Commits for angie
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v337_base to v338_preview (2016-08-15 to 2016-08-22) v338
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53280f702308da193ac7565e25d29d571e06d3b7 Fri Aug 19 10:51:59 2016 -0700
- Added a check for bad chrom name for scaffold-based assemblies. All other checks are still skipped for scaffold-based assemblies! refs #17919
- src/hg/checkTableCoords/checkTableCoords.c - lines changed 13, context: html, text, full: html, text
b3fcbb7d6139a1993f5f02261ae3b495bc3edf41 Mon Aug 15 10:43:26 2016 -0700
- Increased verbosity level to 2 for no match & no table info lines.
- src/hg/checkHgFindSpec/checkHgFindSpec.c - lines changed 4, context: html, text, full: html, text
aaf72102b545c05c42f66b7a3fc22d65b1ecf4fe Mon Aug 8 14:12:39 2016 -0700
- Added recognition of a small subset of HGVS terms: coding (c.) SNVs relative to RefSeq NM_ or LRG transcript IDs,
and protein (p.) simple substitutions relative to NP_.
Also accepted (not HGVS but similar and popular): geneSymbol and abbreviated protein subst like "ALK G1494E".
hgFind will map terms to the current genome if possible, and will display warnings about unrecognized accessions,
out-of-bounds coordinates and mismatching reference alleles.
refs #15071, #15554
- src/hg/lib/tests/expected/hgvs/validTerms.txt - lines changed 11, context: html, text, full: html, text
- src/hg/lib/tests/hgvsTester.c - lines changed 72, context: html, text, full: html, text
- src/hg/lib/tests/hgvsTests.mk - lines changed 18, context: html, text, full: html, text
- src/hg/lib/tests/input/hgvs/validTerms.txt - lines changed 16, context: html, text, full: html, text
- src/hg/lib/tests/makefile - lines changed 9, context: html, text, full: html, text
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