Commits for angie

v308_preview2 to v308_base (2014-10-27 to 2014-11-03) v308

• I was under the mistaken impression that VCF header ##INFO andencouraged." This change remove errors about missing descriptions
  that were causing hgTables to give up after 101 errors on a track
  hub VCF. While inspecting the code I found that hgc's vcfClick.c
  printKeysWithDescriptions had never made use of its infoDefs arg
  as intended, so descriptions from ##ALT (symbolic alternate alleles)
  and ##FILTER were not displayed -- fixed that.
  refs #14231
  
  • src/hg/hgTables/vcf.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgc/vcfClick.c - lines changed 33, context: html, text, full: html, text
  • src/lib/vcf.c - lines changed 16, context: html, text, full: html, text
• Removing errors from expected output, after errors were removed from vcf.c in 294e289 because they're not actually errors.
  • src/lib/tests/expected/vcfParseOldV3.out - lines changed 28, context: html, text, full: html, text
• hgLiftOver was missing a call to setUdcCacheDir leading to erroneoususe of /tmp/udcCache instead of hg.conf setting.
  
  • src/hg/hgLiftOver/hgLiftOver.c - lines changed 1, context: html, text, full: html, text
• hgNear, hgVisiGene and phyloGif were missing a call to setUdcCacheDir leading to erroneous use of /tmp/udcCache instead of hg.conf setting.
  • src/hg/near/hgNear/hgNear.c - lines changed 1, context: html, text, full: html, text
  • src/hg/phyloGif/phyloGif.c - lines changed 1, context: html, text, full: html, text
  • src/hg/visiGene/hgVisiGene/hgVisiGene.c - lines changed 1, context: html, text, full: html, text
• Allow start==end in hgTables' user-defined regions BED (valid for insertions).fixes #14238
  
  • src/hg/hgTables/userRegions.c - lines changed 2, context: html, text, full: html, text
• At Jorge's request, adding a FLUSH TABLES to the end of the temporarySQL file that creates tableDescriptions, in hopes that this will end
  myisamchk errors about the table not being closed properly.
  
  • src/test/buildTableDescriptions.pl - lines changed 3, context: html, text, full: html, text
• Made checkTableCoords skip the tests for overlapping blocks andinconsistent ends if the table name starts with bacEnd or cloneEnd,
  because it's legit for those particular tables to have some scrambled
  alignments to the reference genome.
  
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 5, context: html, text, full: html, text
• Adding a couple exemptions to checkTableCoords for {bac,clone}End*Orphan* tracks. Moved the exemptions up to where the comparisons are made (and verbose-mode errors printed out) instead of where summaries are printed.
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 46, context: html, text, full: html, text
• When lookupPosition() returns false (multiple search results), thesubsequent call to doMainPage(conn, TRUE) was causing a popWarnHandler
  underflow errAbort because doMainPage ends with an htmlClose (which
  btw invokes popWarnHandler three times: one directly, once in
  cartWebEnd and once in webEnd). The symptom was that changes made to
  the main page form before looking up a term that returned multiple
  results were lost because the underflow errAbort prevented the cart
  from being saved. The solution is to not use doMainPage(conn, TRUE)
  but instead to call mainPageAfterOpen enclosed by push and pop of
  web warn/error handlers.
  
  Since doMainPage(conn, TRUE) caused trouble that can be avoided by
  calling mainPageAfterOpen, I removed the option.
  
  I also removed dead code doLookupPosition; dispatch is called only
  when lookupPosition() has already returned a single match, so the
  work is already done and it will default to the main page anyway.
  
  refs #12557
  
  • src/hg/hgTables/bedList.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/compositeTrack.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/correlate.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/custom.c - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c - lines changed 18, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h - lines changed 1, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c - lines changed 2, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c - lines changed 2, context: html, text, full: html, text
• Oops, moved something up before a for loop that needed to happen afterwards -- fixed.
  • src/hg/checkTableCoords/checkTableCoords.c - lines changed 21, context: html, text, full: html, text