File Changes for kent

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

• 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
  • lines changed 7, context: html, text, full: html, text
    Adding little script used in encode conversion just to keep this more complete.
• src/hg/encode3/importEncode2/makefile
  • lines changed 5, context: html, text, full: html, text
    Adding new programs to makefile.
• src/hg/encode3/validateManifest/validateManifest.c
  • lines changed 1, context: html, text, full: html, text
    Added comment for Galt.
• src/inc/cheapcgi.h
  • lines changed 9, context: html, text, full: html, text
    Adding cgiEncodeIntoDy into library. Exposing cgiParseInputAbort to public. Improving a comment.
• src/inc/common.h
  • lines changed 57, context: html, text, full: html, text
    Separating into sections with heavyweight comments.
• src/inc/fieldedTable.h
  • lines changed 42, context: html, text, full: html, text
    Moving fieldedTable to a new library module.
• src/inc/hex.h
  • lines changed 4, context: html, text, full: html, text
    Added hexBinaryString and replaced nibbleToHex routine with hexTab lookup.
• src/inc/meta.h
  • lines changed 1, context: html, text, full: html, text
    Improving comment
  • lines changed 1, context: html, text, full: html, text
    Made comment correspond to function, not some other function.
  • lines changed 18, context: html, text, full: html, text
    Tidying up some of the meta code. Ref #10536
• src/inc/net.h
  • lines changed 9, context: html, text, full: html, text
    Added netUrlMustOpenPastHeader
• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 79, context: html, text, full: html, text
    Addint betweens option.
  • lines changed 15, context: html, text, full: html, text
    Adding use count for chain and monomer to between tag.
  • lines changed 3, context: html, text, full: html, text
    Fixing a place where needed a cast to double to avoid 0.82 going to 0. Rearranging debugging output.
• src/lib/asParse.c
  • lines changed 0, context: html, text, full: html, text
    Removing an excess space that Hiram thought was problematic.
• src/lib/cheapcgi.c
  • lines changed 17, context: html, text, full: html, text
    Adding cgiEncodeIntoDy into library. Exposing cgiParseInputAbort to public. Improving a comment.
• src/lib/fieldedTable.c
  • lines changed 102, context: html, text, full: html, text
    Moving fieldedTable to a new library module.
• src/lib/hex.c
  • lines changed 23, context: html, text, full: html, text
    Added hexBinaryString and replaced nibbleToHex routine with hexTab lookup.
  • lines changed 1, context: html, text, full: html, text
    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/makefile
  • lines changed 1, context: html, text, full: html, text
    Moving fieldedTable to a new library module.
• src/lib/meta.c
  • lines changed 64, context: html, text, full: html, text
    Tidying up some of the meta code. Ref #10536
• src/lib/net.c
  • lines changed 28, context: html, text, full: html, text
    Added netUrlMustOpenPastHeader
• src/meta/makefile
  • lines changed 2, context: html, text, full: html, text
    Adding metaHoist to build.
• src/meta/metaFlatten/metaFlatten.c
  • lines changed 1, context: html, text, full: html, text
    Tidying up some of the meta code. Ref #10536
• src/meta/metaHoist/expected.out
  • lines changed 27, context: html, text, full: html, text
    Standalone meta hoister seems to work.
• src/meta/metaHoist/makefile
  • lines changed 22, context: html, text, full: html, text
    Standalone meta hoister seems to work.
• src/meta/metaHoist/metaHoist.c
  • lines changed 170, context: html, text, full: html, text
    Standalone meta hoister seems to work.
  • lines changed 3, context: html, text, full: html, text
    Implementing heavy tag option.
  • lines changed 1, context: html, text, full: html, text
    Tidying up some of the meta code. Ref #10536
• src/meta/metaHoist/test.in
  • lines changed 33, context: html, text, full: html, text
    Standalone meta hoister seems to work.
• src/meta/metaReformat/metaReformat.c
  • lines changed 1, context: html, text, full: html, text
    Tidying up some of the meta code. Ref #10536