Commits for angie

b98e1d0ccffb3a4c1d69f6c69ab98a842840aa57 Fri Apr 24 13:58:33 2020 -0700

Adding VCF subtrack for David: filter to recurrent bi-allelic variants only. refs #25188
- src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 4, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 33, context: html, text, full: html, text

7ae5638cd51f8a67da9dbfa08781d3a1baa4e614 Fri Apr 24 15:20:39 2020 -0700

Adding nextstrainSamplesRb (recurrent bi-allelic) subtrack to trackDb. refs #25188
- src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 11, context: html, text, full: html, text

1ad98d1567578b8ceb7db30bf0be128b225edd1d Mon Apr 27 14:59:36 2020 -0700

lineFileNext for udc file didn't bother to set retSize and apparently it didn't matter until I wanted to use lineFile with udc in phyloOpenTree.
- src/lib/linefile.c - lines changed 2, context: html, text, full: html, text

cdb062c333ee1200f4a744fd0736d9a27933629c Mon Apr 27 15:01:01 2020 -0700

Use lineFileUdc instead of just lineFile, so URLs work. Now I can make a custom track with hapClusterMethod treeFile <url>.
- src/lib/phyloTree.c - lines changed 3, context: html, text, full: html, text

8523f0b59275db50e5f84bceb61040431ea57155 Tue Apr 28 13:28:17 2020 -0700

Applying Braney's fix for vcfTabixLoadItems in 0de7cb7d to vcfLoadItems for consistency. refs #25462
- src/hg/hgTracks/vcfTrack.c - lines changed 2, context: html, text, full: html, text

c35d862713639e092261001c5a1d6e74d725a1e1 Wed Apr 29 17:18:24 2020 -0700

Oops, since nextstrainSamplesRb is not yet on beta/RR, use release tags so nextstrainSamplesAll is off by default on dev but on by default on beta/RR. refs #25475
- src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 12, context: html, text, full: html, text

769a92cab2445edae6ab5209e93162c1e7036dee Thu Apr 30 11:59:54 2020 -0700

Make sure python doesn't gak if no submitting_lab is provided for some sample. refs #25188
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 5, context: html, text, full: html, text

72730b6971500837e39e21461e8fce00eebfc008 Fri May 1 10:21:30 2020 -0700

Add internal node labels to the newick tree files that encode clade and the sequence of mutations leading to the node. This actually does not affect the track at this point, but helps in comparing the trees from different releases. refs #25188
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 23, context: html, text, full: html, text