefile.in | 169 +-
src/io/annotationmappings.C | 348 +
src/io/annotationmappings.H | 175 +
src/io/exp.C | 41 +-
src/io/exp.H | 160 +-
src/io/fasta.C | 71 +-
src/io/fasta.H | 56 +-
src/io/fastq-lh.H | 164 +-
src/io/fastq-mira.C | 278 +-
src/io/fastq-mira.H | 82 +-
src/io/gap4_ft_so_map.xxd | 99 +
src/io/gbf.H | 128 -
src/io/generalio.C | 26 +-
src/io/generalio.H | 17 +-
src/io/mira_ft_set.xxd | 54 +
src/io/ncbiinfoxml.C | 99 +-
src/io/ncbiinfoxml.H | 36 +-
src/io/oldso2so.xxd | 2 +
src/io/phd.C | 31 +-
src/io/phd.H | 38 +-
src/io/scf.C | 205 +-
src/io/scf.H | 58 +-
src/io/so.obo | 18725 +++++++++++++++++++
src/io/so2xgap4map.xxd | 2068 ++
src/knn_abi373/Makefile.am | 6 -
src/knn_abi373/Makefile.in | 510 -
src/knn_abi373/add.c | 224 -
src/knn_abi373/add.h | 14 -
src/knn_abi373/missing.c | 238 -
src/knn_abi373/missing.h | 14 -
src/knn_abi373/ncall.c | 176 -
src/knn_abi373/ncall.h | 14 -
src/knn_abi373/nplus.c | 159 -
src/knn_abi373/nplus.h | 14 -
src/knn_abi373/over.c | 224 -
src/knn_abi373/over.h | 14 -
src/knn_abi373/under.c | 224 -
src/knn_abi373/under.h | 14 -
src/knn_abi373/wrong.c | 176 -
src/knn_abi373/wrong.h | 14 -
src/knn_alf/Makefile.am | 6 -
src/knn_alf/Makefile.in | 510 -
src/knn_alf/add.c | 224 -
src/knn_alf/add.h | 14 -
src/knn_alf/missing.c | 238 -
src/knn_alf/missing.h | 14 -
src/knn_alf/ncall.c | 176 -
src/knn_alf/ncall.h | 14 -
src/knn_alf/nplus.c | 159 -
src/knn_alf/nplus.h | 14 -
src/knn_alf/over.c | 224 -
src/knn_alf/over.h | 14 -
src/knn_alf/under.c | 224 -
src/knn_alf/under.h | 14 -
src/knn_alf/wrong.c | 176 -
src/knn_alf/wrong.h | 14 -
src/lec/Makefile.am | 6 -
src/lec/Makefile.in | 388 -
src/memorc/Makefile.am | 23 +
src/{test/io/scf => memorc}/Makefile.in | 161 +-
src/memorc/main.C | 101 +
src/memorc/memorc.C | 564 +
src/memorc/memorc.H | 91 +
src/mira/CHANGES.txt | 599 +-
src/mira/CHANGES_old.txt | 57 +
src/mira/Makefile.am | 104 +-
src/mira/Makefile.in | 274 +-
src/mira/TODO | 223 +-
src/mira/adaptorsforclip.454.xxd | 6 +-
src/mira/adaptorsforclip.iontor.xxd | 13 +-
src/mira/adaptorsforclip.solexa.xxd | 93 +-
src/mira/adaptorsregex.iontor.xxd | 8 +-
src/mira/adaptorsregex.solexa.xxd | 5 +-
src/mira/ads.C | 529 +-
src/mira/ads.H | 93 +-
src/mira/adsfacts.C | 162 +-
src/mira/adsfacts.H | 93 +-
src/mira/align.C | 265 +-
src/mira/align.H | 52 +-
src/mira/assembly.C | 4353 +++--
src/mira/assembly.H | 1224 +-
src/mira/assembly_info.C | 223 +-
src/mira/assembly_info.H | 50 +-
src/mira/assembly_io.C | 2032 +-
src/mira/assembly_misc.C | 1922 ++
src/mira/assembly_output.C | 4916 ++---
src/mira/assembly_output.H | 358 +-
src/mira/assembly_reduceskimhits.C | 1024 +-
src/mira/assembly_repeatresolve.C | 532 -
src/mira/assembly_swalign.C | 535 +-
src/mira/bloomfilter.C | 98 +
src/mira/bloomfilter.H | 233 +
src/mira/contig.C | 9094 ++++-----
src/mira/contig.H | 1665 +-
src/mira/contig_analysis.C | 3568 ++--
src/mira/contig_consensus.C | 2908 +++
src/mira/contig_covanalysis.C | 287 +
src/mira/contig_edit.C | 1997 +-
src/mira/contig_featureinfo.C | 600 +
src/mira/contig_output.C | 1597 +-
src/mira/contig_pairconsistency.C | 398 +
src/mira/dataprocessing.C | 4114 ++--
src/mira/dataprocessing.H | 287 +
src/mira/dynamic.C | 608 +-
src/mira/dynamic.H | 54 +-
src/mira/enums.H | 22 +-
src/mira/estassembly.C | 87 +-
src/{io/gbf.C => mira/gbf_parse.C} | 639 +-
src/mira/gbf_parse.H | 138 +
src/mira/gff_parse.C | 616 +-
src/mira/gff_parse.H | 76 +-
src/mira/gff_save.C | 301 +
src/mira/gff_save.H | 78 +
src/mira/hashstats.C | 2926 +++
src/mira/hashstats.H | 529 +
src/mira/hdeque.H | 666 +
src/mira/indexed_deque.H | 541 -
src/mira/maf_parse.C | 1246 +-
src/mira/maf_parse.H | 178 +-
src/mira/manifest.C | 577 +
src/mira/manifest.H | 99 +
src/mira/multitag.C | 408 +-
src/mira/multitag.H | 207 +-
src/mira/newpathfinder.C | 5018 -----
src/mira/newpathfinder.H | 405 -
src/mira/overlapedges.H | 82 +
src/mira/parameters.C | 3866 ++--
src/mira/parameters.H | 480 +-
src/mira/parameters_flexer.cc | 10565 ++++++-----
src/mira/parameters_flexer.ll | 384 +-
src/mira/parameters_tokens.h | 165 +-
src/mira/pcrcontainer.C | 890 +
src/mira/pcrcontainer.H | 436 +
src/mira/ppathfinder.C | 2333 +++
src/mira/ppathfinder.H | 465 +
src/mira/preventinitfiasco.C | 338 +
src/mira/read.C | 3658 ++--
src/mira/read.H | 675 +-
src/mira/readgrouplib.C | 850 +
src/mira/readgrouplib.H | 447 +
src/mira/readpool.C | 2453 ++-
src/mira/readpool.H | 341 +-
src/mira/readseqtypes.H | 44 +
src/mira/sam_collect.C | 542 +
src/mira/sam_collect.H | 139 +
src/mira/scaffolder.C | 22 +-
src/mira/scaffolder.H | 20 +-
src/mira/seqforfilter_phix174.solexa.xxd | 2 +
src/mira/seqtohash.C | 46 +
src/mira/seqtohash.H | 102 +
src/mira/simple_2Dsignalprocessing.H | 96 +
src/mira/skim.C | 3446 +---
src/mira/skim.H | 682 +-
src/mira/skim_farc.C | 572 +
src/mira/skim_lowbph.C | 610 +
src/mira/stringcontainer.H | 106 +-
src/mira/structs.H | 335 +-
src/mira/timerestrict.H | 10 +-
src/mira/types_basic.H | 10 +
src/mira/warnings.C | 171 +
src/mira/warnings.H | 117 +
src/modules/Makefile.am | 5 +
src/{test/io/generalio => modules}/Makefile.in | 133 +-
src/modules/misc.C | 162 +
src/{mira/enums.H => modules/misc.H} | 46 +-
src/modules/mod_bait.C | 559 +
src/modules/mod_bait.H | 89 +
src/modules/mod_convert.C | 1919 ++
src/modules/mod_convert.H | 143 +
src/modules/mod_dbgreplay.C | 89 +
src/modules/mod_memestim.C | 438 +
.../timerestrict.H => modules/mod_memestim.H} | 27 +-
src/modules/mod_mira.C | 445 +
src/modules/mod_mira.H | 8 +
src/modules/mod_tagsnp.C | 254 +
src/{mira/enums.H => modules/mod_tagsnp.H} | 48 +-
src/progs/Makefile.am | 113 +-
src/progs/Makefile.in | 225 +-
src/progs/convert_project.C | 2518 ---
src/progs/dbgreplay.C | 124 -
src/progs/fastatool.C | 338 -
src/progs/me_step1.par | 27 -
src/progs/me_step2.par | 140 -
src/progs/me_step3.par | 152 -
