File Changes for angie

v340_preview2 to v340_base (2016-10-10 to 2016-10-17) v340

• src/hg/hgVai/hgVai.c
  • lines changed 1, context: html, text, full: html, text
    7e6fe97d6d581f789137df6a01edb603954608c2 Fri Oct 14 10:18:19 2016 -0700
    hgVai's UI default for whether to match up input variants with dbSNP is true but the execution part's default was false -- making it consistent with UI default.
    
• src/hg/makeDb/doc/hg19.txt
  • lines changed 18, context: html, text, full: html, text
    a2658279f3ea3862ba38e92eb282b6c36e4dff3c Fri Oct 14 11:26:21 2016 -0700
    Build /gbdb/hg{19,38}/vai/snp147.bed4.bb so hgVai queries that include rs# ID aren't horribly slow. This should probably be incorporated into the dbSNP pipeline. refs #18222
    
• src/hg/makeDb/doc/hg38/variation.txt
  • lines changed 18, context: html, text, full: html, text
    a2658279f3ea3862ba38e92eb282b6c36e4dff3c Fri Oct 14 11:26:21 2016 -0700
    Build /gbdb/hg{19,38}/vai/snp147.bed4.bb so hgVai queries that include rs# ID aren't horribly slow. This should probably be incorporated into the dbSNP pipeline. refs #18222
    
• src/lib/vcf.c
  • lines changed 1, context: html, text, full: html, text
    254a0a6357dce9f6659ab9f9dd41553a881a0987 Tue Oct 11 09:22:56 2016 -0700
    As Belinda Giardine pointed out, VCF genotype indexes should be initialized in case they somehow slip through parsing. refs #18219