v296

Code changes:

• Fixed two Custom Track issues: detect and clear truncated bitmap files from the udcCache which would otherwise be stuck forever; Fixed a problem caused by a new glibc malloc policy in which a new heap is created per thread instead of per cpu. A hub with many visible tracks can use hundreds of threads, CGI can waste 15GB or more of RAM and rlimits on RR cause out-of-memory failures. The fix explicitly sets the maximum number of heaps to be shared by all threads. (#12743). Galt
• Fixed bug in lavToPsl that was clipping (#12727). Brian
• Fixed crash in multiWig if individual bigWig is not found (#12644). Brian
• Tweaked genePred reader to tolerate missing exon frames (#12674). Brian
• Fixed bug in bigWig summary calculations (#12558). Brian
• Ongoing work on Genome Browser in a Box (GBiB) including fixing bug in reading MAFs from stdin; fixing bug with lineFile seeks when on top of udc (#11957). Max, Brian
• Fixed bug in drag-highlight that caused the gene name auto-complete dialog to appear beneath hgTracks images (#12589, #12646). Tim
• Fixed a Mac-Safari specific bug in the right-click disable of drag-highlight (#12645). Tim
• Fixed a problem with custom track bed detail files (#12721). Kate
• Fixed problems identified by new gcc compiler on Mac OSX including fixing a javascript makefile install procedure to use rsync instead of cp (#12209). Hiram
• Allow hubs to use pennant icon (#12132). Pauline
• Made improvements to hgc and hgTrackUi to support non-human SNPs (#12490). Angie
• Improved the SNP pipeline for cow and pig (#12490). Angie
• hgLoadBed: when -type=bedN is given, and N < 9, don't assume itemRgb (+refactoring for broader checking of -type=bedN+P vs. actual field count). Angie
• Added missing NULL check in jksql.c. Angie

Data changes:

• Finished minimal browser for GRCh38, hg38 (#11681). Hiram
• Built liftOver from hg18 and hg19 to hg38 (#11681). Hiram
• Added Retroposed Genes v7 to hg19. Rachel
• Lifted GENCODE Genes from hg19 to hg38 (#12674). Brian
• Re-aligned mm10 genbank tracks with new alignment parameters. Brian
• Started work on mm10 UCSC Genes (#12639). Brian
• Started work on hg38 UCSC Genes (#10968). Brian
• Ongoing work on the Cooper Developmental Delay track for hg19 (#9391). Pauline
• Recomputed 100-way Conservation track on hg19 to fix three things: unusual gaps, frame table, Panda alignments (#12260, #12173, #12405). Hiram
• Completed 4-way Conservation track on hg38, including chains/nets to/from canFam3, rheMac3 and mm10 (#11681). Hiram
• Alphabetized all tracks on mm10, hg19 and hg38 browsers except for tracks that are on by default which appear first within each track group (#7343). Hiram
• Completed SNP track (v138) for mm10, bosTau7, galGal4, and susScr3 (#12490). Angie