All File Changes

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

• src/aladdin/aladdin/makefile
  • lines changed 14, context: html, text, full: html, text
    minimalist makefile changes for kentUtils build refs #9104
  • lines changed 1, context: html, text, full: html, text
    moving to minimal makefiles for kentUtils build refs #9104
• src/aladdin/makefile
  • lines changed 3, context: html, text, full: html, text
    minimalist makefile changes for kentUtils build refs #9104
• src/cdnaAli/ali2alx/makefile
  • lines changed 1, context: html, text, full: html, text
    fixup broken 'make test' situation with the makefile changes refs #9104
• src/cdnaAli/binGood/makefile
  • lines changed 1, context: html, text, full: html, text
    fixup broken 'make test' situation with the makefile changes refs #9104
• src/fuse/makefile
  • lines changed 15, context: html, text, full: html, text
    minimalist makefile changes for kentUtils build refs #9104
• src/fuse/udcFuse/makefile
  • lines changed 18, context: html, text, full: html, text
    minimalist makefile changes for kentUtils build refs #9104
• src/getgene/makefile
  • lines changed 15, context: html, text, full: html, text
    minimalist makefile changes for kentUtils build refs #9104
• src/hg/affyTransciptome/makefile
  • lines changed 1, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/agpAllToFaFile/makefile
  • lines changed 14, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/agpCloneCheck/makefile
  • lines changed 14, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/agpCloneList/makefile
  • lines changed 14, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/agpToFa/makefile
  • lines changed 18, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/agpToGl/makefile
  • lines changed 15, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/altSplice/altSplice/makefile
  • lines changed 1, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/altSplice/makefile
  • lines changed 8, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/autoDtd/makefile
  • lines changed 15, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/autoSql/makefile
  • lines changed 22, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
  • lines changed 1, context: html, text, full: html, text
    fixup broken 'make test' situation with the makefile changes refs #9104
• src/hg/autoSql/tests/expected/doc.sql
  • lines changed 0, context: html, text, full: html, text
    an extra blank has been removed from the asParse generator refs #9897
• src/hg/autoSql/tests/expected/symTest.sql
  • lines changed 0, context: html, text, full: html, text
    an extra blank has been removed from the asParse generator refs #9897
• src/hg/autoSql/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    fixup broken 'make test' situation with the makefile changes refs #9104
  • lines changed 2, context: html, text, full: html, text
    fixup make test targets to function with userApp.sh refs #9104
• src/hg/autoXml/makefile
  • lines changed 13, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/bedIntersect/makefile
  • lines changed 15, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/bedItemOverlapCount/makefile
  • lines changed 20, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
  • lines changed 3, context: html, text, full: html, text
    fixup test target to be test:: to avoid conflict with userApp.mk refs #9104
• src/hg/bedOrBlocks/makefile
  • lines changed 13, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
  • lines changed 1, context: html, text, full: html, text
    fixup test target to be test:: to avoid conflict with userApp.mk refs #9104
• src/hg/bedSort/makefile
  • lines changed 15, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/bedSplitOnChrom/makefile
  • lines changed 14, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/bedToGenePred/makefile
  • lines changed 23, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/blastToPsl/makefile
  • lines changed 1, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/borfBig/makefile
  • lines changed 15, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/checkCoverageGaps/makefile
  • lines changed 17, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/checkHgFindSpec/makefile
  • lines changed 20, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/checkTableCoords/makefile
  • lines changed 21, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
  • lines changed 7, context: html, text, full: html, text
    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/hg/ctgFaToFa/makefile
  • lines changed 17, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/ctgToChromFa/makefile
  • lines changed 19, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/dbTrash/makefile
  • lines changed 19, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/embossToPsl/makefile
  • lines changed 17, context: html, text, full: html, text
    minimal makefiles now in place for kentUtils build refs #9104
  • lines changed 1, context: html, text, full: html, text
    fixup broken 'make test' situation with the makefile changes refs #9104
  • lines changed 6, context: html, text, full: html, text
    fixup make test targets to function with userApp.sh refs #9104
• src/hg/embossToPsl/tests/makefile
  • lines changed 2, context: html, text, full: html, text
    fixup make test targets to function with userApp.sh refs #9104
• src/hg/encode3/bigDataWarehouse/README
  • lines changed 13, context: html, text, full: html, text
    Starting design of bigDataWarehouse
  • lines changed 1, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 13, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/bdwCreateUser/bdwCreateUser.c
  • lines changed 74, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 2, context: html, text, full: html, text
    Starting to develop bdwSubmit program.
