Commits for angie

v391_preview to v391_preview2 (2019-11-11 to 2019-11-18) v391

3d835ba54509284ec08b63dc527bd114c9467afc Tue Nov 12 10:55:41 2019 -0800

• Update counts of diffMajor, refIs{Minor,Rare,Singleton}, freqNotRefAlt after fixing VCF allele normalization in dbSnpJsonToTab. refs #23283
  • src/hg/makeDb/trackDb/human/dbSnp153Composite.html - lines changed 10, context: html, text, full: html, text

b49e61be4ad54a46e01be904fa8a8985e9850f0d Tue Nov 12 12:27:30 2019 -0800

• dbSnp153: add a bigBed4 subtrack of coordinate ranges for mappings that we dropped due to inconsistent SPDI. refs #23283 Overall counts increased because we used to bail on an entire variant when we discovered an inconsistent SPDI, losing some valid mappings. Now we go through all mappings, and the bad ones are stored instead of dropped.
  • src/hg/makeDb/doc/bigDbSnp.txt - lines changed 44, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/dbSnp153Composite.html - lines changed 46, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 45, context: html, text, full: html, text
  • src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c - lines changed 94, context: html, text, full: html, text
  • src/hg/utils/automation/doBigDbSnp.pl - lines changed 77, context: html, text, full: html, text

54452ec022a6073410955c04e110a1784f71fb57 Wed Nov 13 17:37:34 2019 -0800

• dbSnp153: add new ucscNote otherMapErr for mappings with the same rs# as a mapping w/inconsistent SPDI in BadCoords/Map Err subtrack. refs #23283
  • src/hg/inc/bigDbSnp.h - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/bigDbSnp.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/hui.c - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/bigDbSnp.txt - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/dbSnp153Composite.html - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 18, context: html, text, full: html, text
  • src/hg/snp/checkBigDbSnp/checkBigDbSnp.c - lines changed 65, context: html, text, full: html, text
  • src/hg/utils/automation/doBigDbSnp.pl - lines changed 9, context: html, text, full: html, text

fe90471e3c0b3556be22777fc6ff9ff3c0f4ea7f Thu Nov 14 11:29:24 2019 -0800

• dbSnp153Composite minor tweak: move detailsTabUrls from top level to view level. refs #23283
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 3, context: html, text, full: html, text

2735c94211fbf200b2aaf0d349c4f5ceb74fe633 Thu Nov 14 14:48:08 2019 -0800

• hg38 finally gets 1000Genomes Phase 3 Variants, yay! refs #21805
  • src/hg/makeDb/doc/hg38/variation.txt - lines changed 41, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/tgpPhase3.html - lines changed 133, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 10, context: html, text, full: html, text

bcd29eb2ea0e1cddcc525174445423f712c9d377 Fri Nov 15 10:23:50 2019 -0800

• Typo in type declaration, doh.
  • src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)