All File Changes

v235_base to v236_preview (2010-07-06 to 2010-07-13) v236

• src/hg/autoSql/autoSql.c
  • lines changed 1, context: html, text, full: html, text
    Fixed handling of lstring.
• src/hg/encode/DAFs/1.0/AffyRnaChip.daf
  • lines changed 36, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/AffyRnaChipExample.ddf
  • lines changed 5, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/BroadChipSeq.daf
  • lines changed 39, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/BroadChipSeqControl.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/CshlLongRnaSeq.daf
  • lines changed 41, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/CshlLongRnaSeq.ddf
  • lines changed 1, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/CshlRnaSeq.daf
  • lines changed 48, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/CshlRnaSeqExample.ddf
  • lines changed 14, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/DukeDNaseSeq.DAF
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/DukeDNaseSeq.DDF
  • lines changed 12, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/DukeExons.daf
  • lines changed 21, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/ElnitskiNRE.DAF
  • lines changed 25, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/ElnitskiNRE.DDF
  • lines changed 2, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/GisChiaPet.daf
  • lines changed 35, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/GisChiaPetExample.ddf
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/GisDnaPet.daf
  • lines changed 74, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/GisPet.daf
  • lines changed 42, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/GisPetExample.ddf
  • lines changed 8, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/GisRnaSeq.daf
  • lines changed 62, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/HAIBChIPseq.daf
  • lines changed 38, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/HAIBChIPseqExample.ddf
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/HAIBRnaSeq.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/HelicosRnaSeq.daf
  • lines changed 48, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/RikenCage.daf
  • lines changed 53, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/RikenCage.ddf
  • lines changed 16, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/RikenCageExample.ddf
  • lines changed 13, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/RikenCageSolexa.daf
  • lines changed 49, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/SangerGencode.daf
  • lines changed 28, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/SangerGencode.ddf
  • lines changed 3, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/SunyRipGeneChip.daf
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/SunyRipGeneChip.ex.ddf
  • lines changed 3, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UMass5C.DAF
  • lines changed 27, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UMass5C.DDF
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UMassTfbsAll.daf
  • lines changed 23, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UMassTfbsAll.ddf
  • lines changed 2, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UMassTfbsValid.daf
  • lines changed 22, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UMassTfbsValid.ddf
  • lines changed 2, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UncFAIREseq.DAF
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UncFAIREseq.DDF
  • lines changed 12, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UtaChIPseq.DAF
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UtaChIPseq.DDF
  • lines changed 12, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UtaInput.DAF
  • lines changed 32, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UtaInput.DDF
  • lines changed 1, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UwChIPseq.daf
  • lines changed 50, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UwDgf.daf
  • lines changed 56, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UwDnaseSeq.daf
  • lines changed 51, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UwDnaseSeqExample.ddf
  • lines changed 11, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UwDnaseValid.daf
  • lines changed 20, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UwDnaseValid.ddf
  • lines changed 7, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/UwExons.daf
  • lines changed 21, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/WoldRnaSeq.daf
  • lines changed 97, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/WoldRnaSeq.ex.ddf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YDHChipSeq.daf
  • lines changed 39, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YDHChipSeqInput.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YDHChipSeqTreatment.daf
  • lines changed 39, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YDHRnaSeq.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YDHRnaSeqTreatment.daf
  • lines changed 35, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YaleChipSeq.DAF
  • lines changed 42, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YaleChipSeq.DDF
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/1.0/YaleChipSeqInput.DAF
  • lines changed 36, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/2.0/haibMethylRrbs.daf
  • lines changed 3, context: html, text, full: html, text
    Adding the word growthProtocol to fields.ra and HAIB RRBS. I would like to validate this using the esisting growth protocol names in the cell line CV. Currently I am not validating.
