kent: changes by commit

branch to review (2010-03-02 to 2010-03-16) v227

• Putting in check for uniqueness of target sequence names.
  • src/jkOwnLib/genoFind.c 1.27 - lines changed: 15, context: html, text, full: html, text
• Bumping version number.
  • src/inc/genoFind.h 1.82 - lines changed: 1, context: html, text, full: html, text
• Describing new input sanity check.
  • src/blat/version.doc 1.76 - lines changed: 2, context: html, text, full: html, text
• Adding new blat test case.
  • src/blat/test/dupeTargetName/q.fa 1.1 - lines changed: 2, context: html, text, full: html, text
  • src/blat/test/dupeTargetName/t.fa 1.1 - lines changed: 34, context: html, text, full: html, text
• Improving handling of release tags. Case where have alpha and beta in composite tracks works better.
  • src/hg/utils/tdbQuery/tdbQuery.c 1.30 - lines changed: 114, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.c 1.8 - lines changed: 10, context: html, text, full: html, text
  • src/hg/utils/tdbQuery/tdbRecord.h 1.4 - lines changed: 3, context: html, text, full: html, text
• Getting rid of some records that mix releases at different levels.
  • src/hg/makeDb/trackDb/apis/trackDb.ra 1.15 - lines changed: 24, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/dp1/trackDb.ra 1.16 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droAna1/trackDb.ra 1.15 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droMoj1/trackDb.ra 1.14 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droVir1/trackDb.ra 1.14 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/droYak1/trackDb.ra 1.17 - lines changed: 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/drosophila/trackDb.ra 1.87 - lines changed: 13, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/trackDb.ra 1.523 - lines changed: 26, context: html, text, full: html, text
• First cut of some code to combine ENCODE regulatory tracks into a single track done.
  • src/hg/regulate/regCluster/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/regulate/regCluster/regCluster.c 1.1 - lines changed: 220, context: html, text, full: html, text
  • src/hg/regulate/regClusterBedExpCfg/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/regulate/regClusterBedExpCfg/regClusterBedExpCfg.c 1.1 - lines changed: 154, context: html, text, full: html, text
  • src/hg/regulate/regClusterMakeTableOfTables/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c 1.1 - lines changed: 162, context: html, text, full: html, text
• Small tweaking to get it to work with real rather than pretend data.
  • src/hg/makeDb/hgBedsToBedExps/bToBeCfg.as 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/hgBedsToBedExps/bToBeCfg.c 1.2 - lines changed: 7, context: html, text, full: html, text
  • src/hg/makeDb/hgBedsToBedExps/bToBeCfg.h 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/hgBedsToBedExps/bToBeCfg.sql 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/makeDb/hgBedsToBedExps/hgBedsToBedExps.c 1.3 - lines changed: 26, context: html, text, full: html, text
  • src/hg/makeDb/hgBedsToBedExps/tests/first/in.cfg 1.2 - lines changed: 12, context: html, text, full: html, text
• Adding a new experimental track.
  • src/hg/makeDb/trackDb/human/hg18/trackDb.ra 1.473 - lines changed: 9, context: html, text, full: html, text
• Making it so that it will break up clusters that are weakly linked.
  • src/hg/regulate/regCluster/makefile 1.2 - lines changed: 5, context: html, text, full: html, text
  • src/hg/regulate/regCluster/regCluster.c 1.2 - lines changed: 166, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/a.bed 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/b.bed 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/c.bed 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/d.bed 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/e.bed 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/expected.bed 1.1 - lines changed: 4, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/expected.cluster 1.1 - lines changed: 22, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/f.bed 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/g.bed 1.1 - lines changed: 3, context: html, text, full: html, text
  • src/hg/regulate/regCluster/tests/needBreak/in.tab 1.1 - lines changed: 7, context: html, text, full: html, text
• Little program to calculate mean/std and quartile stats for a bunch of bed files.
  • src/hg/regulate/regBedStats/makefile 1.1 - lines changed: 18, context: html, text, full: html, text
  • src/hg/regulate/regBedStats/regBedStats.c 1.1 - lines changed: 144, context: html, text, full: html, text
• Adding doubleBoxWhiskerCalc to library.
  • src/inc/common.h 1.167 - lines changed: 8, context: html, text, full: html, text
  • src/lib/common.c 1.144 - lines changed: 35, context: html, text, full: html, text
• Moving doubleBoxWhiskerCalc to library.
  • src/hg/regulate/regBedStats/regBedStats.c 1.2 - lines changed: 35, context: html, text, full: html, text
• Removing -two option.
  • src/hg/regulate/regClusterMakeTableOfTables/regClusterMakeTableOfTables.c 1.2 - lines changed: 35, context: html, text, full: html, text
• Fixing compile errors under Linux.
  • src/lib/common.c 1.145 - lines changed: 2, context: html, text, full: html, text
• Improved an error message.
  • src/hg/lib/customFactory.c 1.117 - lines changed: 1, context: html, text, full: html, text