File Release Notes and Changelog
Notes:
Gap5 1.1.2, April 3rd 2009
===========================
Features
--------
* The template display now sports a "Filter" button. This allows
certain types of data to be filtered in/out by mapping
quality, template consistency, whether it spans contigs and
whether single/paired.
(Future plans here include by ligation and/or instrument type.)
* The template display Y-mode of "stacking" should now be MUCH
faster when given deep data sets.
* Added the ability to select regions of a sequence or a reading
name from the contig editor so that cut and paste works. (From
the editor, but not into it yet.)
* The number of sequences in a contig is now displayed in the
contig selector and contig list windows.
Bug fixes / minor adjustments
-----------------------------
* The template display crosshair now correctly displays the Y
coordinate in the bottom status line.
* Fixed a bug in the consensus algorithm; the last base was
incorrect when the contig was 1 base longer than an exact
multiple of 1024bp.
* Sped up the Save Consensus command when dealing with many
contigs.
* Tweaked the Y-spread function of the template display so that
multiple sequences with both identical X and Y coordinates now
get spread apart.
* The contig editor now instantly displays the impact of making
insertions or deletions instead of only correctly displaying
all sequences on the next scroll.
* Fixed an issue of opening contigs when given a reading name
instead of a contig name.
* The contig editor sequence no longer vanishes temporarily when
scrolling the sequence names.
Changes:
2009-04-03 jkbonfield <jkbonfield@sanger.ac.uk>
* template_display.c:
(11:26:38) Added a filter dialogue to allow the template display to
be filtered by spanning, pair/single or mapping quality.
Adjusted the Y-spread function to also take into account an index
rather than purely X location. This means lines at the same X,Y
coordinate can now be spread too, making duplicated templates
easier to see.
Fixed Y x-hair so that the reported position in the information bar
is now the correct Y position.
* depth.tcl,
* template_display.h:
(11:26:39) Added a filter dialogue to allow the template display to
be filtered by spanning, pair/single or mapping quality.
Adjusted the Y-spread function to also take into account an index
rather than purely X location. This means lines at the same X,Y
coordinate can now be spread too, making duplicated templates
easier to see.
Fixed Y x-hair so that the reported position in the information bar
is now the correct Y position.
* gap.tcl:
(11:33:01) Bumped version to 1.1.2
* template_display.c:
(13:53:44) Fixed the Y crosshair value when using
separate-by-strands mode.
* template_display.c:
(14:05:24) Minor tweaks of out by one errors in Y xhair value.
2009-04-02 jkbonfield <jkbonfield@sanger.ac.uk>
* consen.tcl,
* newgap5_cmds.c:
(14:59:34) Sped up the consensus saving code substantially when
many contigs are output due to an over-zelous addition to the map
passed into string map; this ultimately made the code O(N^2) in
speed.
Added a new tcl_reformat_sequence command in C to convert binary
quality to fastq and to perform line-wrapping. This works around
locale issues and is faster to boot.
Fixed a bug in calc_quality that wrote out one more base than
desired.
* consensus.c:
(15:09:09) Fixed the consensus generation functions when passed a
sequence exactly 1 more than a multiple of 1024 long. Due to a < vs
<= the last base was uninitialised.
* contig_editor.tcl:
(15:11:10) Added clipboard copy for reading names, although at
present without any highlighting.
* tkEdNames.c:
(15:11:11) Added clipboard copy for reading names, although at
present without any highlighting.
* editor_view.c:
(15:12:35) Bug fixed copy(clipboard) of the consensus; it was out
by one sometimes.
* list_proc.tcl:
(15:12:52) Removal of debugging output.
2009-03-31 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_editor.tcl,
* editor_view.c,
* editor_view.h,
* tkEditor.c:
(16:29:54) Added selection (copy) handling for sequences and
consensus.
2009-03-27 jkbonfield <jkbonfield@sanger.ac.uk>
* editor_view.c:
(14:11:02) Fixed a bug with the display in the editor vanishing
whenever the names panel is scrolled.
2009-03-26 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_selector.tcl:
(11:16:16) Fixed searching of contig names via reading names.
* contig_id.tcl,
* gap4_compat.tcl:
(11:16:19) Fixed searching of contig names via reading names.
2009-03-25 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_selector.tcl,
* list_contigs.tcl:
(10:25:23) Now list the number of sequences in a contig.
