v291

Code changes:

• Fixed ajax code to be tolerant of ISPs that strip newlines from content (#11873). Tim
• Fixed a problem where hub assembly lists were not nicely wrapping on hub portal page (#11889). Tim
• Removed an invalid assert in Gene Haplotypes feature that assumed that if only one haplotype is found, it is the reference haplotype (#11894). Tim
• Rewrote some of makeTrackIndex: replaced mdb and cv access with the lib routines that are much more efficient (#11951). Tim
• Added MAF output in Table Browser for HAL data type (#10637). Brian
• Fixed a bug (and added tests)in pslOpen that would hang on files with only comments. Brian
• Tweaked GWAS otto scripts (#5172). Brian
• Changed "genes" field in gwasCatalog to a longblob from a varchar(255). Brian
• Added maxHours option to genbank load scripts. Currently set to 14 for testing. Brian
• Prioritized list of databases for the genbank process to load (most important ones first). Brian
• Fixed problem on genome-euro that was causing genbank loads to be v-e-r-y slow. Brian
• Made some modifications to support the fact that rrnfs1 is not binary-compatible with hgwdev. Brian
• Fixed Ensembl gene update procedure to properly detect if it's identical to previous version (#11675). Hiram
• Updated build system to automatically detect MySQL libraries and build environment (#11899 #9149). Hiram
• Fixed several bugs in anno* libs found by Case Western team (#11775, #11787). Angie & Jonathan.
• Tweaked search position for Artificial Example Variants (#11110). Angie
• Refined old kludge that affected DGV items at beginning of chrom in Table Browser (#11200). Angie
• Updated links to new Galaxy server from Table Browser (#11898). Angie
• Ongoing work to support HAL and halSnakes in assembly hubs including adding a chromosome color mode for HAL snakes (#10637). Brian

Data changes:

• Added XM, XR RefSeq Gene tracks on hgwdev (#11904). Brian
• Finished 100-way Conservation track documentation (#10272). Hiram
• Reloaded snp138 with allele frequency corrections, include 100% non-reference in Common (#11438, #11954). Angie