  • lines changed 12, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 72, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/bdwCreateUser/makefile
  • lines changed 19, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 19, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/bdwSubmit/bdwSubmit.c
  • lines changed 363, context: html, text, full: html, text
    Starting to develop bdwSubmit program.
  • lines changed 64, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 85, context: html, text, full: html, text
    Making license plate generator and upload dir generator
  • lines changed 83, context: html, text, full: html, text
    Working on error handling. If it can't make a proper connection to the submission url, it still creates a submission table entry where the error message is kept. It does not go on to make a file table entry though, which is good, keeping that table uncluttered.
  • lines changed 184, context: html, text, full: html, text
    Cleaning up a bunch. Starting to download files. BdwFile table gets filled out fairly completely.
  • lines changed 62, context: html, text, full: html, text
    Adding more submission and submissionDir info.
  • lines changed 8, context: html, text, full: html, text
    A little further along.
  • lines changed 40, context: html, text, full: html, text
    Making it not fetch files it already has.
  • lines changed 35, context: html, text, full: html, text
    Removing a bunch of debugging statements.
  • lines changed 128, context: html, text, full: html, text
    Improving comment and moving some related functions to be closer together.
  • lines changed 119, context: html, text, full: html, text
    Moving fieldedTable to a new library module.
  • lines changed 26, context: html, text, full: html, text
    Fetching files initially to a temporary file name.
  • lines changed 75, context: html, text, full: html, text
    Making submission of same submission file not create a new file table entry.
  • lines changed 620, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/bdwSubmit/makefile
  • lines changed 18, context: html, text, full: html, text
    Starting to develop bdwSubmit program.
  • lines changed 18, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/bigDataWarehouse.as
  • lines changed 67, context: html, text, full: html, text
    Starting design of bigDataWarehouse
  • lines changed 67, context: html, text, full: html, text
    Moving bigDataWarehouse.as to local library.
• src/hg/encode3/bigDataWarehouse/inc/bdwLib.h
  • lines changed 27, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 7, context: html, text, full: html, text
    Starting to develop bdwSubmit program.
  • lines changed 7, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 34, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/inc/bigDataWarehouse.h
  • lines changed 347, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 226, context: html, text, full: html, text
    Further development of bigDataWarehouse schema.
  • lines changed 1, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 3, context: html, text, full: html, text
    Adding more submission and submissionDir info.
  • lines changed 1, context: html, text, full: html, text
    A little further along.
  • lines changed 3, context: html, text, full: html, text
    Making it not fetch files it already has.
  • lines changed 407, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/lib/bdwLib.c
  • lines changed 80, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 13, context: html, text, full: html, text
    Further developing schema.
  • lines changed 9, context: html, text, full: html, text
    Starting to develop bdwSubmit program.
  • lines changed 21, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 107, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/lib/bigDataWarehouse.as
  • lines changed 67, context: html, text, full: html, text
    Moving bigDataWarehouse.as to local library.
  • lines changed 73, context: html, text, full: html, text
    Further developing schema.
  • lines changed 1, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 2, context: html, text, full: html, text
    Adding more submission and submissionDir info.
  • lines changed 1, context: html, text, full: html, text
    A little further along.
  • lines changed 2, context: html, text, full: html, text
    Making it not fetch files it already has.
  • lines changed 88, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/lib/bigDataWarehouse.c
  • lines changed 851, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 436, context: html, text, full: html, text
    Further development of bigDataWarehouse schema.
  • lines changed 14, context: html, text, full: html, text
    Adding more submission and submissionDir info.
  • lines changed 4, context: html, text, full: html, text
    A little further along.