• src/hg/encode/DAFs/2.0/licrMm9Histone.daf
  • lines changed 2, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/licrMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/psuMm95c.daf
  • lines changed 2, context: html, text, full: html, text
    Updated mouse daf variables to include stain and sex where appropriate
  • lines changed 1, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/psuMm9DnaseSeq.daf
  • lines changed 3, context: html, text, full: html, text
    Updated mouse daf variables to include stain and sex where appropriate
  • lines changed 1, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/psuMm9Histone.daf
  • lines changed 3, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/psuMm9RnaSeq.daf
  • lines changed 2, context: html, text, full: html, text
    Updated mouse daf variables to include stain and sex where appropriate
  • lines changed 2, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/psuMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/stanfordMm9Hist.daf
  • lines changed 2, context: html, text, full: html, text
    Updated DAFs, added input instead of control
  • lines changed 3, context: html, text, full: html, text
    Fully updated all mouse DAFs
  • lines changed 4, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/stanfordMm9Tfbs.daf
  • lines changed 2, context: html, text, full: html, text
    Updated DAFs, added input instead of control
  • lines changed 6, context: html, text, full: html, text
    Fully updated all mouse DAFs
  • lines changed 3, context: html, text, full: html, text
    Updated Mouse Dafs to match controlled vocabulary
• src/hg/encode/DAFs/2.0/stanfordMm9TfbsInput.daf
  • lines changed 4, context: html, text, full: html, text
    Updated DAFs, added input instead of control
• src/hg/encode/DAFs/2.0/stanfordNucleosome.daf
  • lines changed 43, context: html, text, full: html, text
    Support for Nucleosome submissions.
• src/hg/encode/DAFs/2.0/uwMm9DnaseSeq.daf
  • lines changed 1, context: html, text, full: html, text
    Add age variable that will be submitted by UW Mouse
  • lines changed 49, context: html, text, full: html, text
    Updated mouse daf variables to include stain and sex where appropriate
• src/hg/encode/DAFs/2.0/uwMm9Sample.ddf
  • lines changed 10, context: html, text, full: html, text
    Sample DDF for UW Mouse Samples
• src/hg/encode/DAFs/AffyRnaChip.daf
  • lines changed 36, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/AffyRnaChipExample.ddf
  • lines changed 5, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/BroadChipSeq.daf
  • lines changed 39, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/BroadChipSeqControl.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/CshlLongRnaSeq.daf
  • lines changed 41, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/CshlLongRnaSeq.ddf
  • lines changed 1, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/CshlRnaSeq.daf
  • lines changed 48, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/CshlRnaSeqExample.ddf
  • lines changed 14, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/DukeDNaseSeq.DAF
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/DukeDNaseSeq.DDF
  • lines changed 12, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/DukeExons.daf
  • lines changed 21, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/ElnitskiNRE.DAF
  • lines changed 25, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/ElnitskiNRE.DDF
  • lines changed 2, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/GisChiaPet.daf
  • lines changed 35, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/GisChiaPetExample.ddf
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/GisDnaPet.daf
  • lines changed 74, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/GisPet.daf
  • lines changed 42, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/GisPetExample.ddf
  • lines changed 8, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/GisRnaSeq.daf
  • lines changed 62, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/HAIBChIPseq.daf
  • lines changed 38, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/HAIBChIPseqExample.ddf
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/HAIBRnaSeq.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/HelicosRnaSeq.daf
  • lines changed 48, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/RikenCage.daf
  • lines changed 53, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/RikenCage.ddf
  • lines changed 16, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/RikenCageExample.ddf
  • lines changed 13, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/RikenCageSolexa.daf
  • lines changed 49, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/SangerGencode.daf
  • lines changed 28, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/SangerGencode.ddf
  • lines changed 3, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/SunyRipGeneChip.daf
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/SunyRipGeneChip.ex.ddf
  • lines changed 3, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UMass5C.DAF
  • lines changed 27, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UMass5C.DDF
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UMassTfbsAll.daf
  • lines changed 23, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UMassTfbsAll.ddf
  • lines changed 2, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UMassTfbsValid.daf
  • lines changed 22, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UMassTfbsValid.ddf
