Commits for angie
switch to files view, user index
v339_base to v340_preview (2016-09-26 to 2016-10-03) v340
Show details
a1c329068ad18aa4093972b501e6324f8bcdb398 Fri Sep 16 17:19:30 2016 -0700
- Parse HGVS position ranges and coding terms' UTR and intron coordinates.
When the chromAlias table is present, this also now supports NC_*:g. terms.
The sequence change part is no longer parsed -- it's not necessary for mapping
to genomic ranges, although it will be necessary in order for hgVai to take
HGVS input.
This does not yet support ranges-of-ranges but neither does Mutalyzer. This
also doesn't support uncertain positions ('?'). Like complex sequence changes,
those can wait until we have a sophisticated parser.
We also support some new not-quite-HGVS forms: geneSymbol and protein pos only,
or geneSymbol and c.<valid position range>.
refs #15071
- src/hg/lib/tests/expected/hgvs/clinVarHgvs.txt - lines changed 79, context: html, text, full: html, text
- src/hg/lib/tests/expected/hgvs/validTerms.txt - lines changed 17, context: html, text, full: html, text
- src/hg/lib/tests/hgvsTester.c - lines changed 15, context: html, text, full: html, text
- src/hg/lib/tests/hgvsTests.mk - lines changed 5, context: html, text, full: html, text
- src/hg/lib/tests/input/hgvs/clinVarHgvs.txt - lines changed 77, context: html, text, full: html, text
- src/hg/lib/tests/input/hgvs/validTerms.txt - lines changed 10, context: html, text, full: html, text
a096f41962e1fec8b70904bcef41eb5f1d40a922 Mon Sep 26 16:35:17 2016 -0700
- Adding indexes to ncbiRefSeqLink.sql to speed up queries on fields other than id. refs #13673 note-442
- src/hg/lib/ncbiRefSeqLink.sql - lines changed 4, context: html, text, full: html, text
43db133d50ad5cd505cc1ea853b701b271054e91 Mon Sep 26 16:56:04 2016 -0700
- Added support for HGVS-like syntax that b0b got from a user: no '.' and NM_ accession with protein change description. Also, if the new ncbiRefSeq* tables are present, use those instead of refSeqAli and Genbank metadata tables.
At this point, ncbiRefSeqPsl is missing some transcripts that are present in other ncbiRefSeq* tables, so if an accession is not found there, try again in refSeqAli and Genbank.
refs #15071, #13673 note-443
- src/hg/lib/tests/expected/hgvs/validTerms.txt - lines changed 3, context: html, text, full: html, text
- src/hg/lib/tests/input/hgvs/validTerms.txt - lines changed 3, context: html, text, full: html, text
3640a4d6b3303a6bebc7c5b2fc5abcf7f4fae0b2 Wed Sep 28 11:56:00 2016 -0700
- Partial support for changes in VCF4.2 and latest samtools mpileup output:
- Tolerate 'Number=R' and new INFO attributes Source and Version
- Tolerate mpileup's '<X>' alt (no alternate allele was observed)
- The 4.3 spec includes '<*>' from gVCF, also meaning no alt al obsvd.
- GT is no longer required; user's example has PL instead, so parse that
into genotypes.
- hgVai now annotates "variants" with <X> and <*> as no_sequence_alteration
- annoFormatVep now uses html encoding for html output in various places so
that "<X>" is displayed properly (custom track labels and various item
names could also have undesirable characters). I am not encoding the
extras' descriptions because those are internal and some have <a>'s.
refs #15625
- src/hg/inc/annoGratorGpVar.h - lines changed 3, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 52, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 5, context: html, text, full: html, text
f8b7740e1898ae4a2ad289ef043a541c4179e0ae Fri Sep 30 12:05:55 2016 -0700
- Expand vaHtmlSafefNoAbort's newFormatSize 3x instead of 2x to prevent uncaught overflow on format strings composed mostly of %s's, since 3 bytes are added for every %s (two bytes expand to five bytes).
switch to files view, user index