Commits for kate

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

• First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
  • src/hg/utils/bedScore/.bedScore.c.swp - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/bedScore/bedScore - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
  • src/hg/utils/bedScore/bedScore.c - lines changed 267, context: html, text, full: html, text
  • src/hg/utils/bedScore/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/bedScore/tests/expected/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/bedScore/tests/input/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/bedScore/tests/makefile - lines changed 11, context: html, text, full: html, text
• Moving utility up a level in the tree.
  • src/hg/utils/bedScore/bedScore.c - lines changed 267, context: html, text, full: html, text
  • src/hg/utils/bedScore/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/bedScore/tests/expected/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/bedScore/tests/input/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/bedScore/tests/makefile - lines changed 11, context: html, text, full: html, text
  • src/utils/bedScore/bedScore.c - lines changed 267, context: html, text, full: html, text
  • src/utils/bedScore/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 11, context: html, text, full: html, text
• 1. Change default minScore to 0. 2. Improve modularization
  • src/utils/bedScore/bedScore.c - lines changed 106, context: html, text, full: html, text
• Redo path after moving the dir
  • src/utils/bedScore/makefile - lines changed 1, 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/encodeTfbsTest.bed - lines changed 31515, context: html, text, full: html, text
  • 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/makefile - lines changed 6, context: html, text, full: html, text
• Removing bogusly committed tmp file
  • src/hg/utils/bedScore/.bedScore.c.swp - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Removing bogusly committed executable file
  • src/hg/utils/bedScore/bedScore - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change shows no diff)
• Redesign to support the multiple scorers
  • src/utils/bedScore/bedScore.c - lines changed 159, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/miniTest.bed - lines changed 5, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/encodeTest.bed - lines changed 5, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/miniTest.bed - lines changed 5, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 10, context: html, text, full: html, text
• Resolve merge conflict
  • src/utils/bedScore/tests/makefile - lines changed 11, context: html, text, full: html, text
• Add tests
  • src/utils/bedScore/tests/expected/encodeSmallTfbs.bed - lines changed 101, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/encodeSmallTfbs.bed - lines changed 101, context: html, text, full: html, text
• Add scoring method 'reg', used in ENCODE regulatory track
  • src/utils/bedScore/bedScore.c - lines changed 156, context: html, text, full: html, text
  • src/utils/bedScore/tests/expected/encodeRegTest.bed - lines changed 44159, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/hsmmCtcfJan2011.narrowPeak - lines changed 44159, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 8, context: html, text, full: html, text
• Remove code snippet for reg method
  • src/utils/bedScore/bedScore.c - lines changed 30, context: html, text, full: html, text
• Add support for processing multiple files. refs #10569
  • src/utils/bedScore/bedScore.c - lines changed 41, context: html, text, full: html, text
• Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
  • src/utils/bedScore/bedScore.c - lines changed 105, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/uniform1.bed - lines changed 10, context: html, text, full: html, text
  • src/utils/bedScore/tests/input/uniform2.bed - lines changed 10, context: html, text, full: html, text
  • src/utils/bedScore/tests/makefile - lines changed 7, context: html, text, full: html, text
• Tighten up code for multiple files with uniform option. refs #10569
  • src/utils/bedScore/bedScore.c - lines changed 64, context: html, text, full: html, text
• Add test for -uniform option. refs #10569
  • src/utils/bedScore/tests/makefile - lines changed 1, context: html, text, full: html, text
• FIxed problem with pathname interpretation. refs #10569.
  • src/utils/bedScore/bedScore.c - lines changed 11, context: html, text, full: html, text