Commits for angie
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v400_preview2 to v400_base (2020-06-15 to 2020-06-22) v400
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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/doUpdate.sh - lines changed 11, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 142, 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/lineageColors.py - lines changed 36, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/newick.py - lines changed 9, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/nextstrainVcf.py - lines changed 27, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py - lines changed 28, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/sampleLineage.py - lines changed 35, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treeIntersectNextstrain.py - lines changed 24, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treeLineage.py - lines changed 61, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/utils.py - lines changed 16, 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.
- src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 18, 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/hgTracks/vcfTrack.c - lines changed 60, 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/nextstrain.py - lines changed 77, 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/lineageColors.py - lines changed 10, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/newick.py - lines changed 43, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/nextstrainVcf.py - lines changed 1, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/sampleCladeLineage.py - lines changed 1, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/sampleLineage.py - lines changed 4, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treeBranchWithSamples.py - lines changed 69, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treeColorByLineage.py - lines changed 3, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treeIntersectNextstrain.py - lines changed 66, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treeIntersectVcf.py - lines changed 46, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treeLineage.py - lines changed 5, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/treePruneToSamples.py - lines changed 39, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/vcf.py - lines changed 85, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/vcfPruneToSamples.py - lines changed 38, context: html, text, full: html, text
- src/hg/utils/otto/nextstrainNcov/virusNames.py - lines changed 6, 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/faToVcf.c - lines changed 316, context: html, text, full: html, text
- src/hg/utils/faToVcf/makefile - lines changed 3, context: html, text, full: html, text
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