src/progs/mira.C | 1690 +-
src/progs/miramer.C | 494 +
src/progs/miratest.C | 408 +-
src/progs/par2c.pl | 7 -
src/progs/quirks.C | 68 +
src/{mira/timerestrict.H => progs/quirks.H} | 28 +-
src/progs/scftool.C | 510 -
src/progs/sw.C | 140 -
src/progs/version.H | 30 -
src/scripts/Makefile.am | 8 +-
src/scripts/Makefile.in | 66 +-
src/scripts/fasta2frag.tcl | 274 +-
src/scripts/fastaselect.tcl | 125 -
src/scripts/fastqselect.tcl | 170 -
src/stdinc/Makefile.in | 58 +-
src/stdinc/defines.H | 80 +-
src/stdinc/stlincludes.H | 78 +-
src/stdinc/template.C | 22 +-
src/stdinc/template.H | 14 +-
src/stdinc/types.H | 6 +-
src/support/GTAGDB | 52 +-
src/support/Makefile.in | 68 +-
src/test/Makefile.am | 3 -
src/test/Makefile.in | 586 -
src/test/io/Makefile.am | 3 -
src/test/io/Makefile.in | 586 -
src/test/io/fasta/Makefile.am | 19 -
src/test/io/fasta/Makefile.in | 511 -
src/test/io/fasta/tstFASTA.C | 181 -
src/test/io/generalio/Makefile.am | 18 -
src/test/io/generalio/tstgeneralio.C | 67 -
src/test/io/scf/Makefile.am | 19 -
src/test/io/scf/tstSCF.C | 30 -
src/test/mira/Makefile.am | 4 -
src/test/mira/Makefile.in | 588 -
src/test/mira/align/Makefile.am | 20 -
src/test/mira/align/Makefile.in | 511 -
src/test/mira/align/tstAlign.C | 72 -
src/test/mira/read/Makefile.am | 10 -
src/test/mira/read/Makefile.in | 504 -
src/test/mira/read/tstRead.C | 117 -
src/test/mira/readpool/Makefile.am | 10 -
src/test/mira/readpool/Makefile.in | 504 -
src/test/mira/readpool/tstReadPool.C | 107 -
src/util/Makefile.am | 10 +-
src/util/Makefile.in | 91 +-
src/util/boostiostrutil.H | 79 +
src/util/dptools.C | 183 +-
src/util/dptools.H | 86 +-
src/util/fileanddisk.C | 862 +
src/util/fileanddisk.H | 184 +
src/util/fmttext.C | 115 +
src/util/fmttext.H | 42 +
src/util/machineinfo.C | 218 +
src/util/machineinfo.H | 70 +
src/util/memusage.H | 126 +-
src/util/misc.C | 363 +-
src/util/misc.H | 70 +-
src/util/progressindic.H | 50 +-
src/{mira/timerestrict.H => util/stlimprove.H} | 34 +-
src/version.H | 18 +
src/version.stub | 15 +
422 files changed, 121141 insertions(+), 101143 deletions(-)
diff --cc debian/changelog
index 559b4f1,0000000..7d6bc7f
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,51 -1,0 +1,173 @@@
++mira (4.0.2-1) unstable; urgency=low
++
++ * new upstream version
++
++ -- Thorsten Alteholz <debian at alteholz.de> Sat, 26 Apr 2014 19:00:35 +0200
++
++mira (4.0-1) unstable; urgency=low
++
++ [ Thorsten Alteholz ]
++ * New upstream version
++ * debian/rules: add boost dir in auto_configure (Closes: #735798)
++
++ [ Andreas Tille ]
++ * cme fix dpkg-control
++ * debian/patches/{make.patch,spelling.patch}: applied upstream (thus removed)
++
++ -- Thorsten Alteholz <debian at alteholz.de> Sun, 02 Feb 2014 22:51:35 +0100
++
++mira (3.9.18-1) unstable; urgency=low
++
++ * New upstream version (most patches applied by upstream)
++ * debian/copyright: Add Upstream-Contact
++ * debian/control: cme fix dpkg-control
++ * debian/mira-assembler.lintian-overrides: deleted unused override
++ * debian/rules: Prevent installing duplicated data, rather
++ create symlink
++ * debian/mirabait.1: wrote missing manpage
++
++ -- Andreas Tille <tille at debian.org> Fri, 09 Aug 2013 13:59:24 +0200
++
++mira (3.9.17-1) unstable; urgency=low
++
++ [ Thorsten Alteholz ]
++ * new upstream version
++ * debian/control: Standards-Version set to 3.9.4 (no changes)
++ * debian/control: DM-Upload-Allowed: removed
++ * debian/control: use dh 9
++ * debian/control: add dependency to libboost-iostreams-dev
++ * debian/control: improve extended descriptions
++ * debian/control: change VCS-tags according to new lintian
++ * debian/rules: get-orig-source added
++ * debian/watch: do not look at dev-versions
++ * debian/mira-doc.README.Debian: correct path to documentation
++
++ [ Dmitrijs Ledkovs ]
++ * Build depend on libboost-all-dev and libbz2-dev.
++ * Add boost-minimal patch, to add boost-libraries in final linking,
++ fixing FTBFS (Closes: #701322)
++ * Enable parallel builds, to speed up compilation.
++
++ [ Andreas Tille ]
++ * delete debian/README.source which is outdated / wrong
++ * debian/*.1: Wrote / reviewed manpages for all installed programs
++ * debian/miraSearchESTSNPs.1: Wrote manpage but mention that this
++ functionality is deactivated in version 3.9.17
++ * debian/mira-assembler.manpages: Simply install all manpages that can be
++ found
++ * Removed debian/obsolete.mira-assembler.install
++ * debian/control: The actual scripts do not contain the .tcl suffix
++ in our installation
++ * debian/rules:
++ - Currently miraSearchESTSNPs and miraclip claim to be deactivated so
++ why bothering installing these?
++ - Use xz compression for binaries
++
++ -- Andreas Tille <tille at debian.org> Fri, 07 Jun 2013 08:34:21 +0200
++
++mira (3.4.0.1-3) unstable; urgency=low
++
++ [ Charles Plessy ]
++ * Build-depend on libgoogle-perftools-dev instead of libtcmalloc-minimal0
++ (debian/control, debian/README.source, debian/rules).
++ Closes: #673527, #674822
++ * Conforms to Policy 3.9.3 (debian/control, no other changes needed).
++ * Rely on dpkg source format 3.0 (quilt) for the patches, and remove
++ build dependance on quilt (debian/control, debian/rules).
++ * Verbose Debhelper (debian/rules).
++
++ [ Andreas Tille ]
++ * debian/upstream: very small fix to prevent bibcheck warning
++
++ -- Charles Plessy <plessy at debian.org> Mon, 28 May 2012 10:51:01 +0900
++
++mira (3.4.0.1-2) unstable; urgency=low
++
++ [ Andreas Tille ]
++ * Remove two patches:
++ - read_default_constructor.patch which introduces a duplicate
++ bposhashstat_t() definition
++ - fix_duplicate_bposhashstat_t_definition.patch which removes
++ this duplicate afterwards
++
++ [ Charles Plessy ]
++ * Removed unconditional dependency on libtcmalloc-minimal0 (debian/control).
