Commits for angie

0410ce3f2bff7c04762f60551db166f4cae460f7 Tue Jun 22 10:13:57 2021 -0700

faToVcf: added -maxDiff to exclude sequences with too many mismatches w/reference (causes usher mem usage increase, no good placement).
- src/hg/utils/faToVcf/faToVcf.c - lines changed 48, context: html, text, full: html, text

b0914531bd4294d1cf0a746601f080cd53d159a2 Sun Jun 27 20:17:40 2021 -0700

Add link from lineage to outbreak.info. Better labels for subtree links.
- src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 21, context: html, text, full: html, text

b69d77d71d0bf2464ed68a165fd1988a7044753e Sun Jun 27 20:20:21 2021 -0700

Added -includeNoAltN option to include info about Ns in the VCF.
- src/hg/utils/faToVcf/faToVcf.c - lines changed 9, context: html, text, full: html, text

dc65a1eecd5e15e136536571af19bf7ccd77726e Sun Jun 27 20:21:39 2021 -0700

Clean up hardcoded paths a tiny bit.
- src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh - lines changed 2, context: html, text, full: html, text

179775232ff5fe31323f984619b75cbc77204c00 Sun Jun 27 20:22:29 2021 -0700

Update nextclade to 1.0 (new required command line args).
- src/hg/utils/otto/sarscov2phylo/getCogUk.sh - lines changed 12, context: html, text, full: html, text
- src/hg/utils/otto/sarscov2phylo/getNcbi.sh - lines changed 12, context: html, text, full: html, text

83f9e814d5441d0ba86d5fa735aed67d264a771f Sun Jun 27 20:27:52 2021 -0700

Skip building new.masked.vcf.gz if it already exists (go straight to usher). More prevention of empty-grep crashes. Use faToVcf new -maxDiff option to prevent memory usage blowup for sequences that are so diverged/erroneous that we won't keep them anyway. Exclude sequences with 10 or more equally parsimonious placements so we don't keep trying in vain (and wasting time). Handle new nextstrain clade names with spaces etc.
- src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh - lines changed 29, context: html, text, full: html, text

3e968a25a2e9635f916fb3eeac0b3e2147cfba7c Mon Jun 28 08:43:35 2021 -0700

Add links to outbreak.info for lineages in results table & details.
- src/hg/hgPhyloPlace/phyloPlace.c - lines changed 33, context: html, text, full: html, text
- src/hg/hgPhyloPlace/phyloPlace.h - lines changed 1, context: html, text, full: html, text
- src/hg/hgPhyloPlace/treeToAuspiceJson.c - lines changed 1, context: html, text, full: html, text

1e6e36834dceedd5c2cb79834bcc84ee0bac4be5 Mon Jun 28 08:44:36 2021 -0700

Use make -j for pangolin (no multithreading at this point).
- src/hg/utils/otto/sarscov2phylo/gisaidFromChunks.sh - lines changed 2, context: html, text, full: html, text