  • lines changed 2, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UncFAIREseq.DAF
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UncFAIREseq.DDF
  • lines changed 12, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UtaChIPseq.DAF
  • lines changed 44, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UtaChIPseq.DDF
  • lines changed 12, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UtaInput.DAF
  • lines changed 32, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UtaInput.DDF
  • lines changed 1, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UwChIPseq.daf
  • lines changed 50, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UwDgf.daf
  • lines changed 56, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UwDnaseSeq.daf
  • lines changed 51, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UwDnaseSeqExample.ddf
  • lines changed 11, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UwDnaseValid.daf
  • lines changed 20, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UwDnaseValid.ddf
  • lines changed 7, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/UwExons.daf
  • lines changed 21, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/WoldRnaSeq.daf
  • lines changed 97, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/WoldRnaSeq.ex.ddf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YDHChipSeq.daf
  • lines changed 39, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YDHChipSeqInput.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YDHChipSeqTreatment.daf
  • lines changed 39, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YDHRnaSeq.daf
  • lines changed 33, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YDHRnaSeqTreatment.daf
  • lines changed 35, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YaleChipSeq.DAF
  • lines changed 42, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YaleChipSeq.DDF
  • lines changed 9, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/DAFs/YaleChipSeqInput.DAF
  • lines changed 36, context: html, text, full: html, text
    Moved all the old DAfs to 1.0
• src/hg/encode/encodeMkGeoPkg/encodeMkGeoPkg
  • lines changed 68, context: html, text, full: html, text
    adder placeholder for the series SORT
• src/hg/encode/encodeValidate/config/cv.ra
  • lines changed 14, context: html, text, full: html, text
    Adding geo terms for seqPlatform entries and making the term tag more concise
  • lines changed 1, context: html, text, full: html, text
    Add category =L cell Line for mouse cell MEL
  • lines changed 2, context: html, text, full: html, text
    Accidently used number 0 instead of O when registering DMSO_2.0pct
  • lines changed 5, context: html, text, full: html, text
    Updated 5 cell lines that were missing tier designations
  • lines changed 134, context: html, text, full: html, text
    This is the attempt at replacing ripTgtProtien with Antibody. I have most of the work done, but it doesn't work with encodeVocab
  • lines changed 5, context: html, text, full: html, text
    Added new treatment DMSO_2.0pct
  • lines changed 54, context: html, text, full: html, text
    Added new seqPlatform variable to cv.ra and fields.ra to check seqencing platform information for GEO submissions
  • lines changed 18, context: html, text, full: html, text
    Updated hgEncodeVocab to find path for the valdiation documents for the antibodies now mentioned in cv.ra
  • lines changed 2, context: html, text, full: html, text
    Commented out the validation lines that include file names for 2 antibodies
• src/hg/encode/encodeValidate/config/fields.ra
  • lines changed 5, context: html, text, full: html, text
    Adding the word growthProtocol to fields.ra and HAIB RRBS. I would like to validate this using the esisting growth protocol names in the cell line CV. Currently I am not validating.
  • lines changed 5, context: html, text, full: html, text
    Added new seqPlatform variable to cv.ra and fields.ra to check seqencing platform information for GEO submissions
• src/hg/encode/encodeValidate/config/pi.ra
  • lines changed 20, context: html, text, full: html, text
    Added Mouse labs for Hardison and Stam grants
• src/hg/encode/encodeValidate/doEncodeValidate.pl
  • lines changed 1, context: html, text, full: html, text
    Tim noticed that my added category code had a hole in it and stopped some human submissions. To fix I check if category is defined.
  • lines changed 5, context: html, text, full: html, text
    Changed sextype to cellLineSex upon Krishs recomendation
  • lines changed 36, context: html, text, full: html, text
    Updated doEncodeValidate to take Sex from DDF for tissue samples. Currently will be used for mouse tissues
• src/hg/encode/hgEncodeSubmit/app/controllers/pipeline_controller.rb
  • lines changed 1, context: html, text, full: html, text
    making the ftp list be sorted as requested
  • lines changed 25, context: html, text, full: html, text
    add paraFetchStatus monitoring
• src/hg/encode/hgEncodeSubmit/lib/pipeline_background.rb
  • lines changed 3, context: html, text, full: html, text
    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
  • lines changed 24, context: html, text, full: html, text
    convert to using paraFetch instead of wget, fix to allow for mixed-case extension, added function for displaying greek disk-size suffixes for human-friendly display
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 1, context: html, text, full: html, text
    Fixed typo in code that printed Human Cell Line column names the same as mouse.