2009-03-23 jkbonfield <jkbonfield@sanger.ac.uk>
* editor_view.c:
(16:05:46) Temporarily disabled the range caching code in
edview_visible_items as it cannot detect when data is changed (eg
inserting a base to the consensus => identical query range, but
sequences maybe shifted within that range).
* depth.tcl:
(16:09:19) The window title bar is now named after the contig being
displayed.
2009-03-20 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl:
(16:32:35) Small tweaks to make the depth plot work again (as I've
been mainly focusing on the template display).
Adjusted the default parameters for template display (scales,
separate strands now off).
* gap_canvas_box.tcl:
(16:33:35) Copied from gap4 and tweaked. Needed to support zooming
in the contig selector.
* tclIndex:
(16:33:57) *** empty log message ***
* template_display.c:
(16:36:26) Total rewrite of the compute_ypos packing algorithm.
This needs migrating back into tg_contig.c sometime. The new one
uses a pair of splay trees and is massively faster than before.
Adjusted the line width of reads when zoomed >= 150 in Y.
Restructured the plotting function to be more distinct between
querying, allocating Y and plotting. This is a precursor to caching
of data (so we can scroll in Y faster) and better scrolling.
* template_display.h:
(16:36:56) New "colours" (actually just GC line width change) for
fwd/rev.
2009-03-11 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl,
* template_display.c,
* template_display.h:
(17:06:33) Added cross-hairs
* gap.tcl:
(17:35:30) Version number update.
Instead of Gap v5.x.x the program is now called gap5 and has
version 1.x.x. Although a bit of a departure, it's more sane in
that we regain control of the major version number again.
* ng_fb_cmds.tcl:
(17:46:10) Removed the assumption of having a version code in
database names.
2009-03-10 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl,
* template_display.c,
* template_display.h:
(12:35:18) Added a sequence depth and template depth line
(optional). These need moving to their own raster or canvas, but
for now they're functional rather than elegant.
Fixed a bug with the xview coordinates. The raster plot was offset
by the contig start coordinate, so if it didn't start at zero
(clipped) it was shifted in X.
2009-03-09 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl,
* template_display.c,
* template_display.h:
(17:34:01) Ripped out the old canvas based template display code.
Added an init method of plots (implemented for template display)
and adjusted the layout slightly.
Improved (but still not completely fixed) X and Y zooming of plots.
Fixed template_display object "range" method call. It's now the
same coordinates worked out during plotting.
Added a (currently unused) xzoom mode to the template display
window to mirror the (currently used) yzoom control.
2009-03-05 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl,
* template_display.c,
* template_display.h:
(17:01:21) Improvements to the template display:
- background is now black so the reads are more vibrant and show up
easier with low depth data.
- Can separate out by template strand.
- Additional yoffset control used as an offset to the computed Y.
This allows bringing the two halves (when separated) closer or
further apart.
* depth.tcl,
* template_display.c,
* template_display.h:
(17:45:41) Added a control to filter out single ended data.
2009-02-26 jkbonfield <jkbonfield@sanger.ac.uk>
* template_display.c,
* template_display.h:
(12:13:29) Added a red colour for templates that have read-pairs in
inconsistent orientations.
2009-02-25 jkbonfield <jkbonfield@sanger.ac.uk>
* Makefile:
(13:59:35) Added template_display.o
* editor_view.c:
(14:00:46) Changes to sequence_get_position API.
* gap.tcl:
(14:01:09) Better error checking when given invalid DB to open.
* gap4_compat.c:
(14:01:29) Changes due to sequence_get_position API change.
* newgap5_cmds.c:
(14:02:27) Added call to TDisp_Init to register template display
additions.
* qualIO.c:
(14:02:46) Changes due to sequence_get_position API change.
* tman_interface.c:
(14:03:10) Changes due to sequence_get_position API change.
* contig_editor.tcl:
(14:04:01) Missing bracket? How did it work before.
* depth.tcl:
(14:04:53) Major overhaul to use raster widget instead and the new
template_display.c C code. The old canvas widget code is still
there intact, albeit not reachable right now.
This still needs a big tidyup.
* depth.tcl:
(15:30:13) Allow for the old canvas based template display to still
be viewed, so we can do mouse-overs etc. This is a temporary hack
to get a usable interface, but ultimately I'll probably end up
rewriting the raster method to be a canvas object so it can be
combined with canvas overlays and fits in with the rest of the
window.