++ Closes: #654884
++ * Machine-readable debian/copyright file.
++
++ -- Charles Plessy <plessy at debian.org> Sat, 07 Jan 2012 13:24:48 +0900
++
++mira (3.4.0.1-1) unstable; urgency=low
++
++ * New upstream version
++ Closes: #648762 (at least if I'm not mislead - feel free to reopen)
++ * debian/control:
++ - Added myself to Uploaders
++ - Depends: libtcmalloc-minimal0 [i386 amd64]
++ Thanks for the patch to Michael Terry <michael.terry at canonical.com>
++ however I left out powerpc where libtcmalloc-minimal0 is not
++ available
++ Closes: #649093
++ - Fixed Vcs fields
++ * debian/patches/fix_duplicate_bposhashstat_t_definition.patch
++ Remove duplicate definition of bposhashstat_t()
++
++ -- Andreas Tille <tille at debian.org> Thu, 08 Dec 2011 08:50:19 +0100
++
++mira (3.4.0-3ubuntu1) lucid; urgency=low
++
++ * Small fix to dependencies - there is no "mira" binary package
++
++ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 02 Dec 2011 15:00:35 +0000
++
+mira (3.4.0-3) unstable; urgency=low
+
+ * Rendering Tim's additions available for Debian
+
+ -- Steffen Moeller <moeller at debian.org> Sat, 03 Sep 2011 01:02:10 +0200
+
+mira (3.4.0-2ubuntu5) lucid; urgency=low
+
+ * Small fix to clean target and suppress warnings
+ on Lucid backport.
+ * Fixed missing dependency which caused misleading configure
+ failure.
+ * Yet another missing build dep - flex and xxd
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Tue, 30 Aug 2011 17:17:11 +0100
+
+mira (3.4.0-2) unstable; urgency=low
+
+ * Fixing source tree (removed PDF with no source)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 29 Aug 2011 22:54:53 +0200
+
+mira (3.4.0-1) UNRELEASED; urgency=low
+
+ * New upstream version.
+ - added default constructor to avoid FTBFS
- * Sposoring Tim's work for Debian
++ * Sponsoring Tim's work for Debian
+ * Using 3.0 (quilt) source format for bz2 upstream
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 23 Aug 2011 20:46:32 +0200
+
+mira (3.4rc3-2) lucid; urgency=low
+
+ * Version 3.2.1.8 has been removed from SF.net. Packaging the
+ latest RC instead.
+ * Fixed linking against tcmalloc (see README)
+ * Fixed build of docs - HTML is installed in mira-doc
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 19 Aug 2011 12:35:12 +0100
+
+mira (3.2.1.8-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #435915)
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 04 Mar 2011 11:55:25 +0100
+
+mira (3~rc2-1) UNRELEASED; urgency=low
+
+ * Initial packaging.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 08 Sep 2009 13:35:31 +0900
diff --cc debian/compat
index 7f8f011,0000000..ec63514
mode 100644,000000..100644
--- a/debian/compat
+++ b/debian/compat
@@@ -1,1 -1,0 +1,1 @@@
- 7
++9
diff --cc debian/control
index 7bb3473,0000000..20dec37
mode 100644,000000..100644
--- a/debian/control
+++ b/debian/control
@@@ -1,71 -1,0 +1,94 @@@
+Source: mira
++Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
++Uploaders: Charles Plessy <plessy at debian.org>,
++ Steffen Moeller <moeller at debian.org>,
++ Tim Booth <tbooth at ceh.ac.uk>,
++ Andreas Tille <tille at debian.org>,
++ Thorsten Alteholz <debian at alteholz.de>
+Section: science
+Priority: optional
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- DM-Upload-Allowed: yes
- Uploaders: Charles Plessy <plessy at debian.org>, Steffen Moeller <moeller at debian.org>,
- Tim Booth <tbooth at ceh.ac.uk>
- Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl,
- libboost-thread-dev, libboost-regex-dev, libexpat1-dev, libtcmalloc-minimal0, perl,
- quilt (>= 0.46-7~), flex, vim-common, zlib1g-dev
- Standards-Version: 3.9.2
++Build-Depends: debhelper (>= 9),
++ dblatex,
++ dh-autoreconf,
++ autoconf-archive,
++ docbook-xsl,
++ libboost-all-dev,
++ libbz2-dev,
++ libexpat1-dev,
++ libgoogle-perftools-dev [i386 amd64],
++ perl,
++ flex,
++ vim-common,
++ zlib1g-dev
++Standards-Version: 3.9.5
++Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/mira/trunk/
++Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mira/trunk/
+Homepage: http://chevreux.org/projects_mira.html
- Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/?rev=0&sc=0
- Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/
+
+Package: mira-assembler
+Architecture: any
- Depends: ${shlibs:Depends}, ${misc:Depends}, libtcmalloc-minimal0
- Suggests: mira-examples, mira-doc
++Depends: ${shlibs:Depends},
++ ${misc:Depends}
++Suggests: mira-examples,
++ mira-doc
+Description: Whole Genome Shotgun and EST Sequence Assembler
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
+ specialised on reconstructing pristine mRNA transcripts while
+ detecting and classifying single nucleotide polymorphisms (SNP)
+ occuring in different variations thereof.
+ .
+ The assembler is routinely used for such various tasks as mutation
+ detection in different cell types, similarity analysis of transcripts
+ between organisms, and pristine assembly of sequences from various
+ sources for oligo design in clinical microarray experiments.
+ .
+ The package provides the following executables:
+ Binaries provided:
+ * mira: for assembly of genome sequences
+ * miramem: estimating memory needed to assemble projects. Realised through
+ link to mira.
+ * convert_project: for converting project file types into other types
+ * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
+ frequently used file converters (realised through links to convert_project)
+ * scftool: set of tools useful when working with SCF trace files
+ * fastatool: set of tools useful when working with FASTA trace files
+ .
+ Scripts provided:
- * fasta2frag.tcl: fragmenting sequences into smaller, overlapping
++ * fasta2frag: fragmenting sequences into smaller, overlapping
+ subsequences. Useful for simulating shotgun sequences. Can create
+ subsequences in both directions (/default) and also paired-end sequences.
- * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
++ * fastaselect: given a FASTA file (and possibly a FASTA quality file) and
+ a file with names of reads, select the sequences from the input FASTA (and
+ quality file) and writes them to an output FASTA
- * fastqselect.tcl: like fastaselect.tcl, only for FASTQ
- * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
++ * fastqselect: like fastaselect, only for FASTQ
++ * fixACE4consed: Consed has a bug which incapacitates it from reading
+ consensus tags in ACE files written by the MIRA assembler (and possibly
+ other programs). This script massages an ACE file so that consed can read
+ the consensus tags.
+
-
+Package: mira-examples
+Architecture: all
+Depends: ${misc:Depends}
- Suggests: mira
++Suggests: mira-assembler,
++ mira-doc
+Description: files to experiment with the mira assembler
- A series of files to exploit the functionality of mira.
++ The mira genome fragment assembler is a specialised assembler for
++ sequencing projects classified as 'hard' due to high number of similar
++ repeats.
++ .
++ This package contains a series of files to exploit the functionality
++ of mira.
+
+Package: mira-doc
- Section: doc
+Architecture: all
++Section: doc
+Depends: ${misc:Depends}
- Suggests: mira
++Suggests: mira-assembler
+Description: documentation for the mira assembler
- An HTML book introducing to mira.
++ The mira genome fragment assembler is a specialised assembler for
++ sequencing projects classified as 'hard' due to high number of similar
++ repeats.
++ .
++ This package contains an HTML book introducing to mira.
diff --cc debian/convert_project.1
index 0000000,0000000..028746c
new file mode 100644
--- /dev/null
+++ b/debian/convert_project.1
@@@ -1,0 -1,0 +1,302 @@@
++.TH CONVERT_PROJECT "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++convert_project \- convert assembly and sequencing file types
++.SH DESCRIPTION
++This program is part of the MIRA assembler package. It is used to convert
++project file types into other types. Please check out the
++documentation below for more detailed information about convert_project.
