File Changes for kent

v293_preview2 to v293_base (2013-12-02 to 2013-12-09) v293

• src/hg/encode3/encodeDataWarehouse/edwChangeFormat/makk
  • lines changed 3, context: html, text, full: html, text
    Adding script to copy into production.
• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/edwFixBasesInSample.c
  • lines changed 62, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixBasesInSample/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/edwFixCshlSpikeins.c
  • lines changed 77, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixCshlSpikeins/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixGbb2/edwFixGbb2.c
  • lines changed 12, context: html, text, full: html, text
    Simplified to avoid a bug.
  • lines changed 49, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixGbb2/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixRenamed/edwFixRenamed.c
  • lines changed 101, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixRenamed/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixReplaced/edwFixReplaced.c
  • lines changed 284, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixReplaced/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixRevoked/edwFixRevoked.c
  • lines changed 90, context: html, text, full: html, text
    Somehow this stray got lost in directory move.
• src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/edwFixTechRep1.c
  • lines changed 72, context: html, text, full: html, text
    Patch to pull paired_end and technical_replicate out of edwFile and into the appropriate columns of edwValidFile now applied.
  • lines changed 72, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwFixTechRep1/makefile
  • lines changed 4, context: html, text, full: html, text
    Patch to pull paired_end and technical_replicate out of edwFile and into the appropriate columns of edwValidFile now applied.
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/edwMakeContaminationQa/edwMakeContaminationQa.c
  • lines changed 26, context: html, text, full: html, text
    Moving edwMakeTempFastqSample to library where it can be shared.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/edwMakePairedEndQa.c
  • lines changed 120, context: html, text, full: html, text
    Starting to work on program to check read pairing for fastqs. It is maybe 1/3 baked now.
  • lines changed 70, context: html, text, full: html, text
    Further work, maybe 2/3rds baked now.
  • lines changed 168, context: html, text, full: html, text
    Program to add pairedEnd qa seems to work.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/makefile
  • lines changed 4, context: html, text, full: html, text
    Starting to work on program to check read pairing for fastqs. It is maybe 1/3 baked now.
• src/hg/encode3/encodeDataWarehouse/edwMakePairedEndQa/makk
  • lines changed 3, context: html, text, full: html, text
    Script to copy exe to production added.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 2, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makk
  • lines changed 3, context: html, text, full: html, text
    Adding script to copy into production.
• src/hg/encode3/encodeDataWarehouse/fix/README
  • lines changed 3, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/edwFixAddFastq.c
  • lines changed 47, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixAddFastq/makk
  • lines changed 3, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/edwFixBasesInSample.c
  • lines changed 62, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBasesInSample/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBzip/edwFixBzip.c
  • lines changed 73, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixBzip/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/edwFixCshlSpikeins.c
  • lines changed 77, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixCshlSpikeins/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/edwFixGbb2.c
  • lines changed 49, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGbb2/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/edwFixGtfBigBed.c
  • lines changed 134, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixGtfBigBed/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/edwFixQualsAtPos.c
  • lines changed 73, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixQualsAtPos/makk
  • lines changed 3, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/edwFixRenamed.c
  • lines changed 101, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRenamed/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/edwFixReplaced.c
  • lines changed 284, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixReplaced/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/edwFixRevoked.c
  • lines changed 90, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixRevoked/makefile
  • lines changed 4, context: html, text, full: html, text
    Committing some edwFix programs I forgot to add to git, and making a subdirectory for them.
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/edwFixTechRep1.c
  • lines changed 72, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
• src/hg/encode3/encodeDataWarehouse/fix/edwFixTechRep1/makefile
  • lines changed 4, context: html, text, full: html, text
    Moving rest of edwFix programs to subdirectory
  • lines changed 2, context: html, text, full: html, text
    Updating makefile path to reflect new position in source tree.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 3, context: html, text, full: html, text
    Moving edwMakeTempFastqSample to library where it can be shared.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 4, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 74, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 37, context: html, text, full: html, text
    Adding to tables that get records deleted when a file needs revalidation. Moving edwMakeTempfFastqSample here where it can be shared.
  • lines changed 1, context: html, text, full: html, text
    INcreasing buffer size for sql query in edwFileAllIntactBetween.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 4, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 15, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 21, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 178, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 3, context: html, text, full: html, text
    Adding paired_end and technical_replicate tag handling to edwValidFile table.
  • lines changed 17, context: html, text, full: html, text
    Adding edwQaPairedEndFastq table.
• src/hg/encode3/encodeDataWarehouse/lib/resetEdw
  • lines changed 1, context: html, text, full: html, text
    Adding technicalReplicate and pairedEnd to vf view.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 1, context: html, text, full: html, text
    A change that will hopefully make the build utils work again.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/makefile
  • lines changed 3, context: html, text, full: html, text
    Program to build a table based on ENCODED experiments seems to work.
• src/hg/encode3/encodeDataWarehouse/oneShot/rsyncEdwExpDataType/rsyncEdwExpDataType.c
  • lines changed 99, context: html, text, full: html, text
    Program to build a table based on ENCODED experiments seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/README
  • lines changed 3, context: html, text, full: html, text
    Program to figure out how well pairs align together from sam file seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/edwSamPairedEndStats.c
  • lines changed 136, context: html, text, full: html, text
    Program to figure out how well pairs align together from sam file seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/makefile
  • lines changed 3, context: html, text, full: html, text
    Program to figure out how well pairs align together from sam file seems to work.
• src/hg/encode3/encodeDataWarehouse/utils/edwSamPairedEndStats/makk
  • lines changed 4, context: html, text, full: html, text
    Script to copy exe to production added.
• src/hg/hgTrackUi/hgTrackUi.c
  • lines changed 25, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/hg/inc/jsHelper.h
  • lines changed 59, context: html, text, full: html, text
    Adding a bunch of functions to help work with output of jsParse.
  • lines changed 124, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 6, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/hg/lib/jsHelper.c
  • lines changed 270, context: html, text, full: html, text
    Adding a bunch of functions to help work with output of jsParse.
  • lines changed 682, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 14, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/inc/jsonParse.h
  • lines changed 132, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 1, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/inc/linefile.h
  • lines changed 4, context: html, text, full: html, text
    Removing lineFileNextRealWithSize - it was buggy and hard to fix in general case, and only one module was using it. Replaced it with something local to fastqStatsAndSubsample.c.
• src/lib/jsonParse.c
  • lines changed 692, context: html, text, full: html, text
    Separating out generic portable JSON parser from Genome Browser specific stuff in jsHelper module, creating jsonParse module.
  • lines changed 10, context: html, text, full: html, text
    Removing jsonGlabalsHash from library routines. Now it is restricted to hgTrackUi.
• src/lib/linefile.c
  • lines changed 10, context: html, text, full: html, text
    Removing lineFileNextRealWithSize - it was buggy and hard to fix in general case, and only one module was using it. Replaced it with something local to fastqStatsAndSubsample.c.
• src/lib/makefile
  • lines changed 2, context: html, text, full: html, text
    Splitting jsonParse out of jsHelper.
• src/utils/fastqStatsAndSubsample/fastqStatsAndSubsample.c
  • lines changed 30, context: html, text, full: html, text
    Removing lineFileNextRealWithSize - it was buggy and hard to fix in general case, and only one module was using it. Replaced it with something local to fastqStatsAndSubsample.c.
  • lines changed 1, context: html, text, full: html, text
    Actually using seed.
  • lines changed 103, context: html, text, full: html, text
    Simplifying initial step down to make it give consistent result across read pairs.