kent: changes by file

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

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