++.SH SYNOPSIS
++.IP convert_project
++[\-f <fromtype>] [\-t <totype> [\-t <totype> ...]]
++[\-aChimMsuZ]
++[\-AcflnNoqrtvxXyz {...}]
++{infile} {outfile} [<totype> <totype> ...]
++.SH OPTIONS
++.TP
++\fB\-f\fR <fromtype>
++load this type of project files, where fromtype is:
++.TP
++caf
++a complete assembly or single sequences from CAF
++.TP
++maf
++a complete assembly or single sequences from CAF
++.TP
++fasta
++sequences from a FASTA file
++.TP
++fastq
++sequences from a FASTQ file
++.TP
++gbf
++sequences from a GBF file
++.TP
++phd
++sequences from a PHD file
++.TP
++fofnexp
++sequences in EXP files from file of filenames
++.TP
++\fB\-t\fR <totype>
++write the sequences/assembly to this type (multiple
++mentions of \fB\-t\fR are allowed):
++.TP
++ace
++sequences or complete assembly to ACE
++.TP
++caf
++sequences or complete assembly to CAF
++.TP
++maf
++sequences or complete assembly to MAF
++.TP
++sam
++complete assembly to SAM
++.TP
++samnbb
++like above, but leaving out reference (backbones) in mapping assemblies
++.TP
++gbf
++sequences or consensus to GBF
++.TP
++gff3
++consensus to GFF3
++.TP
++wig
++assembly coverage info to wiggle file
++.TP
++gcwig
++assembly gc content info to wiggle file
++.TP
++fasta
++sequences or consensus to FASTA file (qualities to
++.IP
++\&.qual)
++.TP
++fastq
++sequences or consensus to FASTQ file
++.TP
++exp
++sequences or complete assembly to EXP files in
++.IP
++directories. Complete assemblies are suited for gap4
++import as directed assembly.
++Note: using caf2gap to import into gap4 is recommended though
++.TP
++text
++complete assembly to text alignment (only when \fB\-f\fR is
++.IP
++caf, maf or gbf)
++.TP
++html
++complete assembly to HTML (only when \fB\-f\fR is caf, maf or
++.IP
++gbf)
++.TP
++tcs
++complete assembly to tcs
++.TP
++hsnp
++surrounding of SNP tags (SROc, SAOc, SIOc) to HTML
++(only when \fB\-f\fR is caf, maf or gbf)
++.TP
++asnp
++analysis of SNP tags
++(only when \fB\-f\fR is caf, maf or gbf)
++.TP
++cstats
++contig statistics file like from MIRA
++(only when source contains contigs)
++.TP
++crlist
++contig read list file like from MIRA
++(only when source contains contigs)
++.TP
++maskedfasta
++reads where sequencing vector is masked out
++(with X) to FASTA file (qualities to .qual)
++.TP
++scaf
++sequences or complete assembly to single sequences CAF
++.TP
++\fB\-a\fR
++Append to target files instead of rewriting
++.TP
++\fB\-A\fR <string>
++String with MIRA parameters to be parsed
++Useful when setting parameters affecting consensus
++calling like \fB\-CO\fR:mrpg etc.
++E.g.: \fB\-a\fR "454_SETTINGS \fB\-CO\fR:mrpg=3"
++.TP
++\fB\-b\fR
++Blind data
++Replaces all bases in reads/contigs with a 'c'
++.TP
++\fB\-C\fR
++Perform hard clip to reads
++When reading formats which define clipping points, will
++.IP
++save only the unclipped part into the result file.
++.IP
++Applies only to files/formats which do not contain
++.IP
++contigs.
++.TP
++\fB\-d\fR
++Delete gap only columns
++When output is contigs: delete columns that are
++.IP
++entirely gaps (like after having deleted reads during
++editing in gap4 or similar)
++.IP
++When output is reads: delete gaps in reads
++.TP
++\fB\-F\fR
++Filter to read groups
++Special use case, do not use yet.
++.TP
++\fB\-m\fR
++Make contigs (only for \fB\-t\fR = caf or maf)
++Encase single reads as contig singlets into the CAF/MAF
++file.
++.TP
++\fB\-n\fR <filename>
++when given, selects only reads or contigs given by
++name in that file.
++.TP
++\fB\-i\fR
++when \fB\-n\fR is used, inverts the selection
++.TP
++\fB\-o\fR
++fastq quality Offset (only for \fB\-f\fR = 'fastq')
++Offset of quality values in FASTQ file. Default of 0
++tries to automatically recognise.
++.TP
++\fB\-Q\fR <quality>
++Set default quality for bases in file types without quality values
++Furthermore, do not stop if expected quality files are missing (e.g. '.fasta')
++.TP
++\fB\-R\fR <name>
++Rename contigs/singlets/reads with given name string
++to which a counter is appended.
++Known bug: will create duplicate names if input
++.IP
++contains contigs/singlets as well as free reads, i.e.
++reads not in contigs nor singlets.
++.TP
++\fB\-S\fR <name>
++(name)Scheme for renaming reads, important for paired\-ends
++Only 'solexa' is currently supported.
++.SS The following switches work only when input (CAF or MAF) contains contigs.
++Beware: CAF and MAf can also contain just reads.
++.TP
++\fB\-M\fR
++Do not extract contigs (or their consensus), but the
++sequence of the reads they are composed of.
++.TP
++\fB\-N\fR <filename>
++like \fB\-n\fR, but sorts output according to order given
++in file.
++.TP
++\fB\-r\fR [cCqf]
++Recalculate consensus and / or consensus quality values
++and / or SNP feature tags.
++\&'c' recalc cons & cons qualities (with IUPAC)
++\&'C' recalc cons & cons qualities (forcing non\-IUPAC)
++\&'q' recalc consensus qualities only
++\&'f' recalc SNP features
++Note: only the last of cCq is relevant, f works as a
++.IP
++switch and can be combined with cQq (e.g. "\-r C \fB\-r\fR f")
++.IP
++Note: if the CAF/MAF contains multiple strains,
++recalculation of cons & cons qualities is forced, you
++.IP
++can just influence whether IUPACs are used or not.
++.TP
++\fB\-s\fR
++split output into multiple files instead of creating a
++single file
++.TP
++\fB\-u\fR
++\&'fillUp strain genomes'
++Fill holes in the genome of one strain (N or @)
++with sequence from a consensus of other strains
++Takes effect only with \fB\-r\fR and \fB\-t\fR gbf or fasta/q
++in FASTA/Q: bases filled up are in lower case
++in GBF: bases filled up are in upper case
++.TP
++\fB\-q\fR <integer>
++Defines minimum quality a consensus base of a strain
++must have, consensus bases below this will be 'N'
++Default: 0
++Only used with \fB\-r\fR, and \fB\-f\fR is caf/maf and \fB\-t\fR is (fasta
++.IP
++or gbf)
++.TP
++\fB\-v\fR
++Print version number and exit
++.TP
++\fB\-x\fR <integer>
++Minimum contig or read length
++When loading, discard all contigs / reads with a
++length less than this value. Default: 0 (=switched off)
++Note: not applied to reads in contigs!
++.TP
++\fB\-X\fR <integer>
++Similar to \fB\-x\fR but applies only to reads and
++then to the clipped length.
++.TP
++\fB\-y\fR <integer>
++Minimum average contig coverage
++When loading, discard all contigs with an
++average coverage less than this value.
++Default: 1
++.TP
++\fB\-z\fR <integer>
++Minimum number of reads in contig
++When loading, discard all contigs with a
++number of reads less than this value.
++Default: 0 (=switched off)
++.TP
++\fB\-l\fR <integer>
++when output as text or HTML: number of bases shown in
++one alignment line. Default: 60.
++.TP
++\fB\-c\fR <character>
++when output as text or HTML: character used to pad
++endgaps. Default: ' ' (blank)
++.PP
++Aliases:
++caf2html, exp2fasta, ... etc. Any combination of "<validfromtype>2<validtotype>"
++can be used as program name (also using links) so as that convert_project
++automatically sets \fB\-f\fR and \fB\-t\fR accordingly.
