File Changes for angie

v400_preview2 to v400_base (2020-06-15 to 2020-06-22) v400

• src/hg/hgTracks/vcfTrack.c
  • lines changed 60, context: html, text, full: html, text
    8d9367da0e57755641dbbf6498093f7e44f14f12 Sat Jun 20 13:27:08 2020 -0700
    VCF: support up to 64k genotypes, including haplotype+tree display. sorta refs #25278 The VCF parser currently has a hardcoded upper limit on the number of genotype columns. I increased that from 16k to 64k to support Rob Lanfear's SARS-CoV-2 tree w/40k nodes. It will keep growing, so I will probably want to revisit so that we allocate the array size needed instead of a hardcoded huge size when most VCF tracks don't have anywhere near that many. In vcfTracks.c, using 'unsigned short' for the gtHapOrder array limits the number of samples to 32k because the index into gtHapOrder is gtIx<<1+hapIx. Changed all the shorts to ints because we now have VCF with more than 32k genotype columns.
• src/hg/utils/faToVcf/faToVcf.c
  • lines changed 316, context: html, text, full: html, text
    aa03a541ef25d83f1542202f784c53500c434c2d Sat Jun 20 14:35:04 2020 -0700
    New util faToVcf for extracting single-nucleotide variants from multi-sequence FASTA alignment.
• src/hg/utils/faToVcf/makefile
  • lines changed 3, context: html, text, full: html, text
    aa03a541ef25d83f1542202f784c53500c434c2d Sat Jun 20 14:35:04 2020 -0700
    New util faToVcf for extracting single-nucleotide variants from multi-sequence FASTA alignment.
• src/hg/utils/otto/nextstrainNcov/doUpdate.sh
  • lines changed 11, context: html, text, full: html, text
    1af2fddea7e6ede49cc2b334a6c8e78df998c9fa Mon Jun 8 16:15:28 2020 -0700
    Nextstrain changed to a new set of clade definitions, but they still keep the old clade assignments around in a different tag. Make subtracks for both old and new sets of clades. refs #25188
• src/hg/utils/otto/nextstrainNcov/lineageColors.py
  • lines changed 36, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
  • lines changed 10, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/newick.py
  • lines changed 9, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
  • lines changed 43, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/nextstrain.py
  • lines changed 142, context: html, text, full: html, text
    1af2fddea7e6ede49cc2b334a6c8e78df998c9fa Mon Jun 8 16:15:28 2020 -0700
    Nextstrain changed to a new set of clade definitions, but they still keep the old clade assignments around in a different tag. Make subtracks for both old and new sets of clades. refs #25188
  • lines changed 18, context: html, text, full: html, text
    a113d7fcbb275fcfda2b51c2bc359900531a8c0d Tue Jun 9 13:26:57 2020 -0700
    Adding more tolerance for missing data in ncov.json so I can run on a dev build of Nextstrain.
  • lines changed 77, context: html, text, full: html, text
    abf5dba0ce1f1cf2d3f15624272bde0854aec681 Sat Jun 20 14:24:44 2020 -0700
    Don't ignore the 'mutations' that are changes between [ACGT] and '-' (missing info), because they can occasionally happen in the path of a nucleotide change, for example T28144- to -T28144C. fixes #25751
• src/hg/utils/otto/nextstrainNcov/nextstrainVcf.py
  • lines changed 27, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
  • lines changed 1, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py
  • lines changed 28, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
  • lines changed 1, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/sampleLineage.py
  • lines changed 35, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
  • lines changed 4, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeBranchWithSamples.py
  • lines changed 69, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeColorByLineage.py
  • lines changed 3, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeIntersectNextstrain.py
  • lines changed 24, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
  • lines changed 66, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeIntersectVcf.py
  • lines changed 46, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treeLineage.py
  • lines changed 61, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
  • lines changed 5, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/treePruneToSamples.py
  • lines changed 39, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/utils.py
  • lines changed 16, context: html, text, full: html, text
    775f8e290daefbb3312fd1d8962344690550c887 Mon Jun 8 16:20:24 2020 -0700
    Extending and updating tree manipulation & SARS-CoV-2 lineage coloring python scripts and modules that I've been working on for David et al. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/vcf.py
  • lines changed 85, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/vcfPruneToSamples.py
  • lines changed 38, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/hg/utils/otto/nextstrainNcov/virusNames.py
  • lines changed 6, context: html, text, full: html, text
    b226cb3af001057dea4635de2d4c6c52f0ebe047 Sat Jun 20 14:34:08 2020 -0700
    New scripts & vcf module for working with non-Nextstrain VCF and trees, e.g. Rob Lanfear's 40k sample build. Updates to other VCF & tree utils. sorta refs #25278, #25382
• src/inc/iupac.h
  • lines changed 33, context: html, text, full: html, text
    aa03a541ef25d83f1542202f784c53500c434c2d Sat Jun 20 14:35:04 2020 -0700
    New util faToVcf for extracting single-nucleotide variants from multi-sequence FASTA alignment.
• src/lib/vcf.c
  • lines changed 1, context: html, text, full: html, text
    8d9367da0e57755641dbbf6498093f7e44f14f12 Sat Jun 20 13:27:08 2020 -0700
    VCF: support up to 64k genotypes, including haplotype+tree display. sorta refs #25278 The VCF parser currently has a hardcoded upper limit on the number of genotype columns. I increased that from 16k to 64k to support Rob Lanfear's SARS-CoV-2 tree w/40k nodes. It will keep growing, so I will probably want to revisit so that we allocate the array size needed instead of a hardcoded huge size when most VCF tracks don't have anywhere near that many. In vcfTracks.c, using 'unsigned short' for the gtHapOrder array limits the number of samples to 32k because the index into gtHapOrder is gtIx<<1+hapIx. Changed all the shorts to ints because we now have VCF with more than 32k genotype columns.