File Changes for angie

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

• src/hg/inc/bigDbSnp.h
  • lines changed 1, 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/lib/bigDbSnp.c
  • lines changed 2, 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/lib/hui.c
  • lines changed 2, 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/makeDb/doc/bigDbSnp.txt
  • lines changed 44, 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.
  • lines changed 17, 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/makeDb/doc/hg38/variation.txt
  • lines changed 41, 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/trackDb/human/dbSnp153Composite.html
  • lines changed 10, context: html, text, full: html, text
    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
  • lines changed 46, 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.
  • lines changed 16, 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/makeDb/trackDb/human/hg38/tgpPhase3.html
  • lines changed 133, 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/trackDb/human/hg38/trackDb.ra
  • lines changed 10, 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/trackDb/human/trackDb.ra
  • lines changed 45, 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.
  • lines changed 18, 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
  • lines changed 3, 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
  • lines changed 0, context: html, text, full: html, text
    bcd29eb2ea0e1cddcc525174445423f712c9d377 Fri Nov 15 10:23:50 2019 -0800
    Typo in type declaration, doh.
• src/hg/snp/checkBigDbSnp/checkBigDbSnp.c
  • lines changed 65, 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/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
  • lines changed 94, 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/utils/automation/doBigDbSnp.pl
  • lines changed 77, 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.
  • lines changed 9, 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