v266

Code changes:

• Moved copyright information from kent/src/README to kent/README since this is now the top level directory people check out. Jim
• Updated style guide section of kent/src/README. Jim
• Made programs to convert ENCODE cv.ra, metaDb table, and encodeExp table to a Django-managed database. Jim
• Created verticalSplitSqlTable utility program to help normalize (in the relational sense) the antibody information from ENCODE. Should be good for other databases too if the need ever comes up. Jim
• Created textBetween and replaceTextBetween command line utilities that let you extract or replace text between two strings. Jim
• Fix problem where context menu disappeared off the top of the screen (#7687). Larry
• Add a JSON parser (#6152). Larry
• Continuing work on geoMirrors (#3000). Larry
• Fix problem where bigBeds weren't being shown properly (#7272). Larry
• Disable inPlaceUpdate when either left or center labels are turned off (see #6944). Larry
• Change priorities for oligo and cutter track to ensure they appear after tracks which get the default of 100 (#7309). Larry
• Ongoing work on gpFx library to predict disruption of genePred given a variant (#6152). Brian
• Tweak to omim generation to avoid checking a field that changes dramatically between versions (#6943). Brian
• Variant annotation integrator: wig and VCF support, basic web UI, bugfixes (#6152). Angie
• Checked in cpgIslandExt code into the kent source tree and fixed up to compile in this environment. Hiram
• Updated the doCpgIslands.pl script to use kluster runs to get done much faster and handle high contig count assemblies. Hiram
• Created ENCODE Data Matrix: A new set of web pages that display a real-time summary of ENCODE datasets in tabular and matrix format (#5149). Kate
• Revamped validateFiles, bedToBigBed, hgLoadBed, and customTracks to use a shared validator routine. Also added support for BedPlus validation via .as files. Revamped help usage messages. Removed unneeded options and variables. Updated validateFiles tests. Now correctly tests that fields do not overflow invisibly, or contain trailing trash, and field strings do not overrun their size. Enforces the BED standard. Galt
• Added lineFileOnBigBed capability, now used by validateFiles to validate bigBeds directly. Galt
• Added library and utility routines to compare .as (autoSql) files. Galt
• MySQL Local Data Infile loading now checks for mysql warnings and treats them as errors by default. hgLoadBed (via jksql.c) to start checking for hg.conf flag so we can turn it on soon on the RR, to make sure there are no unanticipated problems with it. Galt

Data changes:

• Fixed /gbdb/oviAri1/oviAri1.2bit symlink to point to masked sequence (#7486). Chin
• Finished tRNA Genes track for mm10 (#7504). Chin
• Finished Naked mole-rat browser (hetGla1) (#4632). Chin
• GWAS Catalog update (#1656). Angie
• Ongoing work on mm10 UCSC genes (#7045). Brian
• Removed the old Merck PolyA-seq track from the trackDb of several genomes because it was confusing to have two (#2356). Andy
• Started browsers for Budgerigar: melUnd1, Manatee: triMan1, Painted Turtle: chrPic1, Tilapia: oreNil2, Armadillo: dasNov3, Pig: susScr3, Cat: felCat5, Dolphin: turTru2, Gibbon: nomLeu2, Naked Mole Rat: hetGla2. Hiram
• Fixed broken GRC Incident track processing
• Initial 60-way MAF for mm10. Hiram
• Added cpgIsland and Genscan tracks to fr3 browser. Hiram
• Added windowMasker track to hg19. Hiram