File Changes for kent

v344_preview to v344_preview2 (2017-01-16 to 2017-01-23) v344

• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    5eee234b477ed74599b35af7cbad1de195fae16b Sat Jan 21 14:18:32 2017 -0800
    Adding cmpStringOrder routine to force order to conform to a predefined explicit nonalphabetical order.
• src/inc/fieldedTable.h
  • lines changed 1, context: html, text, full: html, text
    1a3364b243b46f7cf3afe58688d6a8cc85e726cf Fri Jan 20 09:58:44 2017 -0800
    Adding rowCount to fieldedTable and refactoring tagStormFromTab a bit.
• src/inc/tagStorm.h
  • lines changed 4, context: html, text, full: html, text
    cdfb695ee8fc4dcb613e443f602cd526b4d250aa Thu Jan 19 23:47:48 2017 -0800
    Adding tagStormHoist to tagSTorm.h, also making it so that the function will put in a single root node for forests, so can have a place to hoist tags shared by all in that case.
  • lines changed 6, context: html, text, full: html, text
    387fdf87c4514e568a9c4c4685fba8d0b0f3c7cd Sat Jan 21 14:19:54 2017 -0800
    Adding sort routines for fields in stanzas.
• src/inc/tagToSql.h
  • lines changed 9, context: html, text, full: html, text
    6762c9714af0d2d3fd83a9a10597d92ab6e170d6 Sat Jan 21 08:00:29 2017 -0800
    Exposing tagType functions tagTypeInfoNew and tagTypeInfoAdd to other modules and writing tagTypeInfoFree for benefit of tagStormFromTab.
• src/lib/common.c
  • lines changed 19, context: html, text, full: html, text
    5eee234b477ed74599b35af7cbad1de195fae16b Sat Jan 21 14:18:32 2017 -0800
    Adding cmpStringOrder routine to force order to conform to a predefined explicit nonalphabetical order.
• src/lib/fieldedTable.c
  • lines changed 1, context: html, text, full: html, text
    1a3364b243b46f7cf3afe58688d6a8cc85e726cf Fri Jan 20 09:58:44 2017 -0800
    Adding rowCount to fieldedTable and refactoring tagStormFromTab a bit.
• src/lib/tagStorm.c
  • lines changed 109, context: html, text, full: html, text
    cec3ab53880681ae1792a643f9c9e81fb9325571 Thu Jan 19 19:19:38 2017 -0800
    Moving tagStormHoist code to library.
  • lines changed 13, context: html, text, full: html, text
    cdfb695ee8fc4dcb613e443f602cd526b4d250aa Thu Jan 19 23:47:48 2017 -0800
    Adding tagStormHoist to tagSTorm.h, also making it so that the function will put in a single root node for forests, so can have a place to hoist tags shared by all in that case.
  • lines changed 1, context: html, text, full: html, text
    813873c75553cc797a25514a86e3d4f7d9511122 Sat Jan 21 09:32:39 2017 -0800
    Adjusting verbosity levels.
  • lines changed 49, context: html, text, full: html, text
    387fdf87c4514e568a9c4c4685fba8d0b0f3c7cd Sat Jan 21 14:19:54 2017 -0800
    Adding sort routines for fields in stanzas.
• src/lib/tagToSql.c
  • lines changed 13, context: html, text, full: html, text
    6762c9714af0d2d3fd83a9a10597d92ab6e170d6 Sat Jan 21 08:00:29 2017 -0800
    Exposing tagType functions tagTypeInfoNew and tagTypeInfoAdd to other modules and writing tagTypeInfoFree for benefit of tagStormFromTab.
• src/tagStorm/tagStormFromTab/tagStormFromTab.c
  • lines changed 112, context: html, text, full: html, text
    f410105db0b3a911e646540347a9f77eacd62923 Wed Jan 18 12:20:23 2017 -0800
    Improving according to Max's feedback. In particular this avoids outputting blank fields, and also weights fields in deciding which one to partition on first in a way that works better for the big data set Max found.