2009-02-19 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl:
(14:57:13) Improved ways to colour and allocate Y positions to
sequences
2009-02-16 jkbonfield <jkbonfield@sanger.ac.uk>
* editor_view.c:
(16:59:13) The contig editor information line now shows data on
read-pairs if the read is paired.
* depth.tcl:
(16:59:56) Added an option to colour the template by mapping
quality. In this mode it doesn't draw the reads for paired data so
the template is more visible.
* gap.tcl:
(17:02:51) Bumped version to 5.0.2
2009-02-13 jkbonfield <jkbonfield@sanger.ac.uk>
* consensus.c:
(16:31:47) Updated calls to contig_seqs_in_range due to argument
changes.
* read_depth.c,
* tkEdNames.c:
(16:31:48) Updated calls to contig_seqs_in_range due to argument
changes.
* contig_editor.tcl:
(16:32:59) Added GUI options for packing multiple sequences per
line.
* depth.tcl:
(16:34:08) Implemented a template Y allocation system similar to
Magnus Manske's plots, where the Y position is based on the size of
insert.
Added some rudimentary GUI controls for this too.
* editor_view.c,
* editor_view.h:
(16:36:06) We now cache the last read rangec_t structs from
contig_seqs_in_range rather than requerying every time the cursor
moves.
Implemented a rough draft of stacking multiple sequences per line.
For now this only works for display and the cursor coordinates do
not function correctly. It also needs the names display removing
too to be sensible.
* tkEditor.c:
(16:36:50) Added -stripe_mode and -stack_mode options. (For use in
the experimental multiple sequences per line mode.)
* tkEditor.h:
(16:36:51) Added -stripe_mode and -stack_mode options. (For use in
the experimental multiple sequences per line mode.)
2009-02-06 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl:
(16:05:25) Improved display of inconsistent templates, so reads and
templates show up differently (may need to fix colours!).
Fixed a bug with ordering of elements in lines sometimes giving tcl
errors.
2009-02-05 jkbonfield <jkbonfield@sanger.ac.uk>
* depth.tcl:
(10:21:44) Changes to the template display following the sequence
and bin/range structure changes.
We now have an accurate and approximate mode. Both need MUCH less
I/O than before, but approximate mode saves further I/O by not
bothering to work out whether the other end of a template, which is
not observed on screen, is in this contig and if so whether it is
to the right or left of the sequence we did observe.
* editor_view.c:
(10:22:13) Changed edGetTemplateReads to use the new
sequence_get_pair function.
* break_contig.c,
* break_contig.h,
* editor_join.c:
(10:29:57) Split break_contig into its own, more appropriately
named, file.
* Makefile:
(10:30:32) Added break_contig.o
* newgap5_cmds.c,
* read_depth.h:
(10:31:03) Minor warning fixes for undefined vars, prototypes, etc.
* break_contig.c:
(17:22:38) Added a bin_invalidate_track() function.
In the course of this discovered and fixed a bug where the track
valid flag was not being set or checked for correctly.
2009-01-28 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_id.tcl,
* contig_selector.tcl,
* gap4_compat.tcl:
(11:19:08) Improvements to contig_id handling. We now accept contig
name, #seq_num and =contig_num. TODO: support reading name too for
when contig name fails.
* gap.tcl:
(12:42:12) Bumped version to 5.0.2
2009-01-27 jkbonfield <jkbonfield@sanger.ac.uk>
* editor_join.c:
(17:12:22) An incomplete update to join contigs (#if-ed out for
now) to determine the optimal bin to reparent, rather than always
duplicating the root node. This will reduce average depth when
making small containment joins.
2009-01-26 jkbonfield <jkbonfield@sanger.ac.uk>
* editor_join.c:
(10:29:52) Improved break contig: It no longer creates new blank
bins for the right hand contig when they are unnecessary.
* editor_join.c:
(16:05:59) More break contig tweaks. We now remove redundant bins
from both left and right contig after breaking.
2009-01-23 jkbonfield <jkbonfield@sanger.ac.uk>
* editor_join.c:
(12:05:08) Bug fixes for break contig.
