Commits for angie
switch to files view, user index
v317_base to v318_preview (2015-06-01 to 2015-06-08) v318
- Add support for ctgPos table type (like bed w/swizzled columns and 'contig' for name)
and possibly other swizzled-bed types if we still have any of those.
refs #15432
- Recognize bigGenePred type and provide better error message for
unrecognized type from hub track (instead of trying to fall back on
getting sql table info which of course fails for a hub).
refs #14579
- Found a couple more places in hAnno.c that also need to recognize bigGenePred.
refs #14579
- Updating test files for changing wiggle column "value" to "valueAverage"
in the tab-sep output since we're now printing out average values.
refs #14579
- src/hg/lib/tests/expected/annoGrator/snpBigWigToTabOut.txt - lines changed 1, context: html, text, full: html, text
- src/hg/lib/tests/expected/annoGrator/snpConsDbToTabOutShort.txt - lines changed 1, context: html, text, full: html, text
- Added support for bigGenePred to anno* libs for hgVai and hgIntegrator.
While updating annoFormatVep.c to use column indices from autoSql instead of
hardcoding genePred indices, I found that I had been using an incorrect index
for strand anyway -- so I removed 3 lines of no-op code.
refs #15439
- src/hg/inc/bigGenePred.h - lines changed 4, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 15, context: html, text, full: html, text
- src/hg/lib/annoGratorGpVar.c - lines changed 9, context: html, text, full: html, text
- src/hg/lib/bigGenePred.c - lines changed 33, context: html, text, full: html, text
- Fix for hgTablesTest checking of commas in join results: it's the
second column, not the first, that should be checked for commas.
refs #15237
- src/hg/hgTablesTest/hgTablesTest.c - lines changed 2, context: html, text, full: html, text
- hgIntegratorModel: schemaUrlFromTrackPath can't assume that mutState
already has db, because it's possible for the groupedTrackDb to
arrive from the server *before* the other query's results with
cladeOrgDb etc. Use the db embedded in groupedTrackDb in that
case.
refs #14579
- src/hg/js/model/hgIntegrator/hgIntegratorModel.js - lines changed 13, context: html, text, full: html, text
- Fleshed out the introduction. Changed file mode bits (chmod a+x) so
that the topbar would be included.
refs #14579
- src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html - lines changed 33, context: html, text, full: html, text
- For GBiB support, we can't simply assume that wib files are on local disk;
we must use hReplaceGbdb and UDC in case they are remote. Following suit
with Max's changes to wigTrack.c wigLoadPreDraw (225c0d55).
refs #14579 note 106
- src/hg/lib/annoStreamWig.c - lines changed 17, context: html, text, full: html, text
- Added an explanation of how we handle multiple overlapping items in
multiple secondary tables. Made an editorial pass over the whole doc
and substituted DNase Clusters for SNPs because I think of genes+snps
as hgVai's domain.
refs #14579
- src/hg/htdocs/goldenPath/help/hgIntegratorHelp.html - lines changed 94, context: html, text, full: html, text
- src/hg/htdocs/images/hgIntegratorDataSourceConfig.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/hgIntegratorFieldsConfig.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/hgIntegratorHgTracksExample.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
- src/hg/htdocs/images/hgIntegratorHgTracksExample2.png - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
switch to files view, user index
