Commits for angie
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v297_preview2 to v297_base (2014-03-10 to 2014-03-17) v297
- Adding a catch-all LRG transcript search as Steve suggested in #12882.Searching for "LRG_321" still won't get the LRG Regions item, but it
will get all transcripts (LRG_321t*) in the LRG Transcripts track.
refs #12882
- src/hg/makeDb/trackDb/human/trackDb.ra - lines changed 9, context: html, text, full: html, text
- Fixing problem with hgVai code not recognizing a genePred whoseasObject was derived from sql field info. Unfortunately, when a sql
field's type is longblob, we don't know whether its autoSql definition
was a list (like exonStarts[exonCount]) or just an lstring. To play
it safe, we call it an lstring which works fine for feeding data
through the annoGrator system. However, when comparing a sql-derived
asObj with lstring to the real autoSql-derived asObj, asCompareObjs
will see different types for the same field and return false. So
for the purposes of recognizing a genePred, we need to simply compare
column names.
- src/hg/hgVai/libifyMe.c - lines changed 1, context: html, text, full: html, text
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 2, context: html, text, full: html, text
- src/hg/lib/annoFormatVep.c - lines changed 1, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 1, context: html, text, full: html, text
- Tweaking bigUrlToTrackLine to handle ".vcf.gz" which has two file extensions.
- minor: use stack instead of needMem for temporary string.
- In code review, Max pointed out that it's non-standard to conditionallyinclude header files in the middle of a .c file. While looking at it,
I realized that there were a lot of unnecessary #ifdef's for KNETFILE_HOOKS
in general, all because there was not yet an #else implementation of
knetUdcInstall, which can be a no-op if KNETFILE_HOOKS is not used.
So I yanked out a lot of unnecessary old stuff, and tested basic bam and
vcf track operations with a few settings:
USE_SAMTABIX USE_BAM USE_TABIX KNETFILE_HOOKS
1 (these tree are all implied by USE_SAMTABIX)
0 1 0 0
0 1 0 1
0 0 1 1
USE_TABIX without KNETFILE_HOOKS doesn't work because the tabix lib
wants to download .tbi files into the current working directory,
cgi-bin, and we don't allow that (and shouldn't!). If we were going
to support that, we could add a change-dir solution as in bamFile.c,
but I don't think we need to support it now that there's samtabix.
refs #6235, refs #12850
- src/hg/hgCustom/hgCustom.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgTables/hgTables.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgTracks/bamTrack.c - lines changed 4, context: html, text, full: html, text
- src/hg/hgTracks/vcfTrack.c - lines changed 10, context: html, text, full: html, text
- src/hg/hgVarAnnogrator/hgVarAnnogrator.c - lines changed 4, context: html, text, full: html, text
- src/hg/lib/tests/annoGratorTester.c - lines changed 6, context: html, text, full: html, text
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