File Changes for kate

v282_preview to v282_preview2 (2013-04-02 to 2013-04-09) v282

• src/hg/utils/bedScore/.bedScore.c.swp
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    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • lines changed 0, context: html, text, full: html, text
    Removing bogusly committed tmp file
• src/hg/utils/bedScore/bedScore
  • lines changed 0, context: html, text, full: html, text
    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • lines changed 0, context: html, text, full: html, text
    Removing bogusly committed executable file
• src/hg/utils/bedScore/bedScore.c
  • lines changed 267, context: html, text, full: html, text
    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • lines changed 267, context: html, text, full: html, text
    Moving utility up a level in the tree.
• src/hg/utils/bedScore/makefile
  • lines changed 3, context: html, text, full: html, text
    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • lines changed 3, context: html, text, full: html, text
    Moving utility up a level in the tree.
• src/hg/utils/bedScore/tests/expected/encodeTest.bed
  • lines changed 5, context: html, text, full: html, text
    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • lines changed 5, context: html, text, full: html, text
    Moving utility up a level in the tree.
• src/hg/utils/bedScore/tests/input/encodeTest.bed
  • lines changed 5, context: html, text, full: html, text
    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • lines changed 5, context: html, text, full: html, text
    Moving utility up a level in the tree.
• src/hg/utils/bedScore/tests/makefile
  • lines changed 11, context: html, text, full: html, text
    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • lines changed 11, context: html, text, full: html, text
    Moving utility up a level in the tree.
• src/utils/bedScore/bedScore.c
  • lines changed 267, context: html, text, full: html, text
    Moving utility up a level in the tree.
  • lines changed 106, context: html, text, full: html, text
    1. Change default minScore to 0. 2. Improve modularization
  • lines changed 159, context: html, text, full: html, text
    Redesign to support the multiple scorers
  • lines changed 156, context: html, text, full: html, text
    Add scoring method 'reg', used in ENCODE regulatory track
  • lines changed 30, context: html, text, full: html, text
    Remove code snippet for reg method
  • lines changed 41, context: html, text, full: html, text
    Add support for processing multiple files. refs #10569
  • lines changed 105, context: html, text, full: html, text
    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
  • lines changed 64, context: html, text, full: html, text
    Tighten up code for multiple files with uniform option. refs #10569
  • lines changed 11, context: html, text, full: html, text
    FIxed problem with pathname interpretation. refs #10569.
• src/utils/bedScore/makefile
  • lines changed 3, context: html, text, full: html, text
    Moving utility up a level in the tree.
  • lines changed 1, context: html, text, full: html, text
    Redo path after moving the dir
• src/utils/bedScore/tests/expected/encodeRegTest.bed
  • lines changed 44159, context: html, text, full: html, text
    Add scoring method 'reg', used in ENCODE regulatory track
• src/utils/bedScore/tests/expected/encodeSmallTfbs.bed
  • lines changed 101, context: html, text, full: html, text
    Add tests
• src/utils/bedScore/tests/expected/encodeTest.bed
  • lines changed 5, context: html, text, full: html, text
    Moving utility up a level in the tree.
  • lines changed 5, context: html, text, full: html, text
    Redesign to support the multiple scorers
• src/utils/bedScore/tests/expected/encodeTfbsTest.bed
  • lines changed 31515, context: html, text, full: html, text
    Add realistic test of encode method (wgEncodeAwgTfbsUwWi38CtcfUniPk, with a few rows dropped where C lib round differs from SQL round function)
• src/utils/bedScore/tests/expected/miniTest.bed
  • lines changed 5, context: html, text, full: html, text
    Redesign to support the multiple scorers
• src/utils/bedScore/tests/input/encodeSmallTfbs.bed
  • lines changed 101, context: html, text, full: html, text
    Add tests
• src/utils/bedScore/tests/input/encodeTest.bed
  • lines changed 5, context: html, text, full: html, text
    Moving utility up a level in the tree.
  • lines changed 5, context: html, text, full: html, text
    Redesign to support the multiple scorers
• src/utils/bedScore/tests/input/encodeTfbsTest.bed
  • lines changed 31515, context: html, text, full: html, text
    Add realistic test of encode method (wgEncodeAwgTfbsUwWi38CtcfUniPk, with a few rows dropped where C lib round differs from SQL round function)
• src/utils/bedScore/tests/input/hsmmCtcfJan2011.narrowPeak
  • lines changed 44159, context: html, text, full: html, text
    Add scoring method 'reg', used in ENCODE regulatory track
• src/utils/bedScore/tests/input/miniTest.bed
  • lines changed 5, context: html, text, full: html, text
    Redesign to support the multiple scorers
• src/utils/bedScore/tests/input/uniform1.bed
  • lines changed 10, context: html, text, full: html, text
    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
• src/utils/bedScore/tests/input/uniform2.bed
  • lines changed 10, context: html, text, full: html, text
    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
• src/utils/bedScore/tests/makefile
  • lines changed 11, context: html, text, full: html, text
    Moving utility up a level in the tree.
  • lines changed 6, context: html, text, full: html, text
    Add realistic test of encode method (wgEncodeAwgTfbsUwWi38CtcfUniPk, with a few rows dropped where C lib round differs from SQL round function)
  • lines changed 10, context: html, text, full: html, text
    Redesign to support the multiple scorers
  • lines changed 11, context: html, text, full: html, text
    Resolve merge conflict
  • lines changed 8, context: html, text, full: html, text
    Add scoring method 'reg', used in ENCODE regulatory track
  • lines changed 7, context: html, text, full: html, text
    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
  • lines changed 1, context: html, text, full: html, text
    Add test for -uniform option. refs #10569