[med-svn] [staden] 04/08: Merge tag 'upstream/2.0.0b11'
Andreas Tille
tille at debian.org
Thu Jul 14 18:29:35 UTC 2016
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tille pushed a commit to branch master
in repository staden.
commit 3ef11e2a008a1eb2b18d517f11250fa6e75edc08
Merge: b343277 6604903
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 14 20:06:48 2016 +0200
Merge tag 'upstream/2.0.0b11'
Upstream version 2.0.0b11
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 +-
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 +
157 files changed, 23382 insertions(+), 2264 deletions(-)
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