  • lines changed 12, context: html, text, full: html, text
    Making it not fetch files it already has.
  • lines changed 1003, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/lib/bigDataWarehouse.sql
  • lines changed 82, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 66, context: html, text, full: html, text
    Further developing schema.
  • lines changed 1, context: html, text, full: html, text
    Changing to base64 encoded hash to simplify code and make mysql browsing of database less funky.
  • lines changed 2, context: html, text, full: html, text
    Adding more submission and submissionDir info.
  • lines changed 1, context: html, text, full: html, text
    A little further along.
  • lines changed 2, context: html, text, full: html, text
    Making it not fetch files it already has.
  • lines changed 99, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/bigDataWarehouse/lib/makefile
  • lines changed 11, context: html, text, full: html, text
    Wrote little program to create users and library routines to check them.
  • lines changed 11, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/encodeDataWarehouse/README
  • lines changed 13, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 1, context: html, text, full: html, text
    Renaming submission to submit just to be more consistent and shroter.
  • lines changed 1, context: html, text, full: html, text
    Working on subscribers.
• src/hg/encode3/encodeDataWarehouse/edwAddSubscriber/edwAddSubscriber.c
  • lines changed 94, context: html, text, full: html, text
    Working on subscribers.
• src/hg/encode3/encodeDataWarehouse/edwCreateUser/edwCreateUser.c
  • lines changed 72, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 25, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
• src/hg/encode3/encodeDataWarehouse/edwCreateUser/makefile
  • lines changed 19, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/encodeDataWarehouse/edwResetPassword/edwResetPassword.c
  • lines changed 45, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 19, context: html, text, full: html, text
    Adding edwResetPassword program.
• src/hg/encode3/encodeDataWarehouse/edwResetPassword/makefile
  • lines changed 4, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 620, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 79, context: html, text, full: html, text
    Renaming submission to submit just to be more consistent and shroter.
  • lines changed 99, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
  • lines changed 121, context: html, text, full: html, text
    Working on subscribers.
  • lines changed 18, context: html, text, full: html, text
    Cleaning out debugging messages
• src/hg/encode3/encodeDataWarehouse/edwSubmit/go
  • lines changed 1, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makefile
  • lines changed 18, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 34, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 10, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 407, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 112, context: html, text, full: html, text
    Renaming submission to submit just to be more consistent and shroter.
  • lines changed 109, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
  • lines changed 4, context: html, text, full: html, text
    Working on subscribers.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 107, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 31, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 88, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 22, context: html, text, full: html, text
    Renaming submission to submit just to be more consistent and shroter.
  • lines changed 30, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
  • lines changed 4, context: html, text, full: html, text
    Working on subscribers.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 1003, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 109, context: html, text, full: html, text
    Renaming submission to submit just to be more consistent and shroter.
  • lines changed 249, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
  • lines changed 23, context: html, text, full: html, text
    Working on subscribers.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 99, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 22, context: html, text, full: html, text
    Renaming submission to submit just to be more consistent and shroter.
  • lines changed 31, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
  • lines changed 3, context: html, text, full: html, text
    Working on subscribers.
• src/hg/encode3/encodeDataWarehouse/lib/makefile
  • lines changed 11, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 7, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 1, context: html, text, full: html, text
    Renaming submission to submit just to be more consistent and shroter.
  • lines changed 1, context: html, text, full: html, text
    Adding a few new fields. Putting submissionDir as part of file record. Testing and simplifying a few things.
  • lines changed 1, context: html, text, full: html, text
    Working on subscribers.
  • lines changed 1, context: html, text, full: html, text
    Adding a subscriber that updates a temp file.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 30, context: html, text, full: html, text
    Renaming 'bigDataWarehouse' to 'encodeDataWarehouse' as decided having to make bigDataWarehouse generic and non-encody was not worth the trouble.
  • lines changed 1, context: html, text, full: html, text
    Adding edwResetPassword program.
• src/hg/encode3/importEncode2/README
  • lines changed 63, context: html, text, full: html, text
    Improving documentation.
