[med-svn] [staden] branch master updated (f24ab60 -> 26dbe3d)
Andreas Tille
tille at debian.org
Thu Jul 14 18:29:34 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch master
in repository staden.
from f24ab60 Update changelog
new 3ca341f Fix issue with min undefined
new b343277 Adpat watch file to new upstream naming scheme
new 6604903 Imported Upstream version 2.0.0b11
new 3ef11e2 Merge tag 'upstream/2.0.0b11'
new 2a1e919 Adapt patches to new upstream version
new 34788e9 Issue is fixed in new upstream version
new a812461 Imported Upstream version 2.0.0+b11
new 26dbe3d Merge tag 'upstream/2.0.0+b11'
The 8 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:
ChangeLog | 2564 +++++++++++++-
Makefile.in | 2 +-
Misc/Makefile | 66 +
Misc/array.c | 25 +
Misc/array.h | 4 +
NEWS | 248 +-
README.build | 4 +-
abi/Makefile | 10 +
alf/Makefile | 1 +
configure | 245 +-
configure.in | 2 +-
convert/Makefile | 73 +
copy_reads/Makefile | 61 +
copy_reads/copy_reads.c | 4 +-
debian/changelog | 7 +-
.../patches/cope_with_modern_windowmanager.patch | 26 -
debian/patches/delete_rpath_from_configure.patch | 25 -
debian/patches/hardening.patch | 15 -
debian/patches/hardening_format-security.patch | 45 -
debian/patches/include_xalloc.patch | 8 +-
debian/patches/make_help_menus_work.patch | 28 -
debian/patches/remove_svnversion_dep.patch | 21 -
debian/patches/series | 6 -
debian/patches/spelling.patch | 68 -
debian/watch | 4 +-
eba/Makefile | 5 +
eba/conf.c | 2 +-
find_renz/Makefile | 8 +
g/Makefile | 82 +
gap4/Makefile | 3694 ++++++++++++++++++++
gap4/contig_editor.tcl | 24 +-
gap4/edMutations.c | 2 +-
gap4/gap-error.c | 2 +-
gap4/gaprc_menu_full | 4 +-
gap4/show_relationships.c | 6 +-
gap5/Makefile | 3406 +++++++++++++++++-
gap5/ace.c | 2 +-
gap5/actf.c | 4 +-
gap5/assemble_single.tcl | 48 +-
gap5/auto_break.c | 77 +-
gap5/b+tree2.c | 2 +
gap5/baf.c | 2 +-
gap5/break_contig.c | 17 +-
gap5/check_assembly.c | 10 +-
gap5/configure.tcl | 101 +-
gap5/consen.c | 147 +-
gap5/consen.h | 2 +-
gap5/consen.tcl | 117 +-
gap5/consensus.c | 381 +-
gap5/consensus.h | 14 +
gap5/contig_editor.tcl | 289 +-
gap5/contig_extend.c | 4 +-
gap5/contig_id.tcl | 6 +-
gap5/cs-object.h | 2 +
gap5/depth.tcl | 267 +-
gap5/dis_readings.c | 9 +-
gap5/dis_readings.tcl | 33 +-
gap5/do_fij.c | 9 +-
gap5/editor_join.c | 2 +-
gap5/editor_search.c | 8 +-
gap5/editor_view.c | 146 +-
gap5/export_contigs.c | 554 ++-
gap5/export_contigs.tcl | 28 +-
gap5/export_snps.c | 350 ++
gap5/export_snps.h | 9 +
gap5/fasta.c | 6 +-
gap5/fij.c | 27 +-
gap5/fij.tcl | 68 +-
gap5/find_haplotypes.0.c | 456 +++
gap5/find_haplotypes.c | 891 +++++
gap5/find_haplotypes.h | 10 +
gap5/find_oligo.c | 4 +-
gap5/find_repeats.c | 2 +-
gap5/g-alloc.c | 6 +-
gap5/g-request.c | 1 +
gap5/gap5.tcl | 15 +-
gap5/gap5_cmd.tcl | 155 +-
gap5/gap5_del_test.tcl | 321 +-
gap5/gap5_thrash.tcl | 5 +-
gap5/gap5rc | 10 +
gap5/gap5rc_menu_full | 18 +-
gap5/gap_canvas_box.c | 3 +-
gap5/gap_globals.c | 8 +-
gap5/gap_globals.h | 3 +
gap5/gap_globals.tcl | 43 +
gap5/gap_range.c | 2 +-
gap5/hash_lib.c | 13 +-
gap5/import_contigs.tcl | 2 +-
gap5/import_gff.c | 2 +-