  • lines changed 65, context: html, text, full: html, text
    Updated hgEncodeVocab to build Mouse Cell Line table according to Mouse specifications. Also made updated links for cell protocols to be ENCODE/protocols/cell/(ogranism) as Melissa. Help from Krish.
  • lines changed 2, context: html, text, full: html, text
    Updated hgEncodeVocab to find path for the valdiation documents for the antibodies now mentioned in cv.ra
• src/hg/hgGene/hgGeneData/D_melanogaster/dm3/otherOrgs.ra
  • lines changed 2, context: html, text, full: html, text
    updated for xxBlastMat tables rebuilds for dm3, sacCer2, and mm9.
• src/hg/hgGene/hgGeneData/Mouse/mm9/otherOrgs.ra
  • lines changed 3, context: html, text, full: html, text
    updated for xxBlastMat tables rebuilds for dm3, sacCer2, and mm9.
• src/hg/hgGene/hgGeneData/S_cerevisiae/sacCer2/otherOrgs.ra
  • lines changed 1, context: html, text, full: html, text
    updated for xxBlastMat tables rebuilds for dm3, sacCer2, and mm9.
• src/hg/hgTracks/hgTracks.c
  • lines changed 39, context: html, text, full: html, text
    Remove subtrack level vis override when composite or view vis comes in.
  • lines changed 3, context: html, text, full: html, text
    Minor cleanup that should have been checked in already
  • lines changed 91, context: html, text, full: html, text
    Initial support of subtrack vis override of composite->view vis using ifdefs
• src/hg/hgTracks/imageV2.h
  • lines changed 10, context: html, text, full: html, text
    SUBTRACKS_HAVE_VIS is dependent upon FLAT_TRACK_LIST which depands upon DRAG_REORDER
  • lines changed 4, context: html, text, full: html, text
    Make sure the ifdef for SUBTRACKS_HAVE_VIS is seen in imageV2.h
• src/hg/hgTracks/pslTrack.c
  • lines changed 2, context: html, text, full: html, text
    fix problem caused by the fact that now colors have the top bit set so they're negative in an int.
• src/hg/hgTracks/simpleTracks.c
  • lines changed 1, context: html, text, full: html, text
    fix problem caused by the fact that now colors have the top bit set so they're negative in an int.
  • lines changed 8, context: html, text, full: html, text
    Initial support of subtrack vis override of composite->view vis using ifdefs
• src/hg/hgc/hgc.c
  • lines changed 1, context: html, text, full: html, text
    Added sorting for DECIPHER phenotype list.
  • lines changed 91, context: html, text, full: html, text
    Built hgIkmc track for hg19 (IKMC track mapped to human genome).
• src/hg/htdocs/ENCODE/antibodies.html
  • lines changed 3, context: html, text, full: html, text
    increased the height of the frame, decreased size of margin on right side to match left side, added top button at bottom
  • lines changed 1, context: html, text, full: html, text
    change absolute paths to cv.ra to relative paths so they work with the sandboxs
• src/hg/htdocs/ENCODE/cellTypes.html
  • lines changed 7, context: html, text, full: html, text
    corrected cell culture protocol info, increased frame height, decreased right margins, added top button to each frame
  • lines changed 3, context: html, text, full: html, text
    change absolute paths to cv.ra to relative paths so they work with the sandboxs
• src/hg/htdocs/ENCODE/cellTypesMouse.html
  • lines changed 3, context: html, text, full: html, text
    change absolute paths to cv.ra to relative paths so they work with the sandboxs
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 10, context: html, text, full: html, text
    added two missing tracks: Mapability and NHGRI Bi-Pro
  • lines changed 5, context: html, text, full: html, text
    added Yale RNA-Seq
• src/hg/htdocs/ENCODE/otherTerms.html
  • lines changed 13, context: html, text, full: html, text
    change absolute paths to cv.ra to relative paths so they work with the sandboxs
• src/hg/htdocs/ENCODE/pubs.html
  • lines changed 21, context: html, text, full: html, text
    added new publication and organized pubs by year
• src/hg/htdocs/ENCODE/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 15, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 6, context: html, text, full: html, text
    "Encode release log update"
  • lines changed 1, context: html, text, full: html, text
    "Encode release log update"
• src/hg/htdocs/goldenPath/help/bam.html
  • lines changed 2, context: html, text, full: html, text
    changed links to reflect examples directory
• src/hg/htdocs/goldenPath/help/bigWig.html
  • lines changed 1, context: html, text, full: html, text
    changed links to reflect examples directory
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 25, context: html, text, full: html, text
    Added news item about 10-yr anniversary; archived a news item.