++.SH EXAMPLES
++.IP
++convert_project source.maf dest.sam
++.IP
++convert_project source.caf dest.fasta wig ace
++.IP
++convert_project \-x 2000 \-y 10 source.caf dest.caf
++.IP
++caf2html \-l 100 \-c . source.caf dest
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/copyright
index 2510d74,0000000..c0b728d
mode 100644,000000..100644
--- a/debian/copyright
+++ b/debian/copyright
@@@ -1,63 -1,0 +1,53 @@@
- Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
-
++Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
++Upstream-Contact: Bastien Chevreux <bach at chevreux.org>
+Source: http://jaist.dl.sourceforge.net/project/mira-assembler/MIRA/V3rc2/mira-3rc2.tar.bz2
+
++Files: *
++Copyright: © 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer, Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecula Biophysics.
++ © 2001-2013 for MIRA V2.x: Bastien Chevreux <bach at chevreux.org>
++License: GPL-2+
++Comment:
++ Author of MIRA
++ .
++ Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches
++ Krebsforschungsinstitut, DKFZ) in Heidelberg, DE
++ Now at DSM Nutritional Products AG, Kaiseraugst, CH
++ .
++ .
++ Author of EdIt
++ .
++ Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches
++ Krebsforschungsinstitut, DKFZ) in Heidelberg. DE
++ Now at MWG Biotech AG, Ebersberg, DE
++
++Files: src/io/scf.H
++Copyright: © Medical Research Council 1994
++License: staden
++ Permission to use, copy, modify and distribute this software and its
++ documentation for any purpose is hereby granted without fee, provided that
++ this copyright and notice appears in all copies.
++ .
++ This file was written by James Bonfield, Simon Dear, Rodger Staden,
++ as part of the Staden Package at the MRC Laboratory of Molecular
++ Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
++ .
++ MRC disclaims all warranties with regard to this software.
++Comment: uses part of a file from the `Staden package'.
++
++License: GPL-2+
++ This package is free software; you can redistribute it and/or modify
++ it under the terms of the GNU General Public License as published by
++ the Free Software Foundation; either version 2 of the License, or
++ (at your option) any later version.
++ .
++ This package is distributed in the hope that it will be useful,
++ but WITHOUT ANY WARRANTY; without even the implied warranty of
++ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
++ GNU General Public License for more details.
++ .
++ You should have received a copy of the GNU General Public License
++ along with this package; if not, write to the Free Software
++ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
++Comment: On Debian systems, the complete text of the GNU General Public
++ License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
- © 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer,
- Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecular
- Biophysics.
- © 2001-2007 for MIRA V2.x: Bastien Chevreux.
-
- Author of MIRA
-
- Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches
- Krebsforschungsinstitut, DKFZ) in Heidelberg, DE
- Now at DSM Nutritional Products AG, Kaiseraugst, CH
-
-
- Author of EdIt
-
- Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches
- Krebsforschungsinstitut, DKFZ) in Heidelberg. DE
- Now at MWG Biotech AG, Ebersberg, DE
-
-
- MIRA, EdIt and accompanying programs of the package are licenced under the GPL
- version 2, both in source code and binaries.
-
- License:
-
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
-
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
-
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
- On Debian systems, the complete text of the GNU General
- Public License can be found in `/usr/share/common-licenses/GPL'.
-
- The file src/io/scf.H uses part of a file from the `Staden package', which is
- released under the following terms:
-
- * Copyright (c) Medical Research Council 1994. All rights reserved.
- *
- * Permission to use, copy, modify and distribute this software and its
- * documentation for any purpose is hereby granted without fee, provided that
- * this copyright and notice appears in all copies.
- *
- * This file was written by James Bonfield, Simon Dear, Rodger Staden,
- * as part of the Staden Package at the MRC Laboratory of Molecular
- * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
- *
- * MRC disclaims all warranties with regard to this software.
-
- The Debian packaging is © 2007, Charles Plessy <charles-debian-nospam at plessy.org> and
- is licensed under as if it were public domain.
diff --cc debian/fasta2frag.1
index 0000000,0000000..cb978c7
new file mode 100644
--- /dev/null
+++ b/debian/fasta2frag.1
@@@ -1,0 -1,0 +1,95 @@@
++.TH FASTA2FRAG "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++.B fasta2frag \- splits a single fasta sequence into several overlapping fragments.
++.SH DESCRIPTION
++This program is part of the MIRA assembler package. The purpose of fasta2frag
++is to fragment sequences into smaller, overlapping
++subsequences. It can be used for simulating shotgun sequences. It can create
++subsequences in both directions (/default) and also paired-end sequences.
++Please check out the
++documentation below for more detailed information about fasta2frag.
++.SH SYNOPSIS
++fasta2frag
++\fI<options> infile outfile\fR
++.SH OPTIONS
++\fB\-l\fR
++int Length of fragments (default=3000)
++.TP
++\fB\-i\fR
++int Increment of fragment start site (default=2500)
++.TP
++\fB\-p\fR
++int Paired end (default=0 is off, 1 is on)
++.TP
++\fB\-P\fR
++int In paired\-end mode, reverse one of the reads
++(0 is off, default=1 is on)
++.TP
++\fB\-s\fR
++int Strobe sequencing (default=0 is off, 1 is on)
++.TP
++\fB\-q\fR
++int Default quality when no quality data present (default=30)
++.TP
++\fB\-r\fR
++int Reverse every nth fragment (default=2)
++.TP
++\fB\-c\fR
++int Circularise fragments so that they form a ring
++.IP
++(default=0 is is off, 1 would be on)
++.TP
++\fB\-qualdivisor\fR
++int Divide quality values by this (default=1)
++.TP
++\fB\-minqual\fR
++int But give it at least this qual (default=0)
++.TP
++\fB\-insert_size\fR
++int paired\-end: insert size (default=3000)
++.TP
++\fB\-insert_stdev\fR int
++paired\-end: standard dev (default=900)
++this is not working at the moment
++.TP
++\fB\-pairednaming\fR string
++naming scheme for paired\-end:
++sanger, 454 (default) or solexa
++.TP
++\fB\-minmut\fR
++int min. number of mutations/seq. errors (def=0)
++.TP
++\fB\-maxmut\fR
++int max. number of mutations/seq. errors (def=0)
++.TP
++\fB\-strobeon\fR
++int number of bases read during strobe on
++.TP
++\fB\-strobeoff\fR
++int number of bases during strobe off
++.TP
++\fB\-startoffset\fR
++int start at offset position
++.TP
++\fB\-namesuffix\fR
++string suffix name with string
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/fastaselect.1
index 0000000,0000000..1a133a8
new file mode 100644
--- /dev/null
+++ b/debian/fastaselect.1
@@@ -1,0 -1,0 +1,47 @@@
++.TH FASTASELECT "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++.B fastaselect \- select fasta sequences in a file
++.SH DESCRIPTION
++This script selects fasta sequences in a file according to names given
++in a name file. Given a FASTA file (and possibly a FASTA quality file) and
++a file with names of reads, select the sequences from the input FASTA (and
++quality file) and writes them to an output FASTA.
++.PP
++If fasta quality file is present (same basename, but with .qual appended),
++then also selects sequences from there.
++.PP
++Please check out the documentation below for more detailed information.
++.SH SYNOPSIS
++fastaselect \fI<options>\fR
++.SH OPTIONS
++.TP
++\fB\-infile\fR
++name filename containing all fasta sequences
++.TP
++\fB\-name\fR
++name filename containing all names of sequences to select
++.TP
++\fB\-outfile\fR name
++filename where to write selcted sequences to
++.SH "SEE ALSO"
++fastqselect(1)
++.PP
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/fastatool.1
index 0000000,0000000..cd3a917
new file mode 100644
--- /dev/null
+++ b/debian/fastatool.1
@@@ -1,0 -1,0 +1,49 @@@
++.TH FASTATOOL "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++.B fastatool \- Provides a set of tools useful when working with FASTA files.
