Commits for angie
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v364_preview2 to v364_base (2018-04-09 to 2018-04-16) v364
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3d834d96bf126177048d391f68a082969a98e243 Mon Apr 9 16:01:03 2018 -0700
- vcfTabOut was missing explainWhyNoResults. Thanks BrianL! refs #21218
17230d72f860c8003411033dad26d9433a65a744 Tue Apr 10 09:04:29 2018 -0700
- Clarify what 'official GENCODE release' means (as opposed to knownGene GENCODE-but-not-really). Thx BrianL refs #21142
77bfb6f5861adb7663082ac74813cbb264cb43fc Tue Apr 10 14:02:15 2018 -0700
- Adding description of no_sequence_alteration to hgVai help, thanks Jairo! refs #21204
- src/hg/htdocs/goldenPath/help/hgVaiHelpText.html - lines changed 7, context: html, text, full: html, text
5b4fcca505f362e2fd288f57d8d8dd2de1148d6c Wed Apr 11 11:47:25 2018 -0700
- Make POST the formMethod default instead of GET, to support long lists of rsIds / HGVS terms. Let the user know that unlike the position/search input that accepts HGVS-ish terms with gene symbols, hgVai needs specific transcript IDs. Thanks Jairo! refs #21142
d7e9c64795289915beea9e389a0218bddd111ba0 Wed Apr 11 12:07:14 2018 -0700
- oops, I omitted part of the regex in 5b4fcca50!
ae875f4d5874c2dec0e6c584a59681e8beed7b64 Wed Apr 11 14:17:58 2018 -0700
- Yikes, was storing an unallocated var from the stack in a hash. Now it's allocated. Thanks Jairo! refs #21142 note-25
- src/hg/lib/annoGratorGpVar.c - lines changed 2, context: html, text, full: html, text
193eba89efc0c2cb8e61e58f75855cff4cae408b Wed Apr 11 17:44:38 2018 -0700
- Filter symbolic alleles out of dbSNP observed alleles and warn user. Make warnings reappear on subsequent queries even when we don't rebuild the VCF file by saving the warnings in a file too.
variantProjector doesn't accept symbolic alleles, and dbSNP has all kinds of cruft in its observed alleles. One kind that occurs frequently is "lengthTooLong" -- sometimes in that case the alleles can be recovered from the allele frequency columns.
Also ignore lines starting with "#" in rsId input using lineFileNextReal .
refs #21142 note-24 -- thanks Jairo for finding the 'lengthTooLong' problem!
4672870e2141c49dc20bf1346f4bac0e0447f6dc Thu Apr 12 14:17:00 2018 -0700
- adding grcHhh38 (test db for adding patch sequences) to genbank build
- src/hg/makeDb/genbank/etc/align.dbs - lines changed 1, context: html, text, full: html, text
- src/hg/makeDb/genbank/etc/genbank.conf - lines changed 26, context: html, text, full: html, text
- src/hg/makeDb/genbank/etc/hgwdev.dbs - lines changed 1, context: html, text, full: html, text
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