gap5/interval_tree.c | 698 ++++
gap5/interval_tree.h | 89 +
gap5/libraries.tcl | 81 +-
gap5/list_proc.tcl | 88 +-
gap5/newgap5_cmds.c | 238 +-
gap5/newgap_structs.h | 5 +
gap5/ng_fb_cmds.tcl | 3 +
gap5/qualIO.c | 21 +-
gap5/quality_plot.c | 46 +-
gap5/replay_log.tcl | 401 +++
gap5/sam_index.c | 158 +-
gap5/sam_pileup.h | 1 +
gap5/shuffle_pads.c | 1730 ++++++++-
gap5/shuffle_pads.h | 14 +-
gap5/shuffle_pads.tcl | 31 +-
gap5/str_finder.c | 341 ++
gap5/str_finder.h | 37 +
gap5/tag_plot.c | 3 -
gap5/tclIndex | 6 +
gap5/template_display.c | 4 +-
gap5/template_draw.c | 6 +
gap5/tg_anno.c | 7 +-
gap5/tg_bin.c | 39 +-
gap5/tg_cache.c | 200 +-
gap5/tg_check.c | 44 +-
gap5/tg_contig.c | 1587 ++++++---
gap5/tg_contig.h | 64 +-
gap5/tg_gio.c | 21 +-
gap5/tg_gio.h | 9 +-
gap5/tg_iface_g.c | 45 +-
gap5/tg_index.c | 11 +-
gap5/tg_index.h | 2 +
gap5/tg_index_common.c | 257 +-
gap5/tg_library.c | 46 +-
gap5/tg_library.h | 18 +
gap5/tg_sequence.c | 205 +-
gap5/tg_sequence.h | 25 +-
gap5/tg_struct.h | 57 +-
gap5/tg_tcl.c | 445 ++-
gap5/tg_utils.c | 42 +-
gap5/tk-io-reg.c | 3 +-
gap5/tkEditor.c | 35 +
gap5/tkEditor.h | 6 +-
gap5/tman_interface.c | 12 +-
gap5/utlist.h | 761 ++++
gap5/zfio.c | 128 -
gap5/zfio.h | 23 -
get_scf_field/Makefile | 3 +
global.mk | 7 +-
haplo/Makefile | 89 +
hetins/hetins.c | 1 +
init_exp/Makefile | 2 +
make_weights/Makefile | 4 +
mutlib/Makefile | 338 ++
polyA_clip/Makefile | 9 +
prefinish/Makefile | 340 ++
primer3/src/ntdpal_main.c | 2 +-
primer3/src/primer3_lib.c | 2 +-
qclip/Makefile | 13 +
screen_seq/Makefile | 5 +
seq_utils/Makefile | 85 +-
seq_utils/align_lib.c | 225 +-
seq_utils/align_lib.h | 13 +-
seq_utils/dna_utils.c | 95 +-
seq_utils/dna_utils.h | 2 +-
spin/Makefile | 765 ++++
staden_config.h.in | 5 +
stops/Makefile | 1 +
system.mk.in | 2 +-
text_utils/Makefile | 4 +
tk_utils/Makefile | 174 +
tk_utils/func_edit.tcl | 25 +
tk_utils/help.tcl | 6 +-
tk_utils/init.tcl | 2 +
tk_utils/tclIndex | 2 +
tk_utils/xcombobox.tcl | 29 +-
tracediff/Makefile | 5 +
tracediff/main.cpp | 38 +-
vector_clip/Makefile | 5 +
168 files changed, 23391 insertions(+), 2508 deletions(-)
delete mode 100644 debian/patches/cope_with_modern_windowmanager.patch
delete mode 100644 debian/patches/delete_rpath_from_configure.patch
delete mode 100644 debian/patches/hardening.patch
delete mode 100644 debian/patches/hardening_format-security.patch
delete mode 100644 debian/patches/remove_svnversion_dep.patch
delete mode 100644 debian/patches/spelling.patch
create mode 100644 gap5/export_snps.c
create mode 100644 gap5/export_snps.h
create mode 100644 gap5/find_haplotypes.0.c
create mode 100644 gap5/find_haplotypes.c
create mode 100644 gap5/find_haplotypes.h
create mode 100644 gap5/gap_globals.tcl
create mode 100644 gap5/interval_tree.c
create mode 100644 gap5/interval_tree.h
create mode 100644 gap5/replay_log.tcl
create mode 100644 gap5/str_finder.c
create mode 100644 gap5/str_finder.h
create mode 100644 gap5/utlist.h
delete mode 100644 gap5/zfio.c
delete mode 100644 gap5/zfio.h
create mode 100644 tk_utils/func_edit.tcl
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