Commits for angie

v295_base to v296_preview (2014-02-03 to 2014-02-10) v296

• In bedAsDef(), use lstring instead of string for those 'undocumented fields' which can be larger than varchar(255).
  • src/lib/basicBed.c - lines changed 1, context: html, text, full: html, text
• Built snp138 tables for bosTau7 and susScr3. Along the way, severalrefinements to doDbSnp.pl and snpNcbiToUcsc were required. refs #12490
  
  • src/hg/makeDb/doc/bosTau7.txt - lines changed 183, context: html, text, full: html, text
  • src/hg/makeDb/doc/susScr3.txt - lines changed 126, context: html, text, full: html, text
  • src/hg/snp/snpLoad/snpNcbiToUcsc.c - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/automation/doDbSnp.pl - lines changed 23, context: html, text, full: html, text
• hgLoadBed's -type=bedN[+[P]] option, when N < 9, should imply thatthe 9th column is not to be treated as itemRgb. (There is also
  a -notItemRgb option, but really, -type=bedN should be enough.)
  I found that -type was processed only inside the main loop of
  loadOneBed, intermixed with some autoSql-processing logic.
  I moved out the autoSql, field-counting, type-parsing and -checking
  logic into separate functions. It turned out that they did not need
  to be inside that loop after all; there is enough information to
  figure them out up front, and the loop needs only to check that each
  line has the predetermined correct number of rows.
  
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 156, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadBed/tests/RunTest.sh - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadBed/tests/bed6plus19.txt.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/makeDb/hgLoadBed/tests/chrom.sizes - lines changed 93, context: html, text, full: html, text
• Updating databasesIgnored with some recent dbSNP build databases.
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• Fixing a couple comments that promise too much.
  • src/inc/hash.h - lines changed 4, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 5, context: html, text, full: html, text
• Adding missing NULL check. On hgwdev, without this fix we get a SEGV:- cartReset
  - hgTables
  - change group to "all tables" --> page draws halfway
  Fortunately I don't see that on hgwbeta.
  
  • src/hg/lib/jksql.c - lines changed 3, context: html, text, full: html, text