2009-01-08 jkbonfield <jkbonfield@sanger.ac.uk>
* editor_join.c:
(14:05:48) Bug fix in break_contig_reparent_seqs: we no longer die
when finding a bin with no Range data.
* gap_hash.c:
(14:06:29) Protect against a match in find repeats extending 1 past
the end of the sequence. I'm not sure why this occurs, but at least
we handle the problem gracefully now.
* tk-io-reg.c:
(14:07:18) Removed a heinous programming crime of returning the
address of a local variable.
This fixed the crosshairs in the contig selector/comparator window.
* contig_editor.tcl:
(14:22:05) Added temporary fix to shut down the contig selector
when making a join. It's not what I want to do, but it works around
the bug (and crash) that I'm not yet sending the appropriate
notifications to force the plots to update upon a join.
Will revert this when that code is in place.
* contig_editor.tcl:
(14:32:11) Fixed the window title to display the contig name(s).
* editor_join.c:
(14:32:44) When splitting contigs we now name the newly produce
right-hand side contig with a derived name (#1, #2, etc).
* contig_id.tcl,
* contig_selector.tcl:
(14:50:26) Improvements to the contig selector / id UI components.
We still need more work here to support #read_num and =contig_num,
but for that to work we need a way of validating them first.
2009-01-07 jkbonfield <jkbonfield@sanger.ac.uk>
* Makefile:
(11:26:57) Huge tidyup - more Gap5 now than a hacked gap4
* consen.c,
* consen.h,
* fij.c,
* find_repeats.c:
(11:30:54) make_consensus() now allocates memory for the consensus
itself, rather than relying on something passed in. This removes
the need to use a max_consensus parameter.
* contig_editor.tcl:
(11:31:23) Now shutdowns the editor windows after a join.
* contig_selector.tcl:
(11:31:56) Bug fixes to zooming and scrolling.
* editor_join.c,
* newgap5_cmds.c,
* newgap_structs.h:
(11:32:58) Added first draft of the Break Contig function.
* tk-io-reg.c:
(11:33:42) Fixed parsing in the reg_init_args function. This fix is
part of the contig selector zooming/scrolling bug fixes.
* list_contigs.tcl:
(11:34:05) *** empty log message ***
* list_proc.tcl:
(11:34:24) gap_defs vs gap5_defs changes
* tclIndex:
(11:34:43) Added result_manager.tcl
* editor_view.c:
(12:27:24) Make sure we always set xx->link->lockOffset in
set_displayPos for a join editor, even if lock is turned off.
This fixes a bug in the join editor where turning off lock,
scrolling, not hitting "align" and then hitting "join" will result
in the incorrect join as it uses the starting lock offset instead
of the current visible one.
* editor_view.c:
(15:15:31) Better error checking in the status line updates.
* editor_join.c:
(15:16:19) Fixed break contig: when sequences were moved from one
bin to another bin I forgot to edit the sequence itself to relink
the bin pointer to the new parent.
2008-12-09 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_selector.tcl,
* tclIndex:
(12:48:23) Moved GetItemInfo from template_display.tcl (not used)
to here.
* depth.tcl:
(12:49:13) Split the GUI dialogue into separate template displays
and reading depth plots.
* gap_utils.tcl:
(12:49:42) New utility function "counter". Used for generating
unique window names.
2008-12-03 jkbonfield <jkbonfield@sanger.ac.uk>
* consensus.c,
* contig_editor.tcl,
* editor_view.c:
(12:08:05) Modified the sequence_*_base() functions to take an
extra argument named contig_orient. This controls whether we wish
to make this change in the orientation that the sequence resides
within the contig (requiring a bin traversal) or whether we already
know and have taken that into account (such as from a former
contig_seqs_in_range query).
This allowed for multiple bug fixes relating to insertion/deletion
of bases in the contig editor both within sequences and the
consensus.
* editor_view.c:
(12:22:03) Fixed '%b' brief format (base call).
2008-12-02 jkbonfield <jkbonfield@sanger.ac.uk>
* consen.tcl:
(12:32:30) Removal of debugging output.
Added close of fd in get_consensus.
* consensus.c:
(12:33:45) Removal of now unnecessary complementing code (see
tg_contig.c changes).
Bug fix to consensus_valid_range (param cons).
* contig_selector.c:
(12:34:19) Added header files.
