v290

Code changes:

• Added db.neverLocal to hg.conf to help mirrors debug their mysql problems (#11733) Max
• Fixed a problem with Ubuntu and other systems where load data LOCAL infile has been disabled by default for mysql clients (#11733). Galt
• Improved mysql setup documentation regarding both setting the default storage engine to myisam and turning on local-infile in my.cnf. Galt
• Added information and links about mysql prevention in our coding standards in src/README (#9107). Galt
• Improved git-reports to handle white-space-only file changes better, and changed the plain-text extension from .diff to .diff.txt which works better with most browsers. Galt
• Improved paraFetch timeouts and retries. Galt
• Improved hdb.c and hgc to handle bed4 and bed9 when element has size=0 start==end such as a SNP insertion point (#7472). Galt
• Fixed a small problem with the sql-injection prevention code in hgTables which was producing messages in the error_log. Now it works properly and is secure. Galt
• Fixed a couple of small issues with the login code (#8293). Chin
• Added new options to pslCDnaFilter to ignore introns and repeat masked sequence (#7568). Brian
• Fixed bug in pslMap where mappings would be missed if multiple mapping alignments mapped to the same rangetree node (#7568). Mark
• Added support for version numbers in genbank tables (#5438). Brian
• Fixed bug in bigBed item search (bad allocation in bPlusTree code). Brian
• Ongoing improvements to the VAI: Added auto-generated example variants; now UI isn't hidden if there are no variant tracks in hubs/CTs; IE9 now keeps user's settings when back button is clicked (#11443, #11110). Angie
• Bug fixes to the VAI: off-by-one intron numbers, skipped rows in VCF, extra line-break in header under certain conditions, header wording tweak, URL correction. Angie
• Ongoing libs support for annoGrator: annoStreamVcf: internally sort indels and substitutions that appear at the same VCF base, because indels are actually one base to the right of their VCF base. In order to satisfy our internal sorting requirements, save indels aside until we see a record at a later VCF base (or EOF). Putting indels after substitutions at the same base satisfies both UCSC and VCF sorting constraints (#11787). Angie
• Ongoing libs support for annoGrator: gpFx.c: major restructuring to accommodate indels that span multiple exons/introns (#11771). Angie
• Ongoing work to support HAL and halSnakes in assembly hubs (#10637). Brian

Data changes:

• Started work on track for NCBI clinVar database (#10956). Max
• Data update for DGV: new composite track (#11200). Angie