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Commits : Listings

Analyzed about 7 hours ago. based on code collected about 7 hours ago.
Aug 22, 2024 — Aug 22, 2025
Commit Message Contributor Files Modified Lines Added Lines Removed Code Location Date
Continous tracks were failing to update because requested range differs from LocationController's range.
Eric Smith
More... over 13 years ago
Updated IGVTools code to 2.0.34. Updated Picard to 1.61.
Eric Smith
More... over 13 years ago
Updated IGVTools code to 2.0.34. Updated Picard to 1.61.
Eric Smith
More... over 13 years ago
Version string changed back to "beta".
Eric Smith
More... over 13 years ago
Fighting with svn.
Eric Smith
More... over 13 years ago
1000 Genomes plugin can now point to a root URL other than the default. Updated commons-net to 3.0.1. PluginController now actually calls shutDown() methods for all plugins.
Eric Smith
More... over 13 years ago
Fixed packing of reads when Scale to Fit is active.
Eric Smith
More... over 13 years ago
Divided variation package into core variation classes and Swing-specific variation classes. Implemented popups and selection for LDPlot.
Eric Smith
More... over 13 years ago
Divided variation package into core variation classes and Swing-specific variation classes. Implemented popups and selection for LDPlot.
Eric Smith
More... over 13 years ago
Arc mode now draws unpaired reads as black spikes with a loop on top.
Eric Smith
More... over 13 years ago
Added labels to allele frequency plot indicate which side is Control and which side is Case.
Eric Smith
More... over 13 years ago
Added scrollability to Allele Frequency Plot.
Eric Smith
More... over 13 years ago
When displaying a variant for a participant, made it clearer that the alleles are specific to the participant.
Eric Smith
More... over 13 years ago
Selecting a VariantRecord using a VariantPopup is now reflected in the Data Table.
Eric Smith
More... over 13 years ago
Allele frequency plot with Cases and Controls. Updated Data Table to cope with changes to VariantRecord.
Eric Smith
More... over 13 years ago
Proper saving/restoring of case/control flags. Popups for allele frequency plot.
Eric Smith
More... over 13 years ago
When running against a whole genome, GATK expects the .fai file to have valid offsets for all contigs listed in the BAM file's sequence dictionary.
Eric Smith
More... over 13 years ago
More meaningful exception when trying to get length of a nonexistent ref.
Eric Smith
More... over 13 years ago
Added dialog to allow user to specify case vs. control for allele frequency.
Eric Smith
More... over 13 years ago
Cancel button on Tool panel now kills the subprocess.
Eric Smith
More... over 13 years ago
Added participant-specific information to VariantPopup for VariantMap.
Eric Smith
More... over 13 years ago
Initial implementation of allele frequency display.
Eric Smith
More... over 13 years ago
Support for storing heterozygosity in variants. Not yet sure of the best way to represent it. Add Apache Commons Lang library to project.
Eric Smith
More... over 13 years ago
Tabix formatter was choking on blank lines when trying to create dictionary.
Eric Smith
More... over 13 years ago
Fasta exporter was creating .fai file with invalid offset values. Another long vs. int problem.
Eric Smith
More... over 13 years ago
Fix to avoid NullPointerException trying to get sequence for non-existent chrM. SNP and Strand SNP popups now indicate average base quality. When there is sufficient room, BAM tracks now render base letter in mismatches.
Eric Smith
More... over 13 years ago
Data Table is always loaded first so that it appears at the left of the plugin zone and at the top of the Plugins menu.
Eric Smith
More... over 13 years ago
Updating older plugins to 2.0 API.
Eric Smith
More... over 13 years ago
Removed some dead code.
Eric Smith
More... over 13 years ago
VariantTracks and VariationSheet both now honour resolution settings.
Eric Smith
More... over 13 years ago