Commits for hiram

v303_base to v304_preview (2014-07-21 to 2014-07-28) v304

• fixup slAddHead argument reference refs #9741
  • src/hg/hgTracks/joinedRmskTrack.c - lines changed 2, context: html, text, full: html, text
• temporary avoid description field refs #9741
  • src/hg/lib/rmskJoined.c - lines changed 2, context: html, text, full: html, text
• completed the joinedRmsk click handling refs #9741
  • src/hg/hgc/hgc.c - lines changed 4, context: html, text, full: html, text
  • src/hg/hgc/hgc.h - lines changed 3, context: html, text, full: html, text
  • src/hg/hgc/joinedRmskClick.c - lines changed 4, context: html, text, full: html, text
• loader for new style 'joined' rmsk track refs #9741
  • src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c - lines changed 395, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadOutJoined/makefile - lines changed 3, context: html, text, full: html, text
• add hgLoadOutJoined to the utils build refs #9741
  • src/hg/makeDb/makefile - lines changed 1, context: html, text, full: html, text
• eliminate split options and setup correct default table name
  • src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c - lines changed 85, context: html, text, full: html, text
• setup indexes for these new rmsk tables refs #9741
  • src/hg/lib/rmskAlign.sql - lines changed 1, context: html, text, full: html, text
  • src/hg/lib/rmskJoined.sql - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/rmskOut2.sql - lines changed 2, context: html, text, full: html, text
• correctly using sqlDyStringPrintf refs #9741
  • src/hg/hgTracks/joinedRmskTrack.c - lines changed 3, context: html, text, full: html, text
• no longer useful
  • src/hg/htdocs/google/index.html - lines changed 14, context: html, text, full: html, text
  • src/hg/htdocs/google/sitemap.xml.gz - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• trying 0-relative genoStart on rmskAlignBaseline table refs #9741
  • src/hg/hgc/joinedRmskClick.c - lines changed 3, context: html, text, full: html, text
• display alignStart 1-relative for users refs #9741
  • src/hg/hgc/joinedRmskClick.c - lines changed 1, context: html, text, full: html, text
• the extra periods on the end of the sentence fragments show up in the hgc click page refs #13578
  • src/hg/lib/nestedRepeats.as - lines changed 4, context: html, text, full: html, text
  • src/hg/lib/nestedRepeats.sql - lines changed 3, context: html, text, full: html, text
• adding search rule for gold table refs #13578
  • src/hg/makeDb/trackDb/rat/rn6/trackDb.ra - lines changed 8, context: html, text, full: html, text
• eliminating the description field and named as rmskJoinedBaseline for table browser recognition in tableDescriptions refs #9741
  • src/hg/lib/rmskJoined.as - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/rmskJoined.c - lines changed 5, context: html, text, full: html, text
  • src/hg/lib/rmskJoined.sql - lines changed 3, context: html, text, full: html, text
• adding rules for the rmskJoined tables;
  • src/hg/makeDb/schema/all.joiner - lines changed 5, context: html, text, full: html, text
• adding rules for the rmskJoined tables refs #9741;
  • src/hg/makeDb/schema/all.joiner - lines changed 1, context: html, text, full: html, text
• display genoStart 1-relative for users refs #9741
  • src/hg/hgc/joinedRmskClick.c - lines changed 2, context: html, text, full: html, text
• different track group for joinedRmsk refs #9741
  • src/hg/makeDb/trackDb/mouse/mm10/trackDb.ra - lines changed 3, context: html, text, full: html, text
• correct formatting on single statement if() statements refs #9741
  • src/hg/hgTracks/joinedRmskTrack.c - lines changed 14, context: html, text, full: html, text
• correct formatting on single statement if() statements refs #9741
  • src/hg/hgc/joinedRmskClick.c - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• more info on the bad rep range error message refs #9741
  • src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c - lines changed 2, context: html, text, full: html, text
• more information on the table definition creation refs #9741
  • src/hg/makeDb/hgLoadBed/hgLoadBed.c - lines changed 2, context: html, text, full: html, text
• adding RepeatMasker Visualization track build procedure refs #9741
  • src/hg/makeDb/doc/hg38.txt - lines changed 27, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.txt - lines changed 31, context: html, text, full: html, text
• (parens) do not really mean negative numbers refs #9741
  • src/hg/makeDb/hgLoadOutJoined/hgLoadOutJoined.c - lines changed 9, context: html, text, full: html, text
• lift overs rn5<->rn6 both ways refs #13578
  • src/hg/makeDb/doc/rn5.txt - lines changed 13, context: html, text, full: html, text
  • src/hg/makeDb/doc/rn6.txt - lines changed 14, context: html, text, full: html, text
• papAnu2 to hg19 liftOver done refs #13695
  • src/hg/makeDb/doc/hg19.txt - lines changed 10, context: html, text, full: html, text
• papAnu2 to hg19 liftOver done refs #13695
  • src/hg/makeDb/doc/hg19.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/papAnu2.txt - lines changed 21, context: html, text, full: html, text
• v304 preview1 refs #13703
  • src/utils/qa/weeklybld/buildEnv.csh - lines changed 2, context: html, text, full: html, text