v338

Code changes:

• Introduce search support for Human Genome Variation Society (HGVS) simple substitutions such as "c." (Ex. hg38 search: NM_007294.3(BRCA1):c.2231C>A) and "p." (Ex. hg38 search: NP_002993.1:p.Asp92Glu), and pseudo-HGVS (gene symbol and protein change, ex. hg38 search: BRCA1 Ala744Cys) as position/search terms (#15071). Angie
• Added GTEx gene expression to Gene Sorter in 3 columns: GTEx (expression), GTEX ID (ENS), and GTEX Delta (distance). The GTEx expression column is now the default expression column. GNF Atlas 2, is still available but not default (#17288). Kate
• Enhancements to address cross site scripting (XSS) concerns in warn and errAbort via new function htmlSafef, which encodes several cases including html, attribrute, css, js, url or none. The encoding approach is based on OWASP recommendations (#17815 #17782). Galt
• Added configuration option to GTEx track to display gene ID (ENS) and/or gene name to complement the new GTEx columns in gene sorter. Kate
• New cart variable (noWhiteout) to suppress whiteout surrounding GTEX track graph items (useful for screenshots with highlighting that extend through GTEx items). Kate
• New command-line tool, hgMaxExp, shows max and min score values in a BED15 (microarray) format table. Kate
• Parser and file schema for allele-specific expression data (GTEx Analysis Group; NY Genome Center). Kate
• Fix Gene Sorter crash when selecting genes with long descriptions (e.g. FSH on hg38) (#18002). Kate
• Enhance hgIntegrator for necessary call to initGenbankTableNames (#15071). Angie
• Enhance hgVai/dbSNP SO terms: made enum <==> string conversion more consistent (#17897, #17209). Angie
• Enhance checkTableCoords to find unrecognized sequence names for scaffold-based assemblies. Angie
• Fix hgGene links to PFAM (#15342). Jonathan
• Fix hgGene links to rat gene information to go to RGD instead of Ensembl on hg38 and mm10 (#14480). Jonathan
• Fixes to support refGene as a composite, and changes to htslib (#13673). Brian
• Added option to genePredToFakePsl to include RNA size file. Hiram
• Work toward making ncbiRefSeq track on hg38 a reality (#13673). Hiram
• New genePredToProt tool that translates genePred files to protein, which handles cases where there the annotations has frameshifting indels described in the exonFrames column. Partial codons will be skipped, this differs from getRnaPred, which only handles initial, incomplete codons. Mark
• Cache added for twoBit sequence header information for the last sequence accessed to avoid rereading, leading to 20% speedup for pslRecalcMatch. Mark
• Fix for compilation error with C99 style inline used by default by clang on OS/X. Mark
• CIRM: cdw - Added in a wrangler column to an existing SQL table in the cdw database, the column keeps track of who runs the cdwSubmit command. Chris
• CIRM: cdwCleanMetaData, removing columns with a single values and columns that are entirely duplicated (#17918). Chris

Data changes:

• Work on CRISPR tracks (#17235). Max
• GTEx allele-specific expression summary tracks in 53 tissues. Hosted on new UCSC-hosted public GTEx Analysis Hub (#17885). Kate
• Makedoc entry for dbSNP version 148 track on cow bosTau8 (#16846). Jonathan