File Changes for chmalee

v400_base to v401_preview (2020-06-22 to 2020-06-29) v401

• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 1, context: html, text, full: html, text
    0d3b8feb6074f6caccc2d4aadd020961fbd7eb82 Wed Jun 10 14:39:38 2020 -0700
    Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582
• src/hg/hgTracks/vcfTrack.c
  • lines changed 3, context: html, text, full: html, text
    68bec7571e8307853f5e9193503f8561a5eb4310 Mon Jun 22 17:14:18 2020 -0700
    Adding hub support for vcfPhasedTrio track type, refs #18846
  • lines changed 3, context: html, text, full: html, text
    6790e66b73c00a9830b64d5fb2eda5733b4e4b90 Thu Jun 25 16:04:36 2020 -0700
    New trackDb variable for phased trios to default to alternate labels if available, refs #25582
  • lines changed 7, context: html, text, full: html, text
    18eef8c27d7fd3382fb8008b0dd344ca4c6f066b Thu Jun 25 16:56:29 2020 -0700
    Fixes bug I introduced in 6790e66b73 where I forgot to account for user selections on hgTrackUi, refs #25582
  • lines changed 51, context: html, text, full: html, text
    bd53b8dfe0a86f9d1c8ed57289fd409a6c52bd6b Fri Jun 26 10:54:41 2020 -0700
    Add option to shade alleles by inconsitent transmission between child and parent haplotypes
  • lines changed 66, context: html, text, full: html, text
    0d3b8feb6074f6caccc2d4aadd020961fbd7eb82 Wed Jun 10 14:39:38 2020 -0700
    Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582
• src/hg/hgc/vcfClick.c
  • lines changed 1, context: html, text, full: html, text
    451dd3c05586d1f291a36920780488e789777240 Wed Jun 24 09:43:15 2020 -0700
    Remove variant sort option from vcfPhasedTrio hgc pages, refs #25582
• src/hg/inc/vcfUi.h
  • lines changed 1, context: html, text, full: html, text
    6790e66b73c00a9830b64d5fb2eda5733b4e4b90 Thu Jun 25 16:04:36 2020 -0700
    New trackDb variable for phased trios to default to alternate labels if available, refs #25582
  • lines changed 1, context: html, text, full: html, text
    bd53b8dfe0a86f9d1c8ed57289fd409a6c52bd6b Fri Jun 26 10:54:41 2020 -0700
    Add option to shade alleles by inconsitent transmission between child and parent haplotypes
  • lines changed 2, context: html, text, full: html, text
    0d3b8feb6074f6caccc2d4aadd020961fbd7eb82 Wed Jun 10 14:39:38 2020 -0700
    Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582
• src/hg/js/hgTracks.js
  • lines changed 402, context: html, text, full: html, text
    0d3b8feb6074f6caccc2d4aadd020961fbd7eb82 Wed Jun 10 14:39:38 2020 -0700
    Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582
• src/hg/js/jquery.tablednd.js
  • lines changed 2, context: html, text, full: html, text
    0d3b8feb6074f6caccc2d4aadd020961fbd7eb82 Wed Jun 10 14:39:38 2020 -0700
    Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582
• src/hg/js/utils.js
  • lines changed 404, context: html, text, full: html, text
    0d3b8feb6074f6caccc2d4aadd020961fbd7eb82 Wed Jun 10 14:39:38 2020 -0700
    Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582
• src/hg/lib/trackHub.c
  • lines changed 5, context: html, text, full: html, text
    68bec7571e8307853f5e9193503f8561a5eb4310 Mon Jun 22 17:14:18 2020 -0700
    Adding hub support for vcfPhasedTrio track type, refs #18846
• src/hg/lib/vcfUi.c
  • lines changed 1, context: html, text, full: html, text
    18eef8c27d7fd3382fb8008b0dd344ca4c6f066b Thu Jun 25 16:56:29 2020 -0700
    Fixes bug I introduced in 6790e66b73 where I forgot to account for user selections on hgTrackUi, refs #25582
  • lines changed 6, context: html, text, full: html, text
    bd53b8dfe0a86f9d1c8ed57289fd409a6c52bd6b Fri Jun 26 10:54:41 2020 -0700
    Add option to shade alleles by inconsitent transmission between child and parent haplotypes
  • lines changed 121, context: html, text, full: html, text
    0d3b8feb6074f6caccc2d4aadd020961fbd7eb82 Wed Jun 10 14:39:38 2020 -0700
    Add drag reorder of VCF samples to VCF trio display. Also fixes bug in haplotype sort that I didn't discover until adding drag reorder. Sometimes when sorting haplotypes it is the case that the initial best match to a child allele is the same for each parent. Previously I would just advance the first drawn parent to the next best match but now I also check whether advancing the first drawn is actually the best idea and potentially advance the other parent instead, refs #25582
• src/hg/makeDb/trackDb/human/hg38/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    6790e66b73c00a9830b64d5fb2eda5733b4e4b90 Thu Jun 25 16:04:36 2020 -0700
    New trackDb variable for phased trios to default to alternate labels if available, refs #25582
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 1, context: html, text, full: html, text
    6790e66b73c00a9830b64d5fb2eda5733b4e4b90 Thu Jun 25 16:04:36 2020 -0700
    New trackDb variable for phased trios to default to alternate labels if available, refs #25582