Commits for kent
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v281_base to v282_preview (2013-03-25 to 2013-04-02) v282
- Unrolling gff changes that broke some of Mark's tests.
- multiWig.c
- src/hg/hgTracks/multiWig.c - lines changed 4, 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.
- Seems to work.
- src/hg/utils/metaFlatten/makefile - lines changed 18, context: html, text, full: html, text
- src/hg/utils/metaFlatten/metaFlatten.c - lines changed 82, context: html, text, full: html, text
- Adding test case.
- src/hg/utils/metaFlatten/expected.out - lines changed 116, context: html, text, full: html, text
- src/hg/utils/metaFlatten/makefile - lines changed 4, context: html, text, full: html, text
- src/hg/utils/metaFlatten/test.in - lines changed 38, 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/encode2MetaPatchRenamed.c - lines changed 169, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MetaPatchRenamed/expected.out - lines changed 134, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MetaPatchRenamed/makefile - lines changed 22, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MetaPatchRenamed/test.ra - lines changed 121, context: html, text, full: html, text
- src/hg/encode3/importEncode2/encode2MetaPatchRenamed/test.rename - lines changed 3, 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.
- src/hg/encode3/importEncode2/encode2MetaPatchRenamed/encode2MetaPatchRenamed.c - lines changed 5, context: html, text, full: html, text
- Making function that puts an md5sum file into a hash.
- Adding several new functions to meta library.
- Adding meta to makefile.
- Adding sveral new functions to handle short form manifests.
- src/hg/inc/encode3/encode2Manifest.h - lines changed 11, context: html, text, full: html, text
- src/hg/lib/encode3/encode2Manifest.c - lines changed 39, 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/encode2MakeEncode3/encode2MakeEncode3.c - lines changed 51, context: html, text, full: html, text
- Making bit where it checks sizes and prints out validation fields and option.
- src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c - lines changed 39, context: html, text, full: html, text
- Moving hashMd5File to library.
- src/hg/encode3/importEncode2/encode2Md5UpdateManifest/encode2Md5UpdateManifest.c - lines changed 16, context: html, text, full: html, text
- Suppressing hoisting of fileNames.
- src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c - lines changed 1, 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/encode2MetaPatchRenamed.c - lines changed 42, context: html, text, full: html, text
- Testing some meta stuff.
- src/hg/oneShot/freen/freen.c - lines changed 18, context: html, text, full: html, text
- Added test case.
- src/hg/utils/metaFlatten/expected.out - lines changed 116, context: html, text, full: html, text
- src/hg/utils/metaFlatten/makefile - lines changed 22, context: html, text, full: html, text
- src/hg/utils/metaFlatten/metaFlatten.c - lines changed 82, context: html, text, full: html, text
- src/hg/utils/metaFlatten/test.in - lines changed 38, context: html, text, full: html, text
- src/meta/metaFlatten/expected.out - lines changed 116, context: html, text, full: html, text
- src/meta/metaFlatten/makefile - lines changed 22, context: html, text, full: html, text
- src/meta/metaFlatten/metaFlatten.c - lines changed 82, context: html, text, full: html, text
- src/meta/metaFlatten/test.in - lines changed 38, context: html, text, full: html, text
- src/meta/metaReformat/expected.out - lines changed 32, context: html, text, full: html, text
- src/meta/metaReformat/makefile - lines changed 22, context: html, text, full: html, text
- src/meta/metaReformat/test.in - lines changed 28, context: html, text, full: html, text
- Moving meta stuff out of hg. It's not really browser specific yet.
- src/meta/metaFlatten/makefile - lines changed 3, context: html, text, full: html, text
- Moving meta stuff out of hg. It's not really browser specific yet.
- Removing magic number per Kate's suggestion. Ref #10370
- src/hg/hgTracks/multiWig.c - lines changed 10, context: html, text, full: html, text
- Adding whitespace to improve readability. Ref #10370
- src/utils/bedToBigBed/bedToBigBed.c - lines changed 3, context: html, text, full: html, text
- Removing from makefile because it won't build.
- Moving meta module to different library.
- Moving meta module to different library.
- Improved readability and removed unused function parameter. Ref #10428.
- src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 4, context: html, text, full: html, text
- Oops forgot main module.
- src/meta/metaReformat/metaReformat.c - lines changed 51, context: html, text, full: html, text
- Small conservative change to gff/gtf reader, just to count # of each feature in file.
- Adding a high verbosity message that may alleviate some mysteriousness.
- src/hg/utils/gffToBed/gffToBed.c - 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.
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