File Changes for kent

v288_preview to v288_preview2 (2013-08-07 to 2013-08-13) v288

• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/edwFixBasesInSample.c
  • lines changed 62, context: html, text, full: html, text
    Little fixer seems to work.
• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/makefile
  • lines changed 4, context: html, text, full: html, text
    Little fixer seems to work.
• src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c
  • lines changed 177, context: html, text, full: html, text
    Seems to work. Has run on about 1/3 of ENCODE2.
  • lines changed 66, context: html, text, full: html, text
    Making it so it only does work if it hasn't done it already.
  • lines changed 21, context: html, text, full: html, text
    Adding keepTemp command line option. Getting sample from already downsampled file in edwFastqFile table.
• src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Seems to work. Has run on about 1/3 of ENCODE2.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 151, context: html, text, full: html, text
    Making it call external fastqStatsAndSubsample program. Allowing 'unknown' format files to get license plate.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 3, context: html, text, full: html, text
    Allowing mm10 as a ucscDb.
• src/hg/encode3/encodeDataWarehouse/inc/edwFastqFileFromRa.h
  • lines changed 15, context: html, text, full: html, text
    Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 12, context: html, text, full: html, text
    Adding support routines for edwFastqFiles.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 159, context: html, text, full: html, text
    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/edwFastqFileFromRa.c
  • lines changed 305, context: html, text, full: html, text
    Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 58, context: html, text, full: html, text
    Adding support routines for edwFastqFiles.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 45, context: html, text, full: html, text
    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 561, context: html, text, full: html, text
    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 49, context: html, text, full: html, text
    Adding edwFastqFile and edwQaRepeat tables. Making a couple of edwValidFile indexes unique.
• src/hg/encode3/encodeDataWarehouse/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding a code-generated routine that will parse a edwFastqFile out of a .ra file with the right fields in a pretty robust fashion. Hmm, it is a lot of code. I'm glad I didn't clutter autoSql with it.
• src/hg/encode3/encodeDataWarehouse/lib/redoSchema
  • lines changed 2, context: html, text, full: html, text
    Moving code generated .h file _before_ the compile!
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 6, context: html, text, full: html, text
    Moving it back from hive to scratch while hive is being delicate. Adding e. coli contamination target.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding new edwMakeContaminationQa program to build.
• src/inc/raToStruct.h
  • lines changed 31, context: html, text, full: html, text
    Added basesInSample output.
• src/lib/hash.c
  • lines changed 2, context: html, text, full: html, text
    Improving comment.
• src/lib/linefile.c
  • lines changed 4, context: html, text, full: html, text
    Made it so linefile on gzipped files doesn't abort with an error message if you close it before reading it all.
  • lines changed 1, context: html, text, full: html, text
    Removing weak attempt at fix that Mark properly fixed.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    Making raToStruct.c module compile.
• src/lib/pipeline.c
  • lines changed 7, context: html, text, full: html, text
    Made it so linefile on gzipped files doesn't abort with an error message if you close it before reading it all.
• src/lib/raToStruct.c
  • lines changed 63, context: html, text, full: html, text
    Added basesInSample output.
  • lines changed 8, context: html, text, full: html, text
    Making raToStruct.c module compile.
• src/utils/faUniqify/faUniqify.c
  • lines changed 60, context: html, text, full: html, text
    Seems to work. Sadly it does change line length.
• src/utils/faUniqify/makefile
  • lines changed 3, context: html, text, full: html, text
    Seems to work. Sadly it does change line length.
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
  • lines changed 412, context: html, text, full: html, text
    Seems to work.
  • lines changed 11, context: html, text, full: html, text
    Making it write out '@' line again.
  • lines changed 31, context: html, text, full: html, text
    Adding smallOk option.
  • lines changed 93, context: html, text, full: html, text
    Added basesInSample output.
  • lines changed 32, context: html, text, full: html, text
    Making it work ok with /dev/null as fastq output. Fixing an integer overflow bug.
• src/utils/fastqStatsAndSubsample/makefile
  • lines changed 3, context: html, text, full: html, text
    Seems to work.
• src/utils/raToStructGen/makefile
  • lines changed 3, context: html, text, full: html, text
    Main ra parsing function is generate and passes visual inspection. Haven't tried compiling it yet though.
• src/utils/raToStructGen/raToStructGen.c
  • lines changed 261, context: html, text, full: html, text
    Main ra parsing function is generate and passes visual inspection. Haven't tried compiling it yet though.
  • lines changed 4, context: html, text, full: html, text
    Output now compiles.
  • lines changed 41, context: html, text, full: html, text
    Making it generate a new function.