* Attic/dependencies:
(12:34:33) *** empty log message ***
* editor_join.c:
(12:35:33) Update 'offset' based on reach contig_offset value too.
Now also destroys the contig properly.
* editor_view.c:
(12:36:14) Changed arguments to sequence_get_position. Removed
complementing code (see tg_contigs.c change).
* fij.c:
(12:36:57) Now corrects for start positions of the editor; does not
assume starts as bp 1.
* find_repeats.c:
(12:37:12) Added include file.
* gap4_compat.c:
(12:37:44) sequence_get_position() arg changes.
Implemented complement_contig function.
* gap4_compat.h:
(12:37:56) Implemented complement_contig function.
* newgap5_cmds.c:
(12:38:16) Implemented complement_contig function.
* qualIO.c:
(12:38:36) sequence_get_position arg changes.
* read_depth.h:
(12:38:54) Added avg_sequence_depth prototype.
* tman_interface.c:
(12:39:12) sequence_get_position arg changes.
* Attic/dependencies:
(12:41:58) *** empty log message ***
* editor_join.c,
* gap4_compat.c:
(17:29:06) Adjusted the positioning of contig offsets so that the
offset is applied verbatim regardless of orientation of the root
bin. The root bin's position element itself can be used to move
contigs around (ie change the numbering start) instead of the
contig start/end records.
2008-11-25 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_editor.tcl:
(10:01:36) Added a Join button.
The save/cutoffs/quality buttons now apply to both editors when in
join editor mode.
The curr_editor variable is now updated when clicking on another
editor (also in join editor mode).
Fixed the mouse-over text display for the names window.
* editor_join.c,
* editor_view.h,
* tkEditor.c:
(10:02:34) Implemented the edJoin() function and the tkEditor
"join" sub command. Tested and we successfully made our first
join. Yay! Next up, complemented joins.
2008-11-24 jkbonfield <jkbonfield@sanger.ac.uk>
* consensus.c,
* consensus.h:
(10:09:58) New function: consensus_valid_range()
This looks at the cutoff data to work out where the "used" extents
of the contig are rather than the absolute sizes of the contig bins
including cutoffs.
* fij.c,
* find_repeats.c:
(10:18:18) Fixed calls to edit_contig and join_contig. These now
also specify the position in contig to display.
* gap4_compat.c:
(10:19:35) lget_contig_num now returns the default contig range as
the true start and end coordinates rather than 1 to 'length'.
* tclIndex:
(10:19:46) Added join_contig
* tkEditor.c:
(10:20:24) New sub-commands: link_to, lock and join_align. For the
join editor.
* tkEditor.h:
(10:20:39) *** empty log message ***
* Makefile,
* editor_join.c:
(10:24:05) New file: editor_join.c. This is derived from Gap4's
join.c and consists of functions for the Join Editor to implement
the align and join buttons.
* contig_editor.tcl,
* editor_view.c,
* editor_view.h:
(10:24:47) Major works to support the Join Editor.
Removed defunct and commented out calc_cons() call.
Fixed bug in status line display of quality values.
Fixed bug in X scrollbar position - if now compensates for contig
start being negative (cutoff data) so user scrolled position and
displayed position match.
Allowed for editor to be started up with the cursor at a specified
read and position.
2008-11-17 jkbonfield <jkbonfield@sanger.ac.uk>
* tk-io-reg.c:
(11:59:58) Fixed a bug in argument parsing within tcl_quit_displays
* fij.c:
(16:40:29) *** empty log message ***
* depth.tcl:
(16:40:48) Fixed Y scrolling (produced Tk error)
* consensus.c:
(16:41:11) Fixed uninitialised data for zero-depth regions.
2008-11-13 jkbonfield <jkbonfield@sanger.ac.uk>
* read_depth.c,
* read_depth.h:
(17:08:08) *** empty log message ***
2008-11-11 jkbonfield <jkbonfield@sanger.ac.uk>
* Makefile:
(15:12:13) Fixed Makefile to not use ~jkb/work/tgap for the tgap
source - it now correctly uses the Staden local copy. Oops
* trace_display.tcl:
(15:12:55) Protect against trace titles containing dots, which
previously broke the tk pathnames being generated.
2008-10-24 jkbonfield <jkbonfield@sanger.ac.uk>
* consensus.c:
(09:05:18) Added depth to the consensus struct per base.
Improved support for utilising all 4 confidence values when
available.
