Commits for angie

v401_base to v402_preview (2020-07-13 to 2020-07-20) v402

93119a2588afc1810b9c6b819ce35cbb0a45bedc Mon Jul 13 14:34:25 2020 -0700

• bedToBigBed: add a -maxAlloc option to raise needLargeMem's ceiling for enormous bigDbSnp files. refs #24500
  • src/hg/utils/automation/doBigDbSnp.pl - lines changed 3, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 6, context: html, text, full: html, text

73d02b0696465e3bbc8634b0650ec5230c379caa Wed Jul 15 16:46:09 2020 -0700

• faToVcf: added -ambiguousToN option to treat all IUPAC ambiguous bases as missing info (as opposed to observations of other alleles as with -resolveAmbiguous). refs #25904
  • src/hg/utils/faToVcf/faToVcf.c - lines changed 11, context: html, text, full: html, text

8dc53b643c0defa73465a6027fd19fe741f25b2a Thu Jul 16 11:01:58 2020 -0700

• Adding sarscov2phylo (SARS-CoV-2 Phylogeny) track (Rob Lanfear's 40k-sample tree). refs #25904
  • src/hg/makeDb/doc/wuhCor1/phylogenetics.txt - lines changed 129, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html - lines changed 165, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 36, context: html, text, full: html, text

51c0e3d58eadd12ec2157b8eb123cf37e293fd01 Thu Jul 16 13:08:40 2020 -0700

• Adding 'release alpha' to subtracks of sarsCov2Phylo. refs #25904
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 3, context: html, text, full: html, text

161f75600a7d002b587651e28c25bd5034322bfa Thu Jul 16 14:14:34 2020 -0700

• AJAX update of VCF track with color-by-function was losing the colors because the whole track list isn't loaded; load geneTrack tdb separately in that case. refs #25870
  • src/hg/hgTracks/vcfTrack.c - lines changed 17, context: html, text, full: html, text

85c7a88f8bc6294728c555e778aa681b932c0f83 Thu Jul 16 14:27:39 2020 -0700

• Better longLabels for SARS-CoV-2 Phylogeny subtracks. refs #25904
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 4, context: html, text, full: html, text

101a3f1fef03c64b66a2ae970e81c358b7803ac3 Thu Jul 16 14:34:08 2020 -0700

• Added note for SARS-CoV-2 Phylogeny about increasing the left label area width in order to see the full tree. refs #25904
  • src/hg/makeDb/trackDb/virus/wuhCor1/sarsCov2Phylo.html - lines changed 3, context: html, text, full: html, text

5fed0fb5652dec1db7546410bd50271b404f4f45 Thu Jul 16 14:55:13 2020 -0700

• Adding Chris's new vcfDoQual and vcfDoFilter trackDb settings for Nextstrain Variants and SARS-CoV-2 Phylogeny. refs #25188, #25904, #25902
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

d69d994c583af17369b899c7e3ff8e4c20fdd8b4 Fri Jul 17 13:09:20 2020 -0700

• Adding trackDb doc for new VCF settings hapClusterMethod, hapClusterColorBy function, and geneTrack. refs #25197, #25278, #25870
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbDoc.html - lines changed 7, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbHub.v2.html - lines changed 7, context: html, text, full: html, text
  • src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml - lines changed 32, context: html, text, full: html, text

90c17c91b1720de15fcb99da8a63b9c6fca4d3b7 Fri Jul 17 13:34:05 2020 -0700

• Remove trackDb.nextstrain.v1.ra and nextstrainSamplesDevOnly.html since they are no longer needed (new tracks have been pushed to RR). Update nextstrainSamples.html with edits made to DevOnly. refs #25782
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html - lines changed 10, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamplesDevOnly.html - lines changed 155, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.v1.ra - lines changed 129, context: html, text, full: html, text