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Commits : Listings

Analyzed 4 months ago. based on code collected over 3 years ago.
Dec 18, 2019 — Dec 18, 2020
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Improved display of inconsistent templates, so reads and templates show up differently (may need to fix colours!).
jkbonfield
More... about 15 years ago
Added a bin_invalidate_track() function.
jkbonfield
More... about 15 years ago
Removal of excessive debugging output
jkbonfield
More... about 15 years ago
Minor warning fixes for undefined vars, prototypes, etc.
jkbonfield
More... about 15 years ago
Added break_contig.o
jkbonfield
More... about 15 years ago
Split break_contig into its own, more appropriately named, file.
jkbonfield
More... about 15 years ago
Changed edGetTemplateReads to use the new sequence_get_pair function.
jkbonfield
More... about 15 years ago
Changes to the template display following the sequence and bin/range structure changes.
jkbonfield
More... about 15 years ago
Updated maq, baf and plain .aln format parsers to cope with the new sequence and bin/range structures.
jkbonfield
More... about 15 years ago
Updates for the contig interface: new dump_ps command; the sequences in range command now returns more data, related to the pairing.
jkbonfield
More... about 15 years ago
Changed the format of the on-disc GT_Seq, GT_Bin and GT_Range structures. NB: *INCOMPATIBLE* file format with previous release.
jkbonfield
More... about 15 years ago
Fixed a bug when working with derived GapIOs. We were often returning a HacheItem from the base GapIO, but then incrementing the reference count in the derived GapIO. We always use the same one now (plus HacheTable checks for consistency of such things too to spot similar bugs).
jkbonfield
More... about 15 years ago
Enabled the bin-prediction code in bin_for_range. Also some small tidy-ups regarding reference counts.
jkbonfield
More... about 15 years ago
Support for maq files with no reference sequence; minor allocation change
jkbonfield
More... about 15 years ago
Added protection against HacheItems being passed into the wrong HacheTable (as this happened in practice due to a bug).
jkbonfield
More... about 15 years ago
removed unused variable
jkbonfield
More... about 15 years ago
Minor prototype fixes
jkbonfield
More... about 15 years ago
Bumped version to 5.0.2
jkbonfield
More... over 15 years ago
Added (currently commented out) bin-estimation code in bin_for_range. It's disabled as I'm not 100% sure it's infalible and it didn't gain as much speed as I hoped. Possibly room for future work though.
jkbonfield
More... over 15 years ago
Protect against no contig_order array in gio_read_contig.
jkbonfield
More... over 15 years ago
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.
jkbonfield
More... over 15 years ago
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.
jkbonfield
More... over 15 years ago
More break contig tweaks. We now remove redundant bins from both left and right contig after breaking.
jkbonfield
More... over 15 years ago
Improved break contig: It no longer creates new blank bins for the right hand contig when they are unnecessary.
jkbonfield
More... over 15 years ago
Bug fixes for break contig.
jkbonfield
More... over 15 years ago
Added a postscript contig output function. It doesn't auto-scale yet, but that's relatively straight forward to manually edit in the ps file afterwards.
jkbonfield
More... over 15 years ago
Updated the Array struct to use size_t, matching the copy in Misc (yes I know, multiple variants is asking for trouble).
jkbonfield
More... over 15 years ago
Fixed some uninitialised memory accesses in the banded version of affine_align_bits. It's possible other variants of this alignment algorithm may also be affected, but they're all subtly different so until I can observe them dying in valgrind I haven't applied the fix elsewhere for fear of introducing new bugs.
jkbonfield
More... over 15 years ago
Correctly handle colours containing spaces during use of Tcl_Eval. Eg "pale turquoise" is now sent as a Tcl list element instead of two arguments. It's not perfect as a colour name with brackets will break things, but it's sufficient.
jkbonfield
More... over 15 years ago
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.
jkbonfield
More... over 15 years ago