• src/hg/htdocs/goldenPath/releaseLog.html
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 15, context: html, text, full: html, text
    "Release log update"
  • lines changed 2, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
  • lines changed 5, context: html, text, full: html, text
    "Release log update"
  • lines changed 1, context: html, text, full: html, text
    "Release log update"
• src/hg/htdocs/images/10yrGraph4.gif
  • lines changed 0, context: html, text, full: html, text
    Committed changes for Bob -- updates to birthday news item, new graphic.
  • lines changed 0, context: html, text, full: html, text
    Added news item about 10-yr anniversary; archived a news item.
• src/hg/htdocs/indexNews.html
  • lines changed 3, context: html, text, full: html, text
    Committed changes for Bob -- updates to birthday news item, new graphic.
  • lines changed 77, context: html, text, full: html, text
    Added news item about 10-yr anniversary; archived a news item.
• src/hg/inc/cart.h
  • lines changed 7, context: html, text, full: html, text
    Remove subtrack level vis override when composite or view vis comes in.
• src/hg/inc/dnaMarkovSql.h
  • lines changed 13, context: html, text, full: html, text
    add dnaMarkSql
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    fix 'trackDbJson' is undefined' message reported by mary
  • lines changed 37, context: html, text, full: html, text
    Fixed side button chrome bug where hgTrackUi wasn't called because of drag reorder
• src/hg/js/hui.js
  • lines changed 7, context: html, text, full: html, text
    Sorting table rows takes time and needs wait masking
• src/hg/js/jquery.tablednd.js
  • lines changed 4, context: html, text, full: html, text
    Fixed side button chrome bug where hgTrackUi wasn't called because of drag reorder
• src/hg/lib/cart.c
  • lines changed 36, context: html, text, full: html, text
    Remove subtrack level vis override when composite or view vis comes in.
• src/hg/lib/dnaMarkovSql.c
  • lines changed 25, context: html, text, full: html, text
    add dnaMarkSql
• src/hg/lib/hgExp.c
  • lines changed 5, context: html, text, full: html, text
    write out PNGs with .png suffix (duh)
• src/hg/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    add dnaMarkovSql.o
• src/hg/lib/mdb.c
  • lines changed 38, context: html, text, full: html, text
    mdbUpdate no longer uses .sql file for table definition. Also tightened usage print. As per Hiram's requests.
• src/hg/makeDb/doc/ce9.txt
  • lines changed 70, context: html, text, full: html, text
    starting ce9, fixing up phyloP run for hg19 and running phyloP for mm9
  • lines changed 106, context: html, text, full: html, text
    starting ce9 WS210
• src/hg/makeDb/doc/dm3.txt
  • lines changed 37, context: html, text, full: html, text
    updated for xxBlastMat tables rebuilds for dm3, sacCer2, and mm9.
• src/hg/makeDb/doc/hg18.txt
  • lines changed 16, context: html, text, full: html, text
    adding DARNED the DAtabase of RNa EDiting
• src/hg/makeDb/doc/hg19.txt
  • lines changed 1, context: html, text, full: html, text
    starting ce9, fixing up phyloP run for hg19 and running phyloP for mm9
  • lines changed 68, context: html, text, full: html, text
    Built hgIkmc track for hg19 (IKMC track mapped to human genome).
