File Changes for hiram

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

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