File Changes for kent

v287_preview to v287_preview2 (2013-07-16 to 2013-07-23) v287

• src/hg/encode3/encPipe/sampleBam/makefile
  • lines changed 3, context: html, text, full: html, text
    Utility to extract a bed subsample of a BAM seems to work.
• src/hg/encode3/encPipe/sampleBam/sampleBam.c
  • lines changed 105, context: html, text, full: html, text
    Utility to extract a bed subsample of a BAM seems to work.
  • lines changed 1, context: html, text, full: html, text
    Actually setting random number seed.
• src/hg/encode3/encodeDataWarehouse/edwMakeReplicateQa/edwMakeReplicateQa.c
  • lines changed 2, context: html, text, full: html, text
    Removing unused options bit of usage statement.
  • lines changed 3, context: html, text, full: html, text
    Fixing merge conflicts with Galt's SQL injection prevention stuff.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/edwMakeValidFile.c
  • lines changed 75, context: html, text, full: html, text
    Adding cursory support (just magic number checking really) for idat and rcc files.
• src/hg/encode3/encodeDataWarehouse/edwMakeValidFile/makk
  • lines changed 3, context: html, text, full: html, text
    Adding little script to copy to SDSC.
• src/hg/encode3/encodeDataWarehouse/edwRunDaemon/edwRunDaemon.c
  • lines changed 1, context: html, text, full: html, text
    Making edwRunDaemon restart more gracefully with a well places sleep.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmit/edwScriptSubmit.c
  • lines changed 1, context: html, text, full: html, text
    Capitalizing HTTPS in usage message to help emphasize that http just won't do.
  • lines changed 20, context: html, text, full: html, text
    Moving password checking for script to library.
  • lines changed 24, context: html, text, full: html, text
    Fixing merge conflicts with Galt's SQL injection prevention stuff.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/edwScriptSubmitStatus.c
  • lines changed 166, context: html, text, full: html, text
    Seems to work.
  • lines changed 26, context: html, text, full: html, text
    Moving edwScriptRegistryFromCgi to library.
• src/hg/encode3/encodeDataWarehouse/edwScriptSubmitStatus/makefile
  • lines changed 16, context: html, text, full: html, text
    Seems to work.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/edwSubmit.c
  • lines changed 2, context: html, text, full: html, text
    Adding rcc and idat to supported formats.
• src/hg/encode3/encodeDataWarehouse/edwSubmit/makk
  • lines changed 3, context: html, text, full: html, text
    Adding little script to copy to SDSC.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/edwWebBrowse.c
  • lines changed 12, context: html, text, full: html, text
    Making it so that edwWebBrowse looks for modification time of file in transit before thinking things are stalled. Upping single file time out to 4 hours to accommodate big files from Barcelona.
  • lines changed 6, context: html, text, full: html, text
    More work to get rid of bogus stalled message.
• src/hg/encode3/encodeDataWarehouse/edwWebBrowse/makk
  • lines changed 3, context: html, text, full: html, text
    Adding little script to copy to SDSC.
• src/hg/encode3/encodeDataWarehouse/edwWebCreateUser/edwWebCreateUser.c
  • lines changed 6, context: html, text, full: html, text
    Improving error handling in case where they have a persona account but are not on white list.
• src/hg/encode3/encodeDataWarehouse/edwWebRegisterScript/edwWebRegisterScript.c
  • lines changed 12, context: html, text, full: html, text
    Improving error handling in case where they have a persona account but are not on white list.
  • lines changed 1, context: html, text, full: html, text
    Capitalizing HTTPS in usage message to help emphasize that http just won't do.
  • lines changed 39, context: html, text, full: html, text
    Fixing merge conflicts with Galt's SQL injection prevention stuff.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/edwWebSubmit.c
  • lines changed 38, context: html, text, full: html, text
    Making it so that edwWebBrowse looks for modification time of file in transit before thinking things are stalled. Upping single file time out to 4 hours to accommodate big files from Barcelona.
• src/hg/encode3/encodeDataWarehouse/edwWebSubmit/makk
  • lines changed 3, context: html, text, full: html, text
    Adding little script to copy to SDSC.
