Commits for angie

v389_preview to v389_preview2 (2019-09-30 to 2019-10-07) v389

b7cb97d2942575d92f6385055e172dcbd979ee05 Tue Oct 1 13:09:29 2019 -0700

• Adding new data type bigDbSnp.as with associated dbSnpDetails.as, for a track based on the new "dbSNP 2.0" schema and JSON downloads. refs #23283
  • src/hg/inc/bigDbSnp.h - lines changed 104, context: html, text, full: html, text
  • src/hg/inc/dbSnpDetails.h - lines changed 71, context: html, text, full: html, text
  • src/hg/lib/bigDbSnp.as - lines changed 21, context: html, text, full: html, text
  • src/hg/lib/bigDbSnp.c - lines changed 299, context: html, text, full: html, text
  • src/hg/lib/dbSnpDetails.as - lines changed 17, context: html, text, full: html, text
  • src/hg/lib/dbSnpDetails.c - lines changed 346, context: html, text, full: html, text
  • src/hg/lib/makefile - lines changed 2, context: html, text, full: html, text

428a47dfc975f02f3c3a97b3273d7b95f9789ff4 Tue Oct 1 13:12:08 2019 -0700

• New util dbSnpJsonToTab converts JSON to bigDbSnp and dbSnpDetails files; checkBigDbSnp flags clustering anomalies. refs #23283
  • src/hg/snp/checkBigDbSnp/checkBigDbSnp.c - lines changed 191, context: html, text, full: html, text
  • src/hg/snp/checkBigDbSnp/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c - lines changed 1738, context: html, text, full: html, text
  • src/hg/snp/dbSnpJsonToTab/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/snp/makefile - lines changed 1, context: html, text, full: html, text

122806164798753fbfbce3cc77411c911a4d9d1e Tue Oct 1 13:15:36 2019 -0700

• Adding automation script doBigDbSnp.pl that downloads dbSNP JSON files, does a cluster run of dbSnpJsonToTab, aggregates results, runs checkBigDbSnp & installs track files. refs #23283
  • src/hg/makeDb/doc/bigDbSnp.txt - lines changed 279, context: html, text, full: html, text
  • src/hg/utils/automation/doBigDbSnp.pl - lines changed 644, context: html, text, full: html, text