• src/hg/encode3/importEncode2/encode2FastqSubdirsInManifest/encode2FastqSubdirsInManifest.c
  • lines changed 70, context: html, text, full: html, text
    removing redundant encode2FastqSubdirsInManifest. Use encode2AddTgzContentsToManifestInstead.
• src/hg/encode3/importEncode2/encode2FastqSubdirsInManifest/makefile
  • lines changed 18, context: html, text, full: html, text
    removing redundant encode2FastqSubdirsInManifest. Use encode2AddTgzContentsToManifestInstead.
• src/hg/encode3/importEncode2/encode2FlattenFastqSubdirs/encode2FlattenFastqSubdirs.c
  • lines changed 2, context: html, text, full: html, text
    Improved help message.
• src/hg/encode3/importEncode2/encode2GffDoctor/encode2GffDoctor.c
  • lines changed 183, context: html, text, full: html, text
    Making GFF doctor substitute something in if there is no transcript_id.
  • lines changed 96, context: html, text, full: html, text
    Refactoring to reduce the parsing work since it looks like I'll have to add one more pass.
  • lines changed 85, context: html, text, full: html, text
    Fixing cases where there are no exons to be found.
• src/hg/encode3/importEncode2/encode2MakeEncode3/encode2MakeEncode3.c
  • lines changed 13, context: html, text, full: html, text
    Improved error message and changed to manifest rather than validated format.
• src/hg/encode3/importEncode2/encode2Manifest/encode2Manifest.c
  • lines changed 12, context: html, text, full: html, text
    Improved usage statement and removed encodeExp load which was never used.
• src/hg/encode3/importEncode2/encode2Meta/encode2Meta.c
  • lines changed 20, context: html, text, full: html, text
    Improving usage statement. Adding maniFields options to include fields normally relagated to manifest/validated file.
• src/hg/encode3/importEncode2/makeTgzDirPatch
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• src/hg/encode3/validateManifest/makefile
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• src/hg/encode3/validateManifest/validateManifest.c
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    Trying to use directory structure jim adopted for encode2-import for the .as files and the chrom.sizes and the .2bit files
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    cleaning up some debugging output for Eurie to use
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    adding #version comment to 1st line of validated.txt output
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    adding support for optional column ucsc_db in manifest.txt to be used as the genome or assembly in place of being implicit in the file_name path
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    incrementing version number to 1.1 -- will provide to Eurie as first alpha test
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    adding warning if genome assembly is not one of the expected values
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    adding a small additional option to have ucsc_db as the first column of the manifest.txt instead of file_name
• src/hg/estOrient/makefile
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• src/hg/geneBounds/orfEnum/makefile
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• src/hg/geneBounds/orfStats/makefile
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• src/hg/genePredHisto/tests/makefile
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• src/hg/genePredSingleCover/makefile
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• src/hg/genePredSingleCover/tests/makefile
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• src/hg/genePredToBed/genePredToBed.awk
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• src/hg/genePredToBed/makefile
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• src/hg/genePredToFakePsl/makefile
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• src/hg/genePredToGtf/tests/makefile
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• src/hg/genePredToMafFrames/makefile
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• src/hg/getFeatDna/makefile
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• src/hg/gigAssembler/checkAgpAndFa/makefile
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• src/hg/gpStats/makefile
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• src/hg/hgGene/pathways.c
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    fix link-out to KEGG (#10481)
• src/hg/hgGetAnn/makefile
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• src/hg/hgKnownGeneList/makefile
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• src/hg/hgLogin/hgLogin.c
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    redmine #9752 #8920 A more secure and sharable sendmail utility mailViaPipe for hgLogin
• src/hg/hgSelect/makefile
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• src/hg/hgc/lowelab.c
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    change Pfam track detail page for HMMER scan
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• src/hg/htdocs/ENCODE/FAQ/index.html
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    Correcting typo Code Review refs #10543
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    Adding organism specification on URL link to avoid broken link if person last browsing different organism Code Review refs #10543
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    Changing document head to match our HTML protocol, and changing button graphic to top following feedback, refs# 9712
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    Lower-casing HTML tags, cleaning up some HTML, making page strict, refs #9712
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    Correcting links where I had cgi-name?&org= to cgi-name?db without
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• src/hg/htdocs/ENCODE/contacts.html
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• src/hg/intronEnds/makefile
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• src/hg/lfsOverlap/makefile
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• src/hg/lib/annoStreamDb.c
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    Performance improvement for annoStreamDb, based on hg/oneShot/timeMysqlHandler.c: instead of using 'SELECT ...ORDER BY' queries to ensure that output is sorted by (chrom, chromStart),
    for tables with (chrom, bin) indices, use the fact that coarser bin numbers
    are lower numerically than finer bin numbers (for example, with the standard
    binRange scheme, the coarsest bin is 0 and the finest bins begin at 585).
