File Changes for angie

v416_base to v417_preview (2021-06-14 to 2021-06-21) v417

• src/hg/utils/otto/sarscov2phylo/fixNcbiFastaNames.pl
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    b90cc537ccb7800ba8dc1caf25e54c835fd653a8 Wed Jun 16 17:50:21 2021 -0700
    Encountered new condition (missing metadata) and found that downstream scripts really expect a space before |.
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 25, context: html, text, full: html, text
    cc57121245fc7a8dd659c359a2f8457a808335b8 Wed Jun 16 17:49:16 2021 -0700
    Use NCBI datasets tool instead of API, more robust and can exclude unwanted files. Handle the previous day's build failing by using ncbi.latest.
• src/hg/utils/otto/sarscov2phylo/updateCombinedTree.sh
  • lines changed 353, context: html, text, full: html, text
    88c5c33485279c9687d7be15a85da2665c16e91d Wed Jun 16 17:52:44 2021 -0700
    Lots of work from the past month. De-dup COG-UK & GenBank; generate public tree from combined gisaidAndPublic tree.
• src/hg/utils/otto/sarscov2phylo/util.sh
  • lines changed 10, context: html, text, full: html, text
    e6e4ac7f750c6e2894752ef008325efee95ae6fc Wed Jun 16 17:47:08 2021 -0700
    Added vcfSamples function (grab VCF sample names from #CHROM header line, print one name per line)
• src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c
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    89e6b5b4e3b7cef642d825fbfca09c6111f3f4cd Wed Jun 16 17:34:53 2021 -0700
    Another case of too many VCF columns to keep an array of them on the stack.
• src/utils/faFrag/faFrag.c
  • lines changed 27, context: html, text, full: html, text
    a31ae2470e4b225665e48c267e22bcca06bc6ddf Wed Jun 16 17:45:59 2021 -0700
    faFrag: support multi-sequence alignment fasta by fetching the same coords from each sequence in file.