File Changes for kent

v281_base to v282_preview (2013-03-25 to 2013-04-02) v282

• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
  • lines changed 51, context: html, text, full: html, text
    Adding a new output - the list of files that we are changing, and what they get changed to.
• src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c
  • lines changed 39, context: html, text, full: html, text
    Making bit where it checks sizes and prints out validation fields and option.
• src/hg/encode3/importEncode2/encode2Md5UpdateManifest/encode2Md5UpdateManifest.c
  • lines changed 16, context: html, text, full: html, text
    Moving hashMd5File to library.
• src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
  • lines changed 1, context: html, text, full: html, text
    Suppressing hoisting of fileNames.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/encode2MetaPatchRenamed.c
  • lines changed 169, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
  • lines changed 5, context: html, text, full: html, text
    Reducing verbosity of a warning. Making it pass through if it has same name after patch rather than suppressing it.
  • lines changed 42, context: html, text, full: html, text
    Making it create subobjects when patching multiples in place of single old one, rather than creating siblings.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/expected.out
  • lines changed 134, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/makefile
  • lines changed 22, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/test.ra
  • lines changed 121, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/encode3/importEncode2/encode2MetaPatchRenamed/test.rename
  • lines changed 3, context: html, text, full: html, text
    Something to patch a meta tree in a particular way needed for encode2 seems to work.
• src/hg/hgTracks/multiWig.c
  • lines changed 4, context: html, text, full: html, text
    multiWig.c
  • lines changed 10, context: html, text, full: html, text
    Removing magic number per Kate's suggestion. Ref #10370
• src/hg/inc/encode3/encode2Manifest.h
  • lines changed 11, context: html, text, full: html, text
    Adding sveral new functions to handle short form manifests.
• src/hg/inc/meta.h
  • lines changed 58, context: html, text, full: html, text
    Writing some utility functions for meta files and related structures. I debated just using existing .ra infrastructure, but decided something smaller and more specialized would be helpful.
  • lines changed 20, context: html, text, full: html, text
    Adding several new functions to meta library.
  • lines changed 76, context: html, text, full: html, text
    Added test case.
• src/hg/lib/encode3/encode2Manifest.c
  • lines changed 39, context: html, text, full: html, text
    Adding sveral new functions to handle short form manifests.
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding meta to makefile.
  • lines changed 1, context: html, text, full: html, text
    Moving meta module to different library.
• src/hg/lib/meta.c
  • lines changed 295, context: html, text, full: html, text
    Writing some utility functions for meta files and related structures. I debated just using existing .ra infrastructure, but decided something smaller and more specialized would be helpful.
  • lines changed 44, context: html, text, full: html, text
    Adding several new functions to meta library.
  • lines changed 339, context: html, text, full: html, text
    Added test case.
• src/hg/oneShot/freen/freen.c
  • lines changed 18, context: html, text, full: html, text
    Testing some meta stuff.
• src/hg/utils/gffToBed/gffToBed.c
  • lines changed 1, context: html, text, full: html, text
    Adding a high verbosity message that may alleviate some mysteriousness.
• src/hg/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    Removing from makefile because it won't build.
• src/hg/utils/metaFlatten/expected.out
  • lines changed 116, context: html, text, full: html, text
    Adding test case.
  • lines changed 116, context: html, text, full: html, text
    Added test case.
• src/hg/utils/metaFlatten/makefile
  • lines changed 18, context: html, text, full: html, text
    Seems to work.
  • lines changed 4, context: html, text, full: html, text
    Adding test case.
  • lines changed 22, context: html, text, full: html, text
    Added test case.
• src/hg/utils/metaFlatten/metaFlatten.c
  • lines changed 82, context: html, text, full: html, text
    Seems to work.
  • lines changed 82, context: html, text, full: html, text
    Added test case.
• src/hg/utils/metaFlatten/test.in
  • lines changed 38, context: html, text, full: html, text
    Adding test case.
  • lines changed 38, context: html, text, full: html, text
    Added test case.
• src/inc/bbiFile.h
  • lines changed 1, context: html, text, full: html, text
    Improved readability and removed unused function parameter. Ref #10428.
• src/inc/gff.h
  • lines changed 1, context: html, text, full: html, text
    Unrolling gff changes that broke some of Mark's tests.
  • lines changed 1, context: html, text, full: html, text
    Small conservative change to gff/gtf reader, just to count # of each feature in file.
• src/inc/md5.h
  • lines changed 3, context: html, text, full: html, text
    Making function that puts an md5sum file into a hash.
• src/inc/meta.h
  • lines changed 76, context: html, text, full: html, text
    Added test case.
• src/lib/bbiWrite.c
  • lines changed 1, context: html, text, full: html, text
    Improved readability and removed unused function parameter. Ref #10428.
• src/lib/bigBed.c
  • lines changed 2, context: html, text, full: html, text
    Improved readability and removed unused function parameter. Ref #10428.
• src/lib/gff.c
  • lines changed 131, context: html, text, full: html, text
    Unrolling gff changes that broke some of Mark's tests.
  • lines changed 2, context: html, text, full: html, text
    Small conservative change to gff/gtf reader, just to count # of each feature in file.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving meta module to different library.
• src/lib/md5.c
  • lines changed 14, context: html, text, full: html, text
    Making function that puts an md5sum file into a hash.
• src/lib/meta.c
  • lines changed 339, context: html, text, full: html, text
    Added test case.
• src/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving meta stuff out of hg. It's not really browser specific yet.
• src/meta/makefile
  • lines changed 14, context: html, text, full: html, text
    Moving meta stuff out of hg. It's not really browser specific yet.
  • lines changed 1, context: html, text, full: html, text
    Added -f flag to rm, so it won't abort when there's nothing to remove.
• src/meta/metaFlatten/expected.out
  • lines changed 116, context: html, text, full: html, text
    Added test case.
• src/meta/metaFlatten/makefile
  • lines changed 22, context: html, text, full: html, text
    Added test case.
  • lines changed 3, context: html, text, full: html, text
    Moving meta stuff out of hg. It's not really browser specific yet.
• src/meta/metaFlatten/metaFlatten.c
  • lines changed 82, context: html, text, full: html, text
    Added test case.
• src/meta/metaFlatten/test.in
  • lines changed 38, context: html, text, full: html, text
    Added test case.
• src/meta/metaReformat/expected.out
  • lines changed 32, context: html, text, full: html, text
    Added test case.
• src/meta/metaReformat/makefile
  • lines changed 22, context: html, text, full: html, text
    Added test case.
• src/meta/metaReformat/metaReformat.c
  • lines changed 51, context: html, text, full: html, text
    Oops forgot main module.
• src/meta/metaReformat/test.in
  • lines changed 28, context: html, text, full: html, text
    Added test case.
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 4, context: html, text, full: html, text
    Improved readability and removed unused function parameter. Ref #10428.
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 3, context: html, text, full: html, text
    Adding whitespace to improve readability. Ref #10370