v292

Code changes:

• Fixed bug that was causing annoStreamDb.c to hang (#11988). Angie
• Fixed memory leak in bigBed.c. Angie
• Fixed exonFrames handling in gpFx.c (#11990). Angie
• Logic fix in hgTables/filterFields.c (#12077). Angie
• Set network default read write timeout for tcp connections to browser defaults of about 2 minutes. Applications can call the new function setReadWriteTimeouts on an open socket if they need them to be longer or shorter. Galt
• Fixed case where strand output in liftOver could be wrong when multiple flag was used with bed6 strands and it hit multiple chains (#12001). Galt
• Added IUPAC support to the oligoMatch utility (#12089). Galt
• Fixed the hgTables gtf-output frame column, at least for tables that have exonFrames column available like refGene and other genePredExt tables (#12107). Galt
• Fixed hgcentral fail over. For years fail over was looking for backupcentral.database instead of backupcentral.db which is what all of our configurations use (#11651). Galt
• Added support for display of motifs in Transcription Factor cluster track, and other factorSource type tracks; Added motif information section to hgc top panel; Added 'Motif display help' link to hgc motif panel; Added trackDb settings: 'motifTable' (localizations), 'motifPwmTable' (position weight matrices). (#9092) Kate
• Fixed bug in genePredCheck to recognize case sensitive chrom names (#11907). Hiram
• Updated build environment to fix bugs and use more static libraries (#11966, #12005). Hiram
• Started work on fixing bugs in source tree so that it can be build on new Mac OSX compiler (#12106). Hiram
• Updated OMIM auto-loading scripts to use new host. Brian
• Ongoing work to support HAL and halSnakes in assembly hubs (#10637). Brian
• More tweaking of Genbank parameters to align miRNAs correctly. Brian
• Genbank changes to support switch from rrnfs1 back to hgnfs1. Brian

Data changes:

• Switched to snp138 for auto-loading GWAS update. Brian
• Fixed allele frequency bug for snp138 (#11954). Angie