• src/hg/makeDb/doc/mm9.txt
  • lines changed 422, context: html, text, full: html, text
    starting ce9, fixing up phyloP run for hg19 and running phyloP for mm9
  • lines changed 27, context: html, text, full: html, text
    Built CGAP tables for mm9.
  • lines changed 40, context: html, text, full: html, text
    updated for xxBlastMat tables rebuilds for dm3, sacCer2, and mm9.
• src/hg/makeDb/doc/sacCer2.txt
  • lines changed 38, context: html, text, full: html, text
    updated for xxBlastMat tables rebuilds for dm3, sacCer2, and mm9.
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 21, context: html, text, full: html, text
    mdbUpdate no longer uses .sql file for table definition. Also tightened usage print. As per Hiram's requests.
• src/hg/makeDb/mdbUpdate/mdbUpdate.c
  • lines changed 27, context: html, text, full: html, text
    mdbUpdate no longer uses .sql file for table definition. Also tightened usage print. As per Hiram's requests.
• src/hg/makeDb/schema/all.joiner
  • lines changed 4, context: html, text, full: html, text
    Added identifier hgIkmcName
  • lines changed 1, context: html, text, full: html, text
    remove felCat4 and felCatV17e from transMap section
  • lines changed 2, context: html, text, full: html, text
    Added lines for knownToKeggEntrez table columns.
• src/hg/makeDb/trackDb/cat/felCat4/trackDb.ra
  • lines changed 17, context: html, text, full: html, text
    remove redundant Cat mRNAs track
• src/hg/makeDb/trackDb/human/darned.html
  • lines changed 22, context: html, text, full: html, text
    darned - the database of rna-editing
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • lines changed 1, context: html, text, full: html, text
    changed the longlabel for Yale RNA-seq
  • lines changed 7, context: html, text, full: html, text
    removed release alpha, beta tags for yaleRnaSeq track
  • lines changed 1, context: html, text, full: html, text
    add pack to the options for YaleRnaSeq
  • lines changed 1, context: html, text, full: html, text
    This is the attempt at replacing ripTgtProtien with Antibody. I have most of the work done, but it doesn't work with encodeVocab
• src/hg/makeDb/trackDb/human/hg18/wgEncodeGisPet.ra
  • lines changed 69, context: html, text, full: html, text
    Made the changes for the long labels for this track LongPolyA to PolyA+
  • lines changed 1, context: html, text, full: html, text
    have made the changes that Antonio wants, maybe so that longPolyA+ is polyA+
• src/hg/makeDb/trackDb/human/hg18/wgEncodeYaleRNAseq.html
  • lines changed 2, context: html, text, full: html, text
    fixed typo and link
  • lines changed 9, context: html, text, full: html, text
    fixed typos
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylSeq.ra
  • lines changed 41, context: html, text, full: html, text
    some trackDb entries and metaData for two tables missing from the methylSeq submission
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyGeneST.ra
  • lines changed 127, context: html, text, full: html, text
    Suny GeneST tracks have added more cell lines`
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    liftOver AffyRnaChip from hg18 to hg19
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeCaltechRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    liftOver AffyRnaChip from hg18 to hg19
  • lines changed 1, context: html, text, full: html, text
    Added noInherit on
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSuny.ra
  • lines changed 1, context: html, text, full: html, text
    This is the fix so that the SUNY track reads the Antibody table not the antibody table in cv.ra. Other changes will need to happen with this.