++.SH DESCRIPTION
++This program is part of the MIRA assembler package.
++Fastatool provides a set of tools useful when working with FASTA trace files.
++.PP
++Please check out the documentation below for more detailed information.
++.SH SYNOPSIS"
++fastatool \fI<toolname>\fR \fI<tool parameters>\fR
++.SH OPTIONS
++.TP
++clip
++Clips bases on the left and right of a FASTA sequence, writes result to STDOUT.
++.IP
++Usage:
++.TP
++ clipFASTA \-l leftclip \-r rightclip fastainfile
++.TP
++sanitize
++Deletes sequences with non-IUPAC bases or empty sequences from a FASTA file,
++writes the 'surviving' sequences to a new file.
++If a quality file is given, a cleaned version of that is also written.
++The sequences in the quality files (if given) MUST be in the same order than
++in the fasta file.
++.IP
++Usage:
++.TP
++ sanitizeFASTA fastainfile fastaoutfile [fastaqualin fastaqualoutfile]
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/fastqselect.1
index 0000000,0000000..dea7157
new file mode 100644
--- /dev/null
+++ b/debian/fastqselect.1
@@@ -1,0 -1,0 +1,47 @@@
++.TH FASTQSELECT "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++.B fastqselect \- select fastq sequences in a file
++.SH DESCRIPTION
++This script selects fastq sequences in a file according to names given
++in a name file. Given a FASTQ file (and possibly a FASTQ quality file) and
++a file with names of reads, select the sequences from the input FASTQ (and
++quality file) and writes them to an output FASTQ.
++.PP
++If fastq quality file is present (same basename, but with .qual appended),
++then also selects sequences from there.
++.PP
++Please check out the documentation below for more detailed information.
++.SH SYNOPSIS
++fastqselect \fI<options>\fR
++.SH OPTIONS
++.TP
++\fB\-infile\fR
++name filename containing all fastq sequences
++.TP
++\fB\-name\fR
++name filename containing all names of sequences to select
++.TP
++\fB\-outfile\fR name
++filename where to write selcted sequences to
++.SH "SEE ALSO"
++fastaselect(1)
++.PP
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/fixACE4consed.1
index 0000000,0000000..b81fa43
new file mode 100644
--- /dev/null
+++ b/debian/fixACE4consed.1
@@@ -1,0 -1,0 +1,32 @@@
++.TH fixACE4consed "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++fixACE4consed \- workaround to allow consed loading the ACE generated by MIRA
++.SH DESCRIPTION
++The ACE output of MIRA is conforming to the file specification given in the
++consed documentation. However, due to a bug in consed, consed cannot correctly
++load tags set by MIRA.
++.PP
++The script fixACE4consed implements a workaround to allow consed loading the
++ACE generated by MIRA.
++.SH SYNOPSIS
++fixACE4consed infile.ace >outfile.ace
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/mira-assembler.lintian-overrides
index 0000000,0000000..2a480bf
new file mode 100644
--- /dev/null
+++ b/debian/mira-assembler.lintian-overrides
@@@ -1,0 -1,0 +1,2 @@@
++# according to www.dict.cc transfering is American English spelling
++mira-assembler: spelling-error-in-binary usr/bin/mira Transfering Transferring
diff --cc debian/mira-assembler.manpages
index 0000000,0000000..0f65186
new file mode 100644
--- /dev/null
+++ b/debian/mira-assembler.manpages
@@@ -1,0 -1,0 +1,1 @@@
++debian/*.1
diff --cc debian/mira-doc.README.Debian
index 88c5ded,0000000..6c502b8
mode 100644,000000..100644
--- a/debian/mira-doc.README.Debian
+++ b/debian/mira-doc.README.Debian
@@@ -1,4 -1,0 +1,4 @@@
+This package provides the Definitive Guide To MIRA book, which is included with
+the default MIRA download, in HTML format.
+
- See: /usr/share/doc/mira/DefinitiveGuideToMIRA.html
++See: /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html
diff --cc debian/mira-doc.doc-base
index 0000000,0000000..2af901e
new file mode 100644
--- /dev/null
+++ b/debian/mira-doc.doc-base
@@@ -1,0 -1,0 +1,12 @@@
++Document: mira-manual
++Title: Sequence assembly wirh mira3
++Author: Bastian Chevreux <bach at chevreux.org
++ Jacqueline Weber
++ Andrea Hoerster
++ Katrina Dlugosch
++Section: Science/Biology
++
++Format: html
++Files: /usr/share/doc/mira-assembler/*
++Index: /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html
++
diff --cc debian/mira.1
index 0000000,0000000..df79ae2
new file mode 100644
--- /dev/null
+++ b/debian/mira.1
@@@ -1,0 -1,0 +1,53 @@@
++.TH 3.9.17 "1" "June 2013" "User Commands"
++.SH NAME
++mira \- The Genome and EST Sequence Assembly System
++.SH DESCRIPTION
++The mira genome fragment assembler is a specialised assembler for
++sequencing projects classified as 'hard' due to high number of similar
++repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
++specialised on reconstructing pristine mRNA transcripts while
++detecting and classifying single nucleotide polymorphisms (SNP)
++occuring in different variations thereof.
++.PP
++The assembler is routinely used for such various tasks as mutation
++detection in different cell types, similarity analysis of transcripts
++between organisms, and pristine assembly of sequences from various
++sources for oligo design in clinical microarray experiments.
++.PP
++The purpose of the \fBmira\fR executable is to assemble sequencing data.
++.SH SYNOPSIS
++mira
++[\fIOPTION\fR] manifest_file [\fImanifest_file\fR] ...
++.SH OPTIONS
++.TP
++\fB\-c\fR / \fB\-\-cwd=\fRdirectory
++Change working directory
++.TP
++\fB\-r\fR / \fB\-\-resume\fR
++Resume an interrupted assembly
++.TP
++\fB\-h\fR / \fB\-\-help\fR
++Print short help and exit
++.TP
++\fB\-v\fR / \fB\-\-version\fR
++Print version and exit
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/miraSearchESTSNPs.1
index 0000000,0000000..0e7cebd
new file mode 100644
--- /dev/null
+++ b/debian/miraSearchESTSNPs.1
@@@ -1,0 -1,0 +1,43 @@@
++.TH miraSearchESTSNPs "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++miraSearchESTSNPs \- Pipeline to discover SNPs in ESTs from different strains
++.SH DESCRIPTION
++The program miraSearchESTSNPs can be used for assembly of EST data from
++different strains (or organisms) and SNP detection within this assembly.
++This is the former miraEST program which was renamed as many people got
++confused regarding whether to use MIRA in est mode or miraEST.
++.PP
++miraSearchESTSNPs is a pipeline that reconstructs the pristine mRNA
++transcript sequences gathered in EST sequencing projects of more than
++one strain, which can be a reliable basis for subsequent analysis steps
++like clustering or exon analysis. This means that even genes that
++contain only one transcribed SNP on different alleles are first treated
++as different transcripts. The optional last step of the assembly process
++can be configured as a simple clusterer that can assemble transcripts
++containing the same exon sequence -- but only differ in SNP positions --
++into one consensus sequence. Such SNPs can then be analysed, classified
++and reliably assigned to their corresponding mRNA transcriptome
++sequence. However, it is important to note that miraSearchESTSNPs is an
++assembler and not a full blown clustering tool.
++.SH SYNOPSIS
++In version 3.9.17 this functionality is deactivated.
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/mirabait.1
index 0000000,0000000..14a66b5
new file mode 100644
--- /dev/null
+++ b/debian/mirabait.1
@@@ -1,0 -1,0 +1,131 @@@
++.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3.
++.TH MIRABAIT: "1" "August 2013" "MIRALIB version 3.9.18" "User Commands"
++.SH NAME
++mirabait \- select reads from a read collection
++.SH SYNOPSIS
++.B mirabait
++[\fI\-f <fromtype>\fR] [\fI\-t <totype> [\-t <totype> ...]\fR] [\fI\-iklor\fR] baitfile infile <basename_for_outfile(s)>
++.SH DESCRIPTION
++\fBmirabait\fR selects reads from a read collection which
++are partly similar or equal to sequences defined as target
++baits. Similarity is defined by finding a user-adjustable number of
++common k-mers (sequences of k consecutive bases) which are the same in
++the bait sequences and the screened sequences to be selected, either in forward
++or reverse complement direction.