    For tables like snp137 with > 50M rows of tiny items, the results from a
    query that uses the (chrom,bin) index typically include a very few items
    from coarser bins, followed by small items from the finest bin levels that
    do come out in chromStart order. So it works out well to save aside the
    initial coarse-bin annoRows in a list, and then as soon as we see a row
    from the finest bin level, sort the list of coarse-bin items and merge
    them into the stream of finest-bin items. This way we produce coordinates
    sorted by chromStart as required by annoGrator, but can start returning
    rows very soon after starting the query.
    For tables that don't have a (chrom,bin) index, if they have a (chrom, end)
    index, tell mysql to ignore that index so it will use the (chrom, start) index
    and produce correctly sorted output.
    refs #6152
    
• src/hg/lib/loweutils.c
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• src/hg/liftAcross/tests/makefile
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• src/hg/makeDb/genbank/etc/hgwbeta.dbs
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    Adding musFur1 assembly to hgwbeta.dbs to turn on GenBank updates refs# 6352
• src/hg/makeDb/hgAar/makefile
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• src/hg/makeDb/hgClonePos/makefile
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• src/hg/makeDb/hgCountAlign/makefile
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• src/hg/makeDb/hgCtgPos/makefile
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• src/hg/makeDb/hgDeleteChrom/makefile
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• src/hg/makeDb/hgExperiment/makefile
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• src/hg/makeDb/hgExtFileCheck/makefile
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• src/hg/makeDb/hgFakeAgp/makefile
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• src/hg/makeDb/hgFindSpec/makefile
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• src/hg/makeDb/hgGeneBands/makefile
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• src/hg/makeDb/hgGenericMicroarray/makefile
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• src/hg/makeDb/hgGoldGapGl/makefile
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• src/hg/makeDb/hgKgGetText/makefile
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• src/hg/pslSwap/tests/makefile
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    fixup test target to be test:: to avoid conflict with userApp.mk refs #9104
• src/hg/pslToBed/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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• src/hg/pslToBed/tests/makefile
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    fixup make test references for userApp.sh refs #9104
• src/hg/pslUnpile/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/qacToWig/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/recycleDb/bedUp/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/rnaStructure/hgLoadRnaFold/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/hg/rnaStructure/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/rnaStructure/rnaFoldBig/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/rnaStructure/rnaPhylo/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/rnaStructure/utrFa/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/snp/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/snp/snpMask/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/snp/snpValid/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/hg/snpException/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/spideyToPsl/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    fixup broken 'make test' situation with the makefile changes refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/hg/spideyToPsl/tests/makefile
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    fixup make test references for userApp.sh refs #9104
• src/hg/splitFa/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/sqlToXml/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/test/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
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    fixup test target to be test:: to avoid conflict with userApp.mk refs #9104
• src/hg/trfBig/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/txCds/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/txGene/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/txGraph/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/uniqSize/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/updateStsInfo/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• 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
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    Removing bogusly committed tmp file
• src/hg/utils/bedScore/bedScore
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    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
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    fixup broken 'make test' situation with the makefile changes refs #9104
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    Removing bogusly committed executable file
• src/hg/utils/bedScore/bedScore.c
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    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
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    Moving utility up a level in the tree.
• src/hg/utils/bedScore/makefile
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    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
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    Moving utility up a level in the tree.