  • lines changed 2, context: html, text, full: html, text
    49d86cd9b0e9281c9f55cf2fe44291cdfe3cea2f Thu Jan 19 11:20:01 2017 -0800
    Cleaning up more memory. Better inclusion of fields.
  • lines changed 206, context: html, text, full: html, text
    1c59685f3b4193f062ea8c52c884593ee5dd5e8d Thu Jan 19 14:34:01 2017 -0800
    Put in a new method for calculating the divs, which is now default. Use the 'local' flag to get the old way. I'm likely to simplify the old way soon.
  • lines changed 99, context: html, text, full: html, text
    cd6894da275f1408964f9e42ba7490c0a4c2b622 Thu Jan 19 15:24:03 2017 -0800
    Cleaning up some memory.
  • lines changed 7, context: html, text, full: html, text
    4f252b105cea62a65ef611f1c122a53ea1b98e9f Thu Jan 19 23:49:18 2017 -0800
    Making it hoist by default at end (but adding a noHoist option). Also makinga debugging dump function go to stderr rather than stdout.
  • lines changed 103, context: html, text, full: html, text
    1a3364b243b46f7cf3afe58688d6a8cc85e726cf Fri Jan 20 09:58:44 2017 -0800
    Adding rowCount to fieldedTable and refactoring tagStormFromTab a bit.
  • lines changed 420, context: html, text, full: html, text
    63969df56a4c7d3728052a8a8a1577ab0cef0c2d Fri Jan 20 11:13:57 2017 -0800
    Making local partitioning use same scoring scheme as global partitioning.
  • lines changed 50, context: html, text, full: html, text
    1a84329d8f1d64d817bb479e6475e64bb7b06eab Fri Jan 20 17:43:37 2017 -0800
    Calculating size of predictor chain to aid partitioning. Adding more info to dumps for debugging.
  • lines changed 45, context: html, text, full: html, text
    9f47439d246bdf7624581fb48e75edcceae8a3e0 Sat Jan 21 08:01:21 2017 -0800
    Discouraging partitioning on numerical fields, especially non-integer ones.
  • lines changed 117, context: html, text, full: html, text
    e9277b1493ec38adef034a36778b3353430e8f16 Sat Jan 21 08:07:56 2017 -0800
    Removing unused routines and making all routines except main static.
  • lines changed 15, context: html, text, full: html, text
    813873c75553cc797a25514a86e3d4f7d9511122 Sat Jan 21 09:32:39 2017 -0800
    Adjusting verbosity levels.
  • lines changed 5, context: html, text, full: html, text
    e3c2c344823583895d01c4ac539d18d96c2558fe Sat Jan 21 09:59:45 2017 -0800
    Fixing memory leaks
  • lines changed 15, context: html, text, full: html, text
    653d5099ccc1a73d3663e6b0b8ad8fcadb8e1c2f Sat Jan 21 14:22:06 2017 -0800
    Making it sort tags in stanzas alphabetically by default, and have an option that explicitly keeps same order as input tab-separated-file. It used to end up with order that largely followed input order, but had some random elements. Had to define a new sorting routine to get back old order in this case.
• src/tagStorm/tagStormHoist/expected.out
  • lines changed 70, context: html, text, full: html, text
    77325cc1b1dc7cde1a835f6163d5a17624d0c958 Thu Jan 19 19:16:02 2017 -0800
    updating test set
• src/tagStorm/tagStormHoist/tagStormHoist.c
  • lines changed 23, context: html, text, full: html, text
    d1ea4d0bc9a04dd97b213728eb9e6682b5826ad2 Thu Jan 19 19:17:19 2017 -0800
    Refactoring a bit in anticipation of moving code to library.
  • lines changed 110, context: html, text, full: html, text
    cec3ab53880681ae1792a643f9c9e81fb9325571 Thu Jan 19 19:19:38 2017 -0800
    Moving tagStormHoist code to library.
• src/tagStorm/tagStormHoist/test.in
  • lines changed 2, context: html, text, full: html, text
    77325cc1b1dc7cde1a835f6163d5a17624d0c958 Thu Jan 19 19:16:02 2017 -0800
    updating test set