• src/hg/encode3/encodeDataWarehouse/inc/edwLib.h
  • lines changed 6, context: html, text, full: html, text
    Improving error handling in case where they have a persona account but are not on white list.
  • lines changed 9, context: html, text, full: html, text
    Making it so that edwWebBrowse looks for modification time of file in transit before thinking things are stalled. Upping single file time out to 4 hours to accommodate big files from Barcelona.
• src/hg/encode3/encodeDataWarehouse/inc/encodeDataWarehouse.h
  • lines changed 1, context: html, text, full: html, text
    Turning replacedBy column to a integer id rather than licensePlate, since the licensePlate really belongs to another table.
• src/hg/encode3/encodeDataWarehouse/lib/edwLib.c
  • lines changed 18, context: html, text, full: html, text
    Improving error handling in case where they have a persona account but are not on white list.
  • lines changed 65, context: html, text, full: html, text
    Making it so that edwWebBrowse looks for modification time of file in transit before thinking things are stalled. Upping single file time out to 4 hours to accommodate big files from Barcelona.
  • lines changed 62, context: html, text, full: html, text
    Fixing merge conflicts with Galt's SQL injection prevention stuff.
  • lines changed 4, context: html, text, full: html, text
    Fixing merge conflicts with Galt's SQL injection prevention stuff.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.as
  • lines changed 1, context: html, text, full: html, text
    Turning replacedBy column to a integer id rather than licensePlate, since the licensePlate really belongs to another table.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.c
  • lines changed 13, context: html, text, full: html, text
    Turning replacedBy column to a integer id rather than licensePlate, since the licensePlate really belongs to another table.
  • lines changed 34, context: html, text, full: html, text
    Fixing merge conflicts with Galt's SQL injection prevention stuff.
• src/hg/encode3/encodeDataWarehouse/lib/encodeDataWarehouse.sql
  • lines changed 1, context: html, text, full: html, text
    Turning replacedBy column to a integer id rather than licensePlate, since the licensePlate really belongs to another table.
• src/hg/encode3/encodeDataWarehouse/makefile
  • lines changed 1, context: html, text, full: html, text
    Adding edwScriptSubmitStatus to makefile.
• src/hg/oneShot/freen/freen.c
  • lines changed 24, context: html, text, full: html, text
    Making freen figure out encode validation key.
• src/inc/obscure.h
  • lines changed 3, context: html, text, full: html, text
    Adding shuffle array of ints.
• src/inc/paraFetch.h
  • lines changed 3, context: html, text, full: html, text
    Adding paraFetchTempUpdateTime for tracking file progress.
• src/kehayden/alphaAsm/alphaAsm.c
  • lines changed 1832, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/kehayden/alphaAsm/makefile
  • lines changed 23, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/kehayden/alphaAsm/yReads.txt
  • lines changed 966, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/kehayden/alphaAsm/yTypeOrder.txt
  • lines changed 34, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/kehayden/linearSat/alphaAsm.c
  • lines changed 1832, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
  • lines changed 1832, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/kehayden/linearSat/linearSat.c
  • lines changed 1832, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
  • lines changed 11, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a better name.
• src/kehayden/linearSat/makefile
  • lines changed 23, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
  • lines changed 5, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/kehayden/linearSat/yReads.txt
  • lines changed 966, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/kehayden/linearSat/yTypeOrder.txt
  • lines changed 34, context: html, text, full: html, text
    Moving alphaAsm to linearSat, a bettern name.
• src/lib/obscure.c
  • lines changed 16, context: html, text, full: html, text
    Adding shuffle array of ints.
• src/lib/paraFetch.c
  • lines changed 18, context: html, text, full: html, text
    Adding paraFetchTempUpdateTime for tracking file progress.
• src/utils/sampleIndexes/makefile
  • lines changed 3, context: html, text, full: html, text
    Little utility seems to work.
• src/utils/sampleIndexes/sampleIndexes.c
  • lines changed 53, context: html, text, full: html, text
    Little utility seems to work.