Commits for chmalee

v408_base to v409_preview (2020-12-07 to 2021-01-04) v409

61c6951478b837ef6dffeb190a780e7579130686 Mon Dec 7 13:06:45 2020 -0800

• Fixing missing south asian population data from gnomad v2.1.1 exomes track, refs #25010
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra - lines changed 1, context: html, text, full: html, text

a8745ce945b6f69b13846cf345fd1f400b252cd1 Tue Dec 8 16:54:37 2020 -0800

• Adding a description page for the new bigBed formatted gnomAD v2.1.1 tracks, refs #25010
  • src/hg/makeDb/trackDb/human/hg19/gnomadExomesGenomes.html - lines changed 170, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/trackDb.gnomad.ra - lines changed 2, context: html, text, full: html, text

9b031666dc8ef873fefdb6201c39366d257f4632 Tue Dec 8 16:58:42 2020 -0800

• Adding gnomAD vcf to bed conversion script, refs #25010, #26652
  • src/hg/makeDb/gnomad/gnomadVcfBedToBigBed - lines changed 329, context: html, text, full: html, text

f83f8061a76cad5ed033b6320f73321cf7b8ffcb Wed Dec 9 11:20:08 2020 -0800

• Fix bug I introduced into bigBed extra field printing when adding bigBed extra field URL substitution, refs #26662
  • src/hg/hgc/bigBedClick.c - lines changed 1, context: html, text, full: html, text

7dea7c645f8ce8892d6d4d162a3cf8295309062f Fri Dec 11 11:22:24 2020 -0800

• Bringing repo copies of omim scripts up to date with the working versions, refs #18151
  • src/hg/utils/otto/clinGen/clinGenWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/decipher/decipherWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/decipher/makefile - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/geneReviews/geneReviewsWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/geneReviews/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/checkGwas.sh - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/gwasWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/otto/gwas/perlParser.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/isca/buildISCA.csh - lines changed 39, context: html, text, full: html, text
  • src/hg/utils/otto/isca/checkISCA.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/isca/iscaWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/isca/makefile - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/otto/isca/validateISCA.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/omim/buildOmimTracks.sh - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/otto/omim/checkOmim.sh - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/omim/makefile - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/otto/omim/omimUploadWrapper.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/omim/omimWrapper.sh - lines changed 1, context: html, text, full: html, text

d8357a44b9fb15ee8262a36d4fbcc43c90fae358 Mon Dec 14 16:42:26 2020 -0800

• Make hgGateway use previously browsed position when changing databases, also fix hgHubConnect assembly redirect to use last used position, refs #14481
  • src/hg/hgGateway/hgGateway.c - lines changed 13, context: html, text, full: html, text
  • src/hg/hgHubConnect/hgHubConnect.c - lines changed 1, context: html, text, full: html, text
  • src/hg/js/hgGateway.js - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/cart.c - lines changed 3, context: html, text, full: html, text

5595f79ea5536f735706cf56966cc3c7be7ca8c1 Mon Dec 28 09:27:58 2020 -0800

• Fixing gnomad v3.1 track name as periods in table names are not allowed or the table browser and data integrator complain, refs #26449
  • src/hg/makeDb/trackDb/human/hg38/gnomad.ra - lines changed 1, context: html, text, full: html, text