braney: changes by commit

branch to review (2010-05-18 to 2010-05-25) v232

• change Tags view back to Alignments, move the Release Notes section
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.html 1.19 - lines changed: 6, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.new.ra 1.3 - lines changed: 1, context: html, text, full: html, text
• make all tier1 cell lines on by default
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeRikenCage.new.ra 1.4 - lines changed: 33, context: html, text, full: html, text
• add primary table and database to schema output
  • src/hg/hgTables/bigBed.c 1.10 - lines changed: 2, context: html, text, full: html, text
• moved into alpha
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/wgEncodeSydhTfbs.ra 1.2 - lines changed: 572, context: html, text, full: html, text
• this is down in metaDb now
  • src/hg/makeDb/trackDb/mouse/mm9/mdbSydhTfbs.ra 1.2 - lines changed: 551, context: html, text, full: html, text
• moved from above
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhHistone.ra 1.1 - lines changed: 29, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeSydhTfbs.ra 1.1 - lines changed: 572, context: html, text, full: html, text
• moved this down to metaDb
  • src/hg/makeDb/trackDb/mouse/mm9/mdbSydhHistone.ra 1.3 - lines changed: 29, context: html, text, full: html, text
• change download directory
  • src/hg/utils/automation/Encode.pm 1.65 - lines changed: 1, context: html, text, full: html, text
  • src/hg/utils/automation/HgAutomate.pm 1.28 - lines changed: 1, context: html, text, full: html, text
• add checking for sex of cell type for BAM's
  • src/hg/encode/encodeValidate/doEncodeValidate.pl 1.225 - lines changed: 26, context: html, text, full: html, text
• allow N's in both reference and query if nMatch is on.
  • src/hg/encode/validateFiles/validateFiles.c 1.42 - lines changed: 2, context: html, text, full: html, text
• add contact
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html 1.9 - lines changed: 9, context: html, text, full: html, text
• change Tags to Alignments in GIS RNA-seq, put space in SplitAligns
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.978 - lines changed: 8, context: html, text, full: html, text
• change SplitAligns to Split Alignments
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html 1.10 - lines changed: 2, context: html, text, full: html, text
• change more tags to alignments
  • src/hg/makeDb/trackDb/human/hg18/wgEncodeGisRnaSeq.html 1.11 - lines changed: 3, context: html, text, full: html, text
• only print out the item count on bigBed's after version 2 when the value is valid
  • src/hg/hgTables/bigBed.c 1.11 - lines changed: 5, context: html, text, full: html, text
• add sqlRenameTable
  • src/hg/inc/jksql.h 1.88 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/jksql.c 1.140 - lines changed: 8, context: html, text, full: html, text
• a utility to swap tables with renames while checking for existance
  • src/hg/hgsqlSwapTables/hgsqlSwapTables.c 1.1 - lines changed: 79, context: html, text, full: html, text
  • src/hg/hgsqlSwapTables/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
• add Ting's ucsfBrainMethyl track
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.488 - lines changed: 168, context: html, text, full: html, text
• description page for Ting's ucsfBrainMethyl track
  • src/hg/makeDb/trackDb/human/hg18/ucsfBrainMethyl.html 1.1 - lines changed: 84, context: html, text, full: html, text
• add bedGraph to dividers
  • src/hg/makeDb/trackDb/tagTypes.tab 1.27 - lines changed: 1, context: html, text, full: html, text
• set visibility modes for UCSF Brain DNA methylation
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.489 - lines changed: 3, context: html, text, full: html, text
• add release alpha to jim's encode regulation supertrack
  • src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra 1.983 - lines changed: 21, context: html, text, full: html, text