[med-svn] [staden] branch upstream updated (d9b0a40 -> a812461)
Andreas Tille
tille at debian.org
Thu Jul 14 18:29:36 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a change to branch upstream
in repository staden.
from d9b0a40 Imported Upstream version 2.0.0+b10
new 6604903 Imported Upstream version 2.0.0b11
new a812461 Imported Upstream version 2.0.0+b11
The 2 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 +-
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(-)
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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