++.SH OPTIONS
++.TP
++\fB\-f\fR <fromtype>
++load this type of project files, where fromtype is:
++.TP
++caf
++sequences from CAF
++.TP
++maf
++sequences from MAF
++.TP
++phd
++sequences from a PHD
++.TP
++gbf
++sequences from a GBF
++.TP
++fasta
++sequences from a FASTA
++.TP
++fastq
++sequences from a FASTQ
++.TP
++\fB\-t\fR <totype>
++write the sequences to this type (multiple mentions
++of \fB\-t\fR are allowed):
++.TP
++fasta
++sequences to FASTA
++.TP
++fastq
++sequences to FASTQ
++.TP
++caf
++sequences to CAF
++.TP
++maf
++sequences to MAF
++.TP
++txt
++sequence names to text file
++.TP
++\fB\-k\fR
++k\-mer, length of bait in bases (<32, default=31)
++.TP
++\fB\-n\fR
++Min. number of k\-mer baits needed (default=1)
++.TP
++\fB\-i\fR
++Inverse hit: writes only sequences that do not hit bait
++.TP
++\fB\-r\fR
++No checking of reverse complement direction
++.TP
++\fB\-o\fR
++fastq quality Offset (only for \fB\-f\fR = 'fastq')
++Offset of quality values in FASTQ file. Default: 33
++A value of 0 tries to automatically recognise.
++.TP
++\fB\-f\fR <fromtype>
++load this type of project files, where fromtype is:
++.TP
++caf
++sequences from CAF
++.TP
++maf
++sequences from MAF
++.TP
++phd
++sequences from a PHD
++.TP
++gbf
++sequences from a GBF
++.TP
++fasta
++sequences from a FASTA
++.TP
++fastq
++sequences from a FASTQ
++.TP
++\fB\-t\fR <totype>
++write the sequences to this type (multiple mentions
++of \fB\-t\fR are allowed):
++.TP
++fasta
++sequences to FASTA
++.TP
++fastq
++sequences to FASTQ
++.TP
++caf
++sequences to CAF
++.TP
++maf
++sequences to MAF
++.TP
++txt
++sequence names to text file
++.TP
++\fB\-k\fR
++k\-mer, length of bait in bases (<32, default=31)
++.TP
++\fB\-n\fR
++Min. number of k\-mer baits needed (default=1)
++.TP
++\fB\-i\fR
++Inverse hit: writes only sequences that do not hit bait
++.TP
++\fB\-r\fR
++No checking of reverse complement direction
++.TP
++\fB\-o\fR
++fastq quality Offset (only for \fB\-f\fR = 'fastq')
++Offset of quality values in FASTQ file. Default: 33
++A value of 0 tries to automatically recognise.
++.SH AUTHOR
++Bastien Chevreux (bach at chevreux.org)
diff --cc debian/miradiff.1
index 0000000,0000000..7085ede
new file mode 100644
--- /dev/null
+++ b/debian/miradiff.1
@@@ -1,0 -1,0 +1,36 @@@
++.TH MIRADIFF "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++miradiff \- diff two data sets of mira(1)
++.SH DESCRIPTION
++This program is part of the MIRA assembler package. Please check out the
++documentation below for more detailed information about miradiff.
++.SH SYNOPSIS
++miradiff
++[\fIOPTION\fR]
++.SH OPTIONS
++.TP
++\fB\-h\fR / \fB\-\-help\fR
++Print short help and exit
++.TP
++\fB\-v\fR / \fB\-\-version\fR
++Print version and exit
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/miramem.1
index 0000000,0000000..edf907d
new file mode 100644
--- /dev/null
+++ b/debian/miramem.1
@@@ -1,0 -1,0 +1,33 @@@
++.TH MIRAMEM "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++miramem \- estimating needed memory for a MIRA assembly project
++.SH DESCRIPTION
++When called from the command line, it will ask a number of questions and
++then print out an estimate of the amount of RAM needed to assemble the
++project. Take this estimate with a grain of salt, depending on the
++sequences properties, variations in the estimate can be +/- 30% for
++bacteria and 'simple' eukaryotes. The higher the number of repeats is,
++the more likely you will need to restrict memory usage in some way or
++another.
++.SH SYNOPSIS
++miramem
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/miramer.1
index 0000000,0000000..bf12ac2
new file mode 100644
--- /dev/null
+++ b/debian/miramer.1
@@@ -1,0 -1,0 +1,36 @@@
++.TH MIRAMER "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++miramer \- handle k-mer statistics of a data set
++.SH DESCRIPTION
++This program is part of the MIRA assembler package. Please check out the
++documentation below for more detailed information about miramer.
++.SH SYNOPSIS
++miramer
++[\fIOPTION\fR]
++.SH OPTIONS
++.TP
++\fB\-h\fR / \fB\-\-help\fR
++Print short help and exit
++.TP
++\fB\-v\fR / \fB\-\-version\fR
++Print version and exit
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/patches/boost-minimal.patch
index 0000000,0000000..1e6d67f
new file mode 100644
--- /dev/null
+++ b/debian/patches/boost-minimal.patch
@@@ -1,0 -1,0 +1,15 @@@
++Author: Thorsten Alteholz <debian at alteholz.de>
++LastChanged: Fri, 09 Aug 2013 13:59:24 +0200
++Description: use minimal set of boost libraries
++
++--- a/src/progs/Makefile.in
+++++ b/src/progs/Makefile.in
++@@ -256,7 +256,7 @@ noinst_HEADERS = quirks.H
++ # EdIt_abi373 EdIt_alf skimmer
++ @BUILDMIRASTATIC_TRUE at AM_LDFLAGS = $(BLOODYDARWINSTATLIBDIRHACK) -L../debuggersupport -L../memorc -L../io/ -L../util/ -L../errorhandling/ -L../mira -L../caf $(LINKEDITDIR) $(BOOST_LDFLAGS) -all-static
++ @BUILDMIRAMEMORC_TRUE at MEMORC = -lmemorc
++-MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport $(LINKEDITLIB)
+++MIRALIBS = -lmiradebuggersupport $(MEMORC) -lmira -lmiraestass -lmiracaf -lmirautil -lmiradptools -lmirafio -lmiraerrorhandling -lmiradebuggersupport -lboost_filesystem -lboost_iostreams -lboost_regex -lboost_thread -lboost_system $(LINKEDITLIB)
++ mira_SOURCES = mira.C
++ mira_LDADD = $(MIRALIBS)
++ convert_project_SOURCES = convert_project.C
diff --cc debian/patches/series
index 244e68e,0000000..2fbda29
mode 100644,000000..100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@@ -1,3 -1,0 +1,1 @@@
- add_shebang_lines
- xsltproc_nonet_for_doc_build
- read_default_constructor.patch
++#boost-minimal.patch
diff --cc debian/rules
index 0e01878,0000000..2c48dd8
mode 100755,000000..100755
--- a/debian/rules
+++ b/debian/rules
@@@ -1,55 -1,0 +1,100 @@@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
- #export DH_VERBOSE=1
++export DH_VERBOSE=1
++#Hacky thing to allow building against tcmalloc without installing
++#troublesome libbgoogle-perftools-dev, see README.Debian
++export DEB_CFLAGS_MAINT_APPEND=-L$(CURDIR)/lib
++
++pkg=mira-assembler
++exampledir=usr/share/doc/mira-examples/examples/minidemo/data/bbdataset1/
++
++include /usr/share/dpkg/default.mk
+
+%:
- dh $@ --with quilt
++ dh $@
+
+override_dh_auto_install :
- make install DESTDIR=$(CURDIR)/debian/mira-assembler
++ make install DESTDIR=$(CURDIR)/debian/$(pkg)
+ #There is no installation target for the docs
- mkdir -p $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler
- cp -r -t $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler doc/docbook/bookfigures doc/docbook/images \
++ mkdir -p $(CURDIR)/debian/tmp/usr/share/doc/$(pkg)
++ cp -r -t $(CURDIR)/debian/tmp/usr/share/doc/$(pkg) doc/docbook/bookfigures doc/docbook/images \
+ doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true
+
++override_dh_installexamples:
++ dh_installexamples
++ # avoid duplicated files
