Commits for angie

v377_preview to v377_preview2 (2019-01-21 to 2019-01-28) v377

f4dbc5c6e419491e0891ae0ee0a1b01261fbe6fb Wed Jan 23 17:49:25 2019 -0800

• Added GRCh38.p11 and p12 sequences to ENCODE Regulation tracks that are not visible by default (DNase HS, DNase Signal). refs #18855, #18853
  • src/hg/makeDb/doc/hg38/patchUpdate.11.txt - lines changed 106, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.12.txt - lines changed 93, context: html, text, full: html, text

6b0f0759060bdea5837b13dea9dc58ee6654f3de Thu Jan 24 12:28:43 2019 -0800

• Changing login.acceptIdx default to false, as I should have done 2 years ago. refs #17327
  • src/hg/lib/wikiLink.c - lines changed 2, context: html, text, full: html, text

7413e7df50cd60ee13b79af99c6acbbe09215530 Fri Jan 25 12:42:25 2019 -0800

• Accept VCF v4.3. We don't implement the full spec, but 1000 Genomes just released very simple VCF for GRCh38 that says it's v4.3 and we have to support them.
  • src/lib/vcf.c - lines changed 2, context: html, text, full: html, text

9d7ae21a4ce62a41658af847358a60be3bb6f742 Fri Jan 25 12:55:33 2019 -0800

• Adding patch sequence annotations to hg38 ncbiRefSeqGenomicDiff. refs #18853, #18855 notes 51, 53
  • src/hg/makeDb/doc/hg38/ncbiRefSeqGenomicDiff.txt - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/hg38/patchUpdate.12.txt - lines changed 24, context: html, text, full: html, text