  • lines changed 25, context: html, text, full: html, text
    This is the attempt at replacing ripTgtProtien with Antibody. I have most of the work done, but it doesn't work with encodeVocab
  • lines changed 71, context: html, text, full: html, text
    Suny GeneST tracks have added more cell lines`
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncodeSunyAlbanyTiling.ra
  • lines changed 1, context: html, text, full: html, text
    This is the attempt at replacing ripTgtProtien with Antibody. I have most of the work done, but it doesn't work with encodeVocab
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.html
  • lines changed 146, context: html, text, full: html, text
    liftOver AffyRnaChip from hg18 to hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeAffyRnaChip.ra
  • lines changed 1106, context: html, text, full: html, text
    liftOver AffyRnaChip from hg18 to hg19
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethyl27.ra
  • lines changed 758, context: html, text, full: html, text
    oops, need to add this as it is referenced in trackDb.wgEncode.ra now
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylSeq.ra
  • lines changed 21, context: html, text, full: html, text
    some trackDb entries and metaData for two tables missing from the methylSeq submission
• src/hg/makeDb/trackDb/human/hgIkmc.html
  • lines changed 13, context: html, text, full: html, text
    updated hgIkmc.html
  • lines changed 117, context: html, text, full: html, text
    Built hgIkmc track for hg19 (IKMC track mapped to human genome).
• src/hg/makeDb/trackDb/human/trackDb.ra
  • lines changed 9, context: html, text, full: html, text
    darned - the database of rna-editing
  • lines changed 28, context: html, text, full: html, text
    Built hgIkmc track for hg19 (IKMC track mapped to human genome).
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding ce9 to the build
• src/hg/makeDb/trackDb/marmoset/calJac3/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    adding bacEndCalJac3Singles
• src/hg/makeDb/trackDb/tagTypes.tab
  • lines changed 2, context: html, text, full: html, text
    adding gc5BaseBw track type
• src/hg/makeDb/trackDb/trackDb.ra
  • lines changed 18, context: html, text, full: html, text
    adding gc5BaseBw track type
• src/hg/makeDb/trackDb/worm/ce9/description.html
  • lines changed 129, context: html, text, full: html, text
    starting ce9 WS210
• src/hg/makeDb/trackDb/worm/ce9/gap.html
  • lines changed 64, context: html, text, full: html, text
    starting ce9 WS210
• src/hg/makeDb/trackDb/worm/ce9/gold.html
  • lines changed 23, context: html, text, full: html, text
    starting ce9 WS210
• src/hg/makeDb/trackDb/worm/ce9/trackDb.ra
  • lines changed 8, context: html, text, full: html, text
    starting ce9 WS210
• src/hg/makeDb/trackDb/zebrafish/danRer6/multiz6way.html
  • lines changed 11, context: html, text, full: html, text
    little bit more cleanup on danRer6 conservation descr page
  • lines changed 218, context: html, text, full: html, text
    re-doing danRer6 description page using hg19.cons46way.html as the model
• src/hg/near/hgNear/hgNearData/kegg.html
  • lines changed 1, context: html, text, full: html, text
    typo
  • lines changed 9, context: html, text, full: html, text
    Created kegg.html, description of the KEGG column.
• src/hg/utils/automation/HgAutomate.pm
  • lines changed 3, context: html, text, full: html, text
    transition cvs to git commands for trackDb build
• src/hg/utils/automation/HgDb.pm
  • lines changed 19, context: html, text, full: html, text
    add update and insert methods
• src/hg/utils/automation/makeGenomeDb.pl
  • lines changed 1, context: html, text, full: html, text
    n need to echo commands in csh scripts
  • lines changed 20, context: html, text, full: html, text
    transition cvs to git commands for trackDb build
  • lines changed 14, context: html, text, full: html, text
    turning gc5Base into a bigWig
• src/hg/utils/motifFinder/motifFinder.c
  • lines changed 16, context: html, text, full: html, text
    change 'multiple hits in a peak' algo to use exponential backoff of the prior
  • lines changed 41, context: html, text, full: html, text
    start adding code to look for multiple binding sites in the same peak
  • lines changed 155, context: html, text, full: html, text
    find largest scoring motif(s) in bed items
• src/hg/utils/mutationClassifier/mutationClassifier.c
  • lines changed 27, context: html, text, full: html, text
    replace mysql order by with in memory sort to get a big speedup
  • lines changed 12, context: html, text, full: html, text
    add pos w/n motif and distance to nearest gene to output
  • lines changed 5, context: html, text, full: html, text
    code cleanup
  • lines changed 5, context: html, text, full: html, text
    fprintf => verbose
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    refactor code into loadMark2
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    look for regulatory mutations w/n introns
  • lines changed 78, context: html, text, full: html, text
    add skipGeneModel option; support 2nd-order markov background model
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    free seq after use
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    scoreDelta -> minDelta
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    print out nearest gene for regulatory mutations
  • lines changed 26, context: html, text, full: html, text
    add scoreDelta option
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    fix bug in handling of multiple files caused by failing to re-initialize lists
• src/hg/utils/mutationClassifier/test/test.bed
  • lines changed 17, context: html, text, full: html, text
    make SNPs zero length
• src/inc/common.h
  • lines changed 7, context: html, text, full: html, text
    Added warnWithBackTrace() to aid simple detective work.
