File Changes for angie

v412_preview2 to v412_base (2021-03-15 to 2021-03-22) v412

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 3, context: html, text, full: html, text
    d6c0b0e804ffa16adefe2703385685945323ca39 Wed Mar 17 11:37:32 2021 -0700
    Added missing NULL check (for uploaded sequences that failed QC checks).
• src/hg/hgTracks/pubsTracks.c
  • lines changed 1, context: html, text, full: html, text
    4d8aafef6108905a734e61f6781600234e72719f Wed Mar 17 12:08:48 2021 -0700
    Fixing compile warning about unused variable that broke the build.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 12, context: html, text, full: html, text
    64ef1345bfa1476ad1c2a1ad7cf413e95556966b Wed Mar 17 11:53:07 2021 -0700
    We can actually end up with more bioSamples than we're looking for due to including past results, so compare IDs instead of counts.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 252, context: html, text, full: html, text
    30ebf52c1ccbd592b814c18d3a68c30624a0f85d Wed Mar 17 11:55:37 2021 -0700
    Adding new updateCombinedTree.sh after updatePublicTree.sh for GISAID+public tree. Eventually, public tree will be derived from combined tree.
• src/hg/utils/otto/sarscov2phylo/updateIdMapping.sh
  • lines changed 1, context: html, text, full: html, text
    e9b05abd1cee4cdf715a0dd725332f507b2141a3 Wed Mar 17 11:52:03 2021 -0700
    Don't need -x anymore, too verbose.
• src/hg/utils/otto/sarscov2phylo/updatePublic.sh
  • lines changed 4, context: html, text, full: html, text
    30ebf52c1ccbd592b814c18d3a68c30624a0f85d Wed Mar 17 11:55:37 2021 -0700
    Adding new updateCombinedTree.sh after updatePublicTree.sh for GISAID+public tree. Eventually, public tree will be derived from combined tree.
• src/hg/utils/otto/sarscov2phylo/updatePublicTree.sh
  • lines changed 3, context: html, text, full: html, text
    02d1894196c846ac4eedfee782ff1bf182f2adbf Wed Mar 17 11:56:18 2021 -0700
    Tolerate another condition where grep finding 0 results crashed the script.
• src/hg/utils/otto/sarscov2phylo/util.sh
  • lines changed 21, context: html, text, full: html, text
    c218231e30bb4cbc6e6536738585b3df1b3f673c Wed Mar 17 11:51:18 2021 -0700
    Make cleanGenbank ~10x more efficient by splitting out sed commands to take advantage of many cores, and adding a test and branch to the slowest command.