Bug fixed some edge cases, such as zero depth regions.
* consensus.h:
(09:05:31) Added depth to the consensus struct per base.
* contig_editor.tcl:
(09:06:24) The status line updates quality information on keyboard
cursor movements now as well as mouse over events.
* editor_view.c:
(09:07:48) The editor "brief" status line format has been updated
to support reporting all 4 confidence values for a sequence base
call.
* gap4_compat.c:
(09:08:23) contig_name_to_number now uses contig_index_query for
btree scanning rather than a brute force search.
* newgap5_cmds.c:
(09:10:06) New function: tcl_sequence_depth, doing pretty much what
you expect.
Start of tcl_find_internal_joins interface. Incomplete right now.
tcl_calc_consensus_full now reports sequence depth too, incase
you're already calculating the consensus anyway.
2008-10-03 jkbonfield <jkbonfield@sanger.ac.uk>
* gap4_compat.c:
(16:23:56) Fixes in get_contig_num. (Done so long ago I forget what
the reasoning was - sorry!)
* fij.c,
* fij.h,
* fij.tcl,
* newgap_structs.h:
(16:25:46) Added Find Internal Joins function.
* depth.tcl,
* tclIndex:
(16:26:50) Added the first draft of a read-depth and template
display. Also tidied up the menus to remove most of the unused
functions somewhat.
* depth.tcl:
(17:56:15) Removed broken bits from the entry dialogue. The window
doesn't yet support multiple contigs anyway.
2008-08-29 jkbonfield <jkbonfield@sanger.ac.uk>
* gap.tcl:
(14:58:13) Removed requirement of database name being
"dbname.version".
2008-08-26 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_editor.tcl,
* tkEditor.c:
(13:30:43) Added an "edits_made" sub-command of the editor. This is
used to implement a warning on editor exit to ask if changes should
be saved.
Also fixed an error with a callback when highlighting non-sequence
objects in the names panel.
2008-08-20 jkbonfield <jkbonfield@sanger.ac.uk>
* Makefile:
(15:49:22) Tidyup to support tgap library being part of the staden
build system now.
* contig_editor.tcl:
(15:50:59) Made the contig editor using a child io for editing in.
The save button now works.
(Previously save/exit did the same thing as we edited the live io
instead of child io.)
* gap.tcl:
(15:51:49) Minor tweaks to replace gap4 with gap5 in strings,
functions and version (gap v5.00 now)
* tkEditor.c:
(15:52:29) Added Editor class save sub-command.
2008-07-14 jkbonfield <jkbonfield@sanger.ac.uk>
* consensus.c:
(15:38:06) Fixes to the consensus algorithm for solexa reads -
specifically calling gaps.
* contig_editor.tcl:
(15:39:22) Added more use of tg_tcl's interfaces - we can now move
reads around and insert/delete bases within readings (not just the
consensus).
2008-06-27 jkbonfield <jkbonfield@sanger.ac.uk>
* consensus.c:
(16:23:43) Improved the consensus algorithm to handle pads. For now
all pads score a fixed amount and we compare them against bases
(any type) also at a fixed score. Having done that we then compute
the base-score from non-pad bases as before, factoring in the
probability of the base even existing right at the end.
These fixed costs of overcall/undercall are reasonable for solexa
where such errors are due to PCR and not related to the data
quality.
For capillary data we need more work to pick appropriate costs.
* contig_editor.tcl:
(16:29:06) Added keybinding to use the new contig insert and delete
base method. (Used for inserting columns of pads.)
2008-05-30 jkbonfield <jkbonfield@sanger.ac.uk>
* contig_editor.tcl,
* editor_view.c,
* editor_view.h,
* tkEditor.c:
(14:22:00) Added code to support read-pair data. For now this is
just the right mouse click in the editor's read name as a proof of
concept.
Fixed the "is the cursor visible?" code too so set X first, fixing
an error in working out the Y display point.
2008-05-27 jkbonfield <jkbonfield@sanger.ac.uk>
* consen.tcl:
(16:25:11) Added code for Gap4's main output consensus function.
Right now it's in simple mode only with no marking or masking.
Formats supported are fastq and fasta, with experiment file to
follow maybe.
* contig_editor.tcl,
* editor_view.c,
* tkEditor.c,
* tkEditor.h:
(16:28:21) Added display of mapping quality to the read-name
section.
