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Analyzed about 11 hours ago. based on code collected about 11 hours ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Aug 17, 2024 — Aug 17, 2025 Showing page 4 of 61 Search / Filter on:
Fixes to rendering of special cases of hanging reads. Support for 'X' and '=' in cigar strings.	Eric Smith	More...				over 13 years ago
Glitch where displaying a GFF popup would subsequently suppress the Group/Attributes column in the data table.	Eric Smith	More...				over 13 years ago
Now correctly retrieves blocks and thickness for GFF and GTF genes which are partially off-screen. Improved display of GFF3 and GTF attributes in popup.	Eric Smith	More...				over 13 years ago
YAOB1E for blocks in BED files. NullPointerException rendering GFF file because name is null.	Eric Smith	More...				over 13 years ago
if Windows use Xerto L&F	Andrew Brook	More...				over 13 years ago
Tweaks to make Linux version run with latest version of JIDE.	Eric Smith	More...				over 13 years ago
Oops. Commented out copyBuiltinPlugins while debugging tool plugins and forgot to uncomment it.	Eric Smith	More...				over 13 years ago
2.0.1 installers.	Eric Smith	More...				over 13 years ago
Miško's ArrayIndexOutOfBoundsException when rendering Strand SNP mode with a deletion at the end of a read.	Eric Smith	More...				over 13 years ago
Small rendering settings	Marc Fiume	More...				over 13 years ago
Added (unnecessary) repaint after dismissing Case/Control dialog, for Linux. Now sets reference properly when selecting using a popper from the variant module.	Eric Smith	More...				over 13 years ago
Now have scroll-bar when "No data in range" or LD plot is being displayed. Fixed race condition involving "Calculating Linkage Disequilibrium" progress-bar.	Eric Smith	More...				over 13 years ago
Variant track now renders all variants at least one pixel wide, to keep them from being anti-aliased to invisibility.	Eric Smith	More...				over 13 years ago
Now renders VariantType.OTHER in grey, rather than throwing an exception. Recognises SNPs with long ALT strings in files created by vcf-merge.	Eric Smith	More...				over 13 years ago
LD calculation revised to work correctly with both phased and unphased data.	Eric Smith	More...				over 13 years ago
Moved LD calculation into worker thread and added progress-bar. Added preferences to control maximum number of loci for LD calculation.	Eric Smith	More...				over 13 years ago
Suppress some labels which Marc found unattractive.	Eric Smith	More...				over 13 years ago
Changed title for unsaved projects to avoid implying that they've actually been saved (reported by Dario).	Eric Smith	More...				over 13 years ago
Fixed NullPointerExceptions in Allele Frequency plot and variant popups. Projects can now be saved while the "Creating track…" progress-bar is up.	Eric Smith	More...				over 13 years ago
Fixed NegativeArrayIndexSize when opening VCF with no participant columns.	Eric Smith	More...				over 13 years ago
If Tool output is a BAM file, it should just be opened (and not formatted).	Eric Smith	More...				over 13 years ago
Tools can now use <download> tag to specify auxiliary files which need to be downloaded as part of the install.	Eric Smith	More...				over 13 years ago
Plugin Repository browser now shows description and optional web-site link.	Eric Smith	More...				over 13 years ago
Initial check-in of two sample tool plugins.	Eric Smith	More...				over 13 years ago
Fixed bug accessing UCSC tables which used to be one-table-per-chromosome but (apparently) are no longer so.	Eric Smith	More...				over 13 years ago
UCSC Explorer and ToolSettingsPanel now do better job of laying out their content when main window is resized.	Eric Smith	More...				over 13 years ago
Mismatches sometimes incorrectly indicated for arc-mode reads (i.e. the two reads which appear hanging off the current arc).	Eric Smith	More...				over 13 years ago
"Deletion" and "Insertion" were swapped in PileupRecord.NUCLEOTIDE_NAMES.	Eric Smith	More...				over 13 years ago
Fixed some problems with VCF export from the Data Table.	Eric Smith	More...				over 13 years ago
WikiPathways - Updated version number	Andrew Brook	More...				over 13 years ago

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