• src/hg/utils/bedScore/tests/expected/encodeTest.bed
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    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
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    Moving utility up a level in the tree.
• src/hg/utils/bedScore/tests/input/encodeTest.bed
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    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
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    Moving utility up a level in the tree.
• src/hg/utils/bedScore/tests/makefile
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    First cut of utility to (re)score BED files based on a column value, with selectable method for normalization/scaling
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    Moving utility up a level in the tree.
• src/hg/utils/gwas/checkGwas.sh
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    first cut at scripts that otto load gwasCatalog #5172
• src/hg/utils/gwas/expectedColumns.txt
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    first cut at scripts that otto load gwasCatalog #5172
• src/hg/utils/gwas/gwasWrapper.sh
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    first cut at scripts that otto load gwasCatalog #5172
• src/hg/utils/gwas/makefile
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    first cut at scripts that otto load gwasCatalog #5172
• src/hg/utils/gwas/perlParser.pl
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    first cut at scripts that otto load gwasCatalog #5172
• src/hg/utils/gwas/validateGwas.sh
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    first cut at scripts that otto load gwasCatalog #5172
• src/hg/utils/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/utils/phyloTrees/97way.commonNames.nh
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    grouped bonobo with chimp, as the consensus is they diverged from each other after humans split from the common ancestor
• src/hg/visiGene/knownToVisiGene/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/xmlCat/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/hg/xmlToSql/makefile
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    minimal makefiles now in place for kentUtils build refs #9104
• src/inc/annoRow.h
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    Moving annoRowCmp from oneShot to annoRow.[ch].
• src/inc/cheapcgi.h
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    Adding cgiEncodeIntoDy into library. Exposing cgiParseInputAbort to public. Improving a comment.
• src/inc/common.h
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    Separating into sections with heavyweight comments.
• src/inc/fieldedTable.h
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    Moving fieldedTable to a new library module.
• src/inc/hex.h
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    Added hexBinaryString and replaced nibbleToHex routine with hexTab lookup.
• src/inc/mailViaPipe.h
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    redmine #9752 #8920 A more secure and sharable sendmail utility mailViaPipe for hgLogin
• src/inc/meta.h
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    Improving comment
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    Made comment correspond to function, not some other function.
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    Tidying up some of the meta code. Ref #10536
• src/inc/net.h
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    Added netUrlMustOpenPastHeader
• src/inc/userApp.mk
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    minimalist makefile changes for kentUtils build refs #9104
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    add comment about preMyLibs
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    adding -lm to all binary build due to Brian's checkin for anti-aliased line drawing refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/kehayden/alphaAsm/alphaAsm.c
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    Addint betweens option.
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    Adding use count for chain and monomer to between tag.
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    Fixing a place where needed a cast to double to avoid 0.82 going to 0. Rearranging debugging output.
• src/lib/annoRow.c
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    Moving annoRowCmp from oneShot to annoRow.[ch].
• src/lib/asParse.c
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    Removing an excess space that Hiram thought was problematic.
• src/lib/cheapcgi.c
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    Adding cgiEncodeIntoDy into library. Exposing cgiParseInputAbort to public. Improving a comment.
• src/lib/fieldedTable.c
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    Moving fieldedTable to a new library module.
• src/lib/hex.c
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    Added hexBinaryString and replaced nibbleToHex routine with hexTab lookup.
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    Making it generate lowercase a-f rather than uppercase. Didn't realize I'd changed case on last commit, and lower case is more compatible with md5sum program.
• src/lib/mailViaPipe.c
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    redmine #9752 #8920 A more secure and sharable sendmail utility mailViaPipe for hgLogin
• src/lib/makefile
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    Moving fieldedTable to a new library module.
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    redmine #9752 #8920 A more secure and sharable sendmail utility mailViaPipe for hgLogin
• src/lib/memgfx.c
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    add simple anti-aliasing to graphics line primitive
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    oops... fixed a little bug in the antialiasing when drawing stuff off screen
• src/lib/meta.c
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    Tidying up some of the meta code. Ref #10536
• src/lib/net.c
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    Added netUrlMustOpenPastHeader
• src/makefile
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    blatSuite actually depends upon hgLib since it is trying to build hg/* programs refs #9104
• src/meta/makefile
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    Adding metaHoist to build.