2008-05-22 jkbonfield <jkbonfield@sanger.ac.uk>
* consen.tcl,
* consensus.c,
* qual.tcl:
(10:25:34) Implemented a new consensus algorithm using log-odds
scores.
* consensus.h:
(10:25:35) Implemented a new consensus algorithm using log-odds
scores.
* Makefile:
(10:26:40) *** empty log message ***
* contig_editor.tcl:
(10:27:55) Changed the mouse highlight on bases to use
BASE_BRIEF_FORMAT[12] instead of the READ_BRIEF_FORMAT format
string.
* editor_view.c,
* editor_view.h:
(10:30:26) Make use of the new consensus algorithm, which gives
quality values so we can now grey-scale the consensus too.
Improved the "brief" status line support, adding a new
edGetBriefCon for consensus status info too.
* qual.c,
* tkEditor.c:
(10:30:30) Make use of the new consensus algorithm, which gives
quality values so we can now grey-scale the consensus too.
Improved the "brief" status line support, adding a new
edGetBriefCon for consensus status info too.
* newgap5_cmds.c:
(10:32:08) Added in List Consensus Confidence and List Base
Confidence functions (the latter still needs major bug fixes
though).
* qualIO.c:
(10:32:09) Added in List Consensus Confidence and List Base
Confidence functions (the latter still needs major bug fixes
though).
* gap.tcl:
(10:32:44) Temporary hack to change maxseq until I update the code
to automatically derive it.
2008-05-12 jkbonfield <jkbonfield@sanger.ac.uk>
* IO.h,
* IO2.h,
* Makefile,
* actf.c,
* actf.h,
* active_tags.c,
* active_tags.h,
* complement.h,
* consen.c,
* consen.h,
* contig_editor.tcl,
* contig_id.tcl,
* contig_selector.c,
* contig_selector.h,
* contig_selector.tcl,
* cs-object.c,
* cs-object.h,
* Attic/dependencies,
* editor_view.c,
* editor_view.h,
* extract.h,
* find_repeats.c,
* find_repeats.h,
* find_repeats.tcl,
* fort.h,
* gap-dbstruct.h,
* gap-error.c,
* gap-error.h,
* gap-if.h,
* gap-tcl.h,
* gap.tcl,
* gap4_compat.c,
* gap4_compat.h,
* gap4_compat.tcl,
* gap_cli_arg.h,
* gap_globals.c,
* gap_globals.h,
* gap_hash.c,
* gap_hash.h,
* gap_utils.tcl,
* hash_lib.c,
* hash_lib.h,
* init.c,
* io-reg.h,
* io_handle.h,
* io_utils.h,
* jog.tcl,
* list.h,
* list_contigs.tcl,
* list_proc.c,
* list_proc.h,
* list_proc.tcl,
* newgap5_cmds.c,
* newgap_cmds.h,
* newgap_structs.h,
* ng_fb_cmds.tcl,
* notedb.c,
* notedb.h,
* qual.c,
* qual.h,
* qualIO.c,
* qualIO.h,
* qualP.h,
* search.tcl,
* sendto.tcl,
* stack_dump.c,
* stack_dump.h,
* tag_checklist.tcl,
* tagdb.c,
* tagdb.h,
* tclIndex,
* template_display.tcl,
* tk-io-reg.c,
* tk-io-reg.h,
* tkAppInit.c:
(11:26:37) Try v2. Initial checkin of gap5 source. Note this
requires the tgap source too, which will be added soon. (It
currently exists in Sanger's own SVN repository.)
* tkEdNames.c,
* tkEdNames.h,
* tkEditor.c,
* tkEditor.h,
* tman_display.c,
* tman_display.h,
* tman_interface.c,
* tman_interface.h,
* trace_display.tcl:
(11:26:38) Try v2. Initial checkin of gap5 source. Note this
requires the tgap source too, which will be added soon. (It
currently exists in Sanger's own SVN repository.)
* contig_editor.tcl,
* contig_id.tcl,
* gap.tcl,
* gap4_compat.tcl,
* ng_fb_cmds.tcl,
* select_contig.tcl:
(16:11:41) Minor tweaks to tidy up gap5 distrib.
* tk-io-reg.c:
(16:11:42) Minor tweaks to tidy up gap5 distrib.
