File Changes for angie

v417_preview to v417_preview2 (2021-06-21 to 2021-06-28) v417

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 33, 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.h
  • lines changed 1, 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/treeToAuspiceJson.c
  • lines changed 21, 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.
  • lines changed 1, 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/utils/faToVcf/faToVcf.c
  • lines changed 48, context: html, text, full: html, text
    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).
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    b69d77d71d0bf2464ed68a165fd1988a7044753e Sun Jun 27 20:20:21 2021 -0700
    Added -includeNoAltN option to include info about Ns in the VCF.
• src/hg/utils/otto/sarscov2phylo/getCogUk.sh
  • lines changed 12, 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/getNcbi.sh
  • lines changed 12, 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/gisaidFromChunks.sh
  • lines changed 2, 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/updateCombinedTree.sh
  • lines changed 29, 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/updateIdMapping.sh
  • lines changed 2, context: html, text, full: html, text
    dc65a1eecd5e15e136536571af19bf7ccd77726e Sun Jun 27 20:21:39 2021 -0700
    Clean up hardcoded paths a tiny bit.