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    minimalist makefile changes for kentUtils build refs #9104
• src/meta/metaFlatten/makefile
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    minimalist makefile changes for kentUtils build refs #9104
• src/meta/metaFlatten/metaFlatten.c
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    Tidying up some of the meta code. Ref #10536
• src/meta/metaHoist/expected.out
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    Standalone meta hoister seems to work.
• src/meta/metaHoist/makefile
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    Standalone meta hoister seems to work.
• src/meta/metaHoist/metaHoist.c
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    Standalone meta hoister seems to work.
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    Implementing heavy tag option.
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    Tidying up some of the meta code. Ref #10536
• src/meta/metaHoist/test.in
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    Standalone meta hoister seems to work.
• src/meta/metaReformat/makefile
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    minimalist makefile changes for kentUtils build refs #9104
• src/meta/metaReformat/metaReformat.c
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    Tidying up some of the meta code. Ref #10536
• src/primeMate/makefile
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    minimalist makefile changes for kentUtils build refs #9104
• src/tracks/makefile
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    adding -lm to all binary build due to Brian's checkin for anti-aliased line drawing refs #9104
• src/utils/addCols/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
• src/utils/bedClip/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
• src/utils/bedCommonRegions/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/utils/bedGeneParts/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/utils/bedGraphToBigWig/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
• src/utils/bedPileUps/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/utils/bedRemoveOverlap/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/utils/bedRestrictToPositions/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
• src/utils/bedScore/bedScore.c
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    Moving utility up a level in the tree.
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    1. Change default minScore to 0. 2. Improve modularization
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    Redesign to support the multiple scorers
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    Add scoring method 'reg', used in ENCODE regulatory track
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    Remove code snippet for reg method
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    Add support for processing multiple files. refs #10569
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    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
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    Tighten up code for multiple files with uniform option. refs #10569
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    FIxed problem with pathname interpretation. refs #10569.
• src/utils/bedScore/makefile
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    Moving utility up a level in the tree.
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    Redo path after moving the dir
• src/utils/bedScore/tests/expected/encodeRegTest.bed
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    Add scoring method 'reg', used in ENCODE regulatory track
• src/utils/bedScore/tests/expected/encodeSmallTfbs.bed
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    Add tests
• src/utils/bedScore/tests/expected/encodeTest.bed
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    Moving utility up a level in the tree.
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    Redesign to support the multiple scorers
• src/utils/bedScore/tests/expected/encodeTfbsTest.bed
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    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
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    Redesign to support the multiple scorers
• src/utils/bedScore/tests/input/encodeSmallTfbs.bed
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    Add tests
• src/utils/bedScore/tests/input/encodeTest.bed
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    Moving utility up a level in the tree.
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    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
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    Add scoring method 'reg', used in ENCODE regulatory track
• src/utils/bedScore/tests/input/miniTest.bed
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    Redesign to support the multiple scorers
• src/utils/bedScore/tests/input/uniform1.bed
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    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
• src/utils/bedScore/tests/input/uniform2.bed
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    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
• src/utils/bedScore/tests/makefile
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    Moving utility up a level in the tree.
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    Add realistic test of encode method (wgEncodeAwgTfbsUwWi38CtcfUniPk, with a few rows dropped where C lib round differs from SQL round function)
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
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    Redesign to support the multiple scorers
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    Resolve merge conflict
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    Add scoring method 'reg', used in ENCODE regulatory track
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    Add -uniform option to normalize uniformly across a set of BED files. #refs 10569
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    Add test for -uniform option. refs #10569
• src/utils/bedToBigBed/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
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    cleaning up test target and adding that generic target in userApp.mk refs #9104
• src/utils/bigBedInfo/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
• src/utils/bigBedNamedItems/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
• src/utils/bigBedSummary/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
• src/utils/bigBedToBed/makefile
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    moving to minimal makefiles for kentUtils build refs #9104
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