• src/inc/common.mk
  • lines changed 4, context: html, text, full: html, text
    oops 64 bit has precedence
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    oops support for PNG path for 32-bit systems
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    trying to autodetect PNG,SSL,BAM; also trying to use PNG statically linked
  • lines changed 2, context: html, text, full: html, text
    cannot yet have png libraries dependency required for default build
• src/inc/dnaMarkov.h
  • lines changed 9, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg
• src/inc/dnaMotif.h
  • lines changed 7, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg
• src/inc/net.h
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    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
• src/lib/dnaMarkov.c
  • lines changed 63, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg
• src/lib/dnaMotif.c
  • lines changed 1, context: html, text, full: html, text
    code cleanup
  • lines changed 72, context: html, text, full: html, text
    add dnaMotifBitScoreWithMarkovBg
• src/lib/errabort.c
  • lines changed 32, context: html, text, full: html, text
    Added warnWithBackTrace() to aid simple detective work.
• src/lib/net.c
  • lines changed 1, context: html, text, full: html, text
    remove unneeded flush
  • lines changed 1, context: html, text, full: html, text
    oops, only need to re-open unfinished parts
  • lines changed 30, context: html, text, full: html, text
    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
• src/product/ex.MySQLUserPerms.sh
  • lines changed 1, context: html, text, full: html, text
    add CREATE TEMPORARY TABLES permission to readonly@localhost
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    added paraFetch
• src/utils/paraFetch/paraFetch.c
  • lines changed 6, context: html, text, full: html, text
    adding retries to paraFetch for greater reliability to finish unattended. sleeps 30 seconds between retries
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v236 preview
  • lines changed 4, context: html, text, full: html, text
    try removing the USE_X settings, should not need them now that autodection is in
  • lines changed 1, context: html, text, full: html, text
    adding PNG
• src/utils/qa/weeklybld/buildUtils.csh
  • lines changed 1, context: html, text, full: html, text
    oops backwards
• src/utils/qa/weeklybld/cherryPickCommits.csh
  • lines changed 2, context: html, text, full: html, text
    more tweaks to cherry-picking
  • lines changed 9, context: html, text, full: html, text
    more fixes and tweaks
  • lines changed 3, context: html, text, full: html, text
    include more detail in the notification about the cherry-picked commit
  • lines changed 4, context: html, text, full: html, text
    sometimes the working dirs do not exist yet when cherrypicking
• src/utils/qa/weeklybld/coBranch.csh
  • lines changed 4, context: html, text, full: html, text
    oops need to change $dir to $branch throughout
• src/utils/qa/weeklybld/defaultBuildSettings.mk
  • lines changed 1, context: html, text, full: html, text
    adding switch for PNG libraries dependency
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 2, context: html, text, full: html, text
    convert to git
  • lines changed 2, context: html, text, full: html, text
    more convert to git doNewBranch.csh
• src/utils/qa/weeklybld/downloadBuildSettings.mk
  • lines changed 3, context: html, text, full: html, text
    static things do not need to be turned off for downloadable utils build
  • lines changed 1, context: html, text, full: html, text
    adding switch for PNG libraries dependency
• src/utils/twoBitInfo/twoBitInfo.c
  • lines changed 3, context: html, text, full: html, text
    fixing help message for twoBitInfo

• lines changed: 9643
• files changed: 328