Commits for angie

d5938e92fec0038d9874c8edf92ba60bc770f4a8 Mon May 24 09:57:40 2021 -0700

Handle Biosample keyword set to empty string.
- src/hg/utils/otto/sarscov2phylo/bioSampleTextToTab.pl - lines changed 3, context: html, text, full: html, text

9875f6c8af94b0f0fcdc5e496515438e6af478b5 Mon May 24 09:59:55 2021 -0700

Add back -x since there have been so many cron failures. Parallelize re-running of pangolin on all sequences (necessary when a new version of pangolin is released).
- src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 23, context: html, text, full: html, text

01388e26d682bc9c0f3b2cf27ae25ff989568e21 Mon May 24 10:01:27 2021 -0700

Set prevDate in this script instead of requiring it from caller.
- src/hg/utils/otto/sarscov2phylo/updatePublic.sh - lines changed 10, context: html, text, full: html, text

95c23a8a25292bec7fd5c853412f0d04d2d44145 Mon May 24 10:03:07 2021 -0700

Preserve older mappings in the case of duplicates -- but allow GenBank dot-version updates. Also, subColumn is way faster than sed.
- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh - lines changed 8, context: html, text, full: html, text

327ff85429911eaa58790c850bc5e83ad4b1548f Wed May 26 19:33:36 2021 -0700

User request (HT Krisandra Allen, WA DOH): add a box in which sequence names/IDs can be pasted instead of uploaded from file.
- src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 25, context: html, text, full: html, text

9da4f41aff8bc9265c4538a3af39736faed03d51 Wed May 26 19:34:38 2021 -0700

Added -minAf (alt allele frequency ignoring N bases).
- src/hg/utils/faToVcf/faToVcf.c - lines changed 8, context: html, text, full: html, text