++ if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.fasta.qual $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual >/dev/null ; then \
++ echo "removing copy of $(exampledir)/cjejuni_demo_in.fasta.qual and create symling" ; \
++ rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual ; \
++ ln -s cjejuni_demo_in.fasta.qual.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual.gz ; \
++ fi
++ if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.fasta $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta >/dev/null ; then \
++ echo "removing copy of $(exampledir)/cjejuni_demo_in.fasta and create symling" ; \
++ rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta ; \
++ ln -s cjejuni_demo_in.fasta.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.gz ; \
++ fi
++ if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_NCTC11168_first40kb.gbf $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf >/dev/null ; then \
++ echo "removing copy of $(exampledir)/cjejuni_NCTC11168_first40kb.gbf and create symling" ; \
++ rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf ; \
++ ln -s cjejuni_NCTC11168_first40kb.gbf.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf.gz ; \
++ fi
++ if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.xml $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml >/dev/null ; then \
++ echo "removing copy of $(exampledir)/cjejuni_demo_traceinfo_in.xml and create symling" ; \
++ rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml ; \
++ ln -s cjejuni_demo_traceinfo_in.xml.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml.gz ; \
++ fi
++
+override_dh_auto_test:
+ make check
+
+#Make the docs
+override_dh_auto_build:
- dh_auto_build
++ dh_auto_build --parallel
+ifneq (,$(findstring mira-doc, $(shell dh_listpackages)))
- dh_auto_build --sourcedir=doc
++ dh_auto_build --sourcedir=doc --parallel
+endif
+
+#Remove unneeded .tcl extensions from scripts
+override_dh_install:
+ dh_install
- if [ -d debian/mira-assembler ] ; then \
- for f in $$(ls debian/mira-assembler/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \
++ if [ -d debian/$(pkg) ] ; then \
++ for f in $$(ls debian/$(pkg)/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \
+ fi
-
- #Hacky thing to allow building against tcmalloc without installing
- #troublesome libbgoogle-perftools-dev, see README.Debian
- export LDFLAGS=-L$(CURDIR)/lib
++ # In version 3.9.17 executing miraSearchESTSNPs just leads to "De-activated atm, sorry."
++ # If this is the case, it should not be installed
++ for deactivated in miraSearchESTSNPs miraclip ; do \
++ if [ -e debian/$(pkg)/usr/bin/$${deactivated} ] ; then \
++ if [ "`debian/$(pkg)/usr/bin/$${deactivated} 2>&1 | tee`" = "De-activated atm, sorry." ] ; then rm -f debian/$(pkg)/usr/bin/$${deactivated} ; fi \
++ else \
++ echo "debian/$(pkg)/usr/bin/$${deactivated} does not exist" ; \
++ fi ; \
++ done
+
+#Must clean up the docs before cleaning out config.status
+#Then scrub some junk not picked up by 'make clean'
+override_dh_auto_clean:
+ ( cd doc ; make clean ) || true
+ dh_auto_clean
+ find * -name Makefile -exec rm '{}' ';'
+ find * -name '*.xxd.H' -exec rm '{}' ';'
+ find * -name '*.par.H' -exec rm '{}' ';'
+ find * -name 'compileinfo.*' -exec rm '{}' ';'
+
+override_dh_clean:
+ dh_clean
+ rm -rf lib
+
+override_dh_auto_configure :
+ mkdir lib
- ln -s /usr/lib/libtcmalloc_minimal.so.0 lib/libtcmalloc_minimal.so
- dh_auto_configure
++ ln -s /usr/lib/libtcmalloc_minimal.so.4 lib/libtcmalloc_minimal.so
++ #dh_auto_configure
++ dh_auto_configure -- --with-boost-libdir=/usr/lib/$(DEB_HOST_MULTIARCH)
++
++override_dh_builddeb:
++ dh_builddeb -- -Z xz
++
++get-orig-source:
++ mkdir -p ../tarballs
++ uscan --verbose --force-download --destdir=../tarballs
+
diff --cc debian/scftool.1
index 0000000,0000000..bb6f431
new file mode 100644
--- /dev/null
+++ b/debian/scftool.1
@@@ -1,0 -1,0 +1,50 @@@
++.TH SCFTOOL "1" "June 2013" "3.9.17" "User Commands"
++.SH NAME
++scftool \- provides a set of tools useful when working with SCF trace files.
++.SH SYNOPSIS
++.IP
++scftool
++<\fBtoolname\fR> <\fBtool parameters\fR>
++.SH OPTIONS
++Available tools:
++.IP convert
++Cuts the given range out of an SCF file and makes a new SCF out of it.
++.IP
++To get help more specific help please type \fIscftool convert\fR
++.IP cut
++Cuts a given range of a SCF file into a new SCF file.
++.IP remix
++Combines trace information of a SCF file with new bases, qualities and peak
++values (either in FASTA or PHD format) into a new SCF file.
++.SH EXAMPLES
++Example for cut:
++.IP
++scftool cut infile lower_base_bound upper_base_bound outfile
++.PP
++Usage of remix (when using PHD files as input for bases, quals and peaks):
++.IP
++scftool remix scf_infile phd_infile scf_outfile
++.PP
++Usage of remix (when using FASTA files as input for bases, quals and peaks):
++.IP
++scftool remix scf_infile bases_infile quals_infile peaks_infile scf_outfile
++.SH "SEE ALSO"
++A more extensive documentation is provided in the mira-doc package and can be found at
++/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html.
++.PP
++You can also subscribe one of the MIRA mailing lists at
++.IP
++http://www.chevreux.org/mira_mailinglists.html
++.PP
++After subscribing, mail general questions to the MIRA talk mailing list:
++.IP
++mira_talk at freelists.org
++.SH BUGS
++To report bugs or ask for features, please use the new ticketing system at:
++.IP
++http://sourceforge.net/apps/trac/mira\-assembler/
++.SH AUTHOR
++The author of the mira code is Bastien Chevreux <bach at chevreux.org>
++.PP
++This manual page was written by Andreas Tille <tille at debian.org> but can be freely used for any other
++distribution.
diff --cc debian/upstream
index 0000000,0000000..0a35427
new file mode 100644
--- /dev/null
+++ b/debian/upstream
@@@ -1,0 -1,0 +1,15 @@@
++Bugs: http://sourceforge.net/apps/trac/mira-assembler/newticket
++Homepage: http://www.chevreux.org/projects_mira.html
++Homepage: http://sourceforge.net/apps/trac/mira-assembler
++Reference:
++ author: Chevreux, Bastien and Pfisterer, Thomas and Drescher, Bernd and Driesel, Albert J. and Müller, Werner E. G. and Wetter, Thomas and Suhai, Sándor
++ title: Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs
++ journal: Genome Research
++ volume: 14
++ number: 6
++ pages: 1147-1159
++ PMID: 15140833
++ doi: 10.1101/gr.1917404
++ year: 2004
++ URL: http://genome.cshlp.org/content/14/6/1147.abstract
++ eprint: http://genome.cshlp.org/content/14/6/1147.full.pdf+htm
diff --cc debian/watch
index acc9210,0000000..2775ae7
mode 100644,000000..100644
--- a/debian/watch
+++ b/debian/watch
@@@ -1,2 -1,0 +1,2 @@@
+version=3
- opts="uversionmangle=s/rc/~rc/" http://sf.net/mira-assembler/mira-(.*).tar.bz2
++http://sf.net/mira-assembler/mira-([\d.]+)\.tar\.bz2
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