All File Changes

v257_preview to v257_preview2 (2011-09-06 to 2011-09-13) v257

• python/programs/DateCheck/dateCheck.py
  • lines changed 43, context: html, text, full: html, text
    streamlined and rewrote some parts that I felt were inefficient
  • lines changed 17, context: html, text, full: html, text
    changed how libraries are handles, and added usage statement
  • lines changed 110, context: html, text, full: html, text
    updated sydh tfbs notes to reflect the mnaseD experiment revocation
• python/programs/dateCheck/dateCheck
  • lines changed 110, context: html, text, full: html, text
    updated sydh tfbs notes to reflect the mnaseD experiment revocation
  • lines changed 141, context: html, text, full: html, text
    added in new functions, check date range in old assembly, check if dateUnrestricted is within 9 months of dateSubmitted in old assembly and cehck if new assembly already has dateResubmitted, also other structural changes, and some necessary secondary functions to make the three main ones work.
• src/hg/encode/encodeExp/listAccessionsHg19.sh
  • lines changed 2, context: html, text, full: html, text
    Trivial script for AWG -- list DCC accessions for all hg19 download files
  • lines changed 1, context: html, text, full: html, text
    Prune composites
• src/hg/encode/encodeRenameObj/encodeRenameObj.c
  • lines changed 1, context: html, text, full: html, text
    fixed minor naming convention
• src/hg/encode/hgEncodeVocab/hgEncodeVocab.c
  • lines changed 523, context: html, text, full: html, text
    Major update to hgEncodeVocab. Little functional change besides sortable tables. Deprecated terms are now marked as such.
  • lines changed 3, context: html, text, full: html, text
    Actually, the document column can be sortable too, since the label is often the lab.
• src/hg/encode/inc/encodePatchTdb.h
  • lines changed 1, context: html, text, full: html, text
    fixed minor naming convention
• src/hg/encode/lib/encodePatchTdb.c
  • lines changed 1, context: html, text, full: html, text
    fixed minor naming convention
• src/hg/encode/md5sumhistory/hg18/wgEncodeAffyRnaChip.md5sum.history
  • lines changed 111, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeBroadChipSeq.md5sum.history
  • lines changed 552, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeBroadHmm.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeBuOrchid.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeCaltechRnaSeq.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeChromatinMap.md5sum.history
  • lines changed 534, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeCshlLoRnaSeq.md5sum.history
  • lines changed 9, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeCshlLongRnaSeq.md5sum.history
  • lines changed 20, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeCshlRnaSeq.md5sum.history
  • lines changed 54, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeCshlShortRnaSeq.md5sum.history
  • lines changed 43, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeDukeAffyExonArray.md5sum.history
  • lines changed 60, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeDukeDNaseSeq.md5sum.history
  • lines changed 8, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeGisDnaPet.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeGisPet.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeGisRnaSeq.md5sum.history
  • lines changed 20, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeHelicosRnaSeq.md5sum.history
  • lines changed 11, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaChipSeq.md5sum.history
  • lines changed 429, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaCnv.md5sum.history
  • lines changed 12, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaMethyl27.md5sum.history
  • lines changed 12, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaMethylSeq.md5sum.history
  • lines changed 93, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaRnaSeq.md5sum.history
  • lines changed 18, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeMapability.md5sum.history
  • lines changed 20, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeMarguliesChai.md5sum.history
  • lines changed 5, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeNhgriBip.md5sum.history
  • lines changed 15, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeNhgriNre.md5sum.history
  • lines changed 11, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeRikenCage.md5sum.history
  • lines changed 92, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeSangerGencode.md5sum.history
  • lines changed 13, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeSunyalbanyRnaGeneChip.md5sum.history
  • lines changed 16, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUc.md5sum.history
  • lines changed 2, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUmassdekker5C.md5sum.history
  • lines changed 11, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUmasshaTfbsValid.md5sum.history
  • lines changed 10, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUncFAIREseq.md5sum.history
  • lines changed 10, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUwAffyExonArray.md5sum.history
  • lines changed 75, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUwChIPSeq.md5sum.history
  • lines changed 554, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUwDGF.md5sum.history
  • lines changed 45, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeUwDnaseSeq.md5sum.history
  • lines changed 386, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg18/wgEncodeYaleChIPseq.md5sum.history
  • lines changed 1133, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeAffyRnaChip.md5sum.history
  • lines changed 56, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeBetaTest.md5sum.history
  • lines changed 6, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeBroadHistone.md5sum.history
  • lines changed 1274, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeBroadHmm.md5sum.history
  • lines changed 13, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeBuOrchid.md5sum.history
  • lines changed 5, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeCaltechRnaSeq.md5sum.history
  • lines changed 573, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeCshlLongRnaSeq.md5sum.history
  • lines changed 1369, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeCshlShortRnaSeq.md5sum.history
  • lines changed 408, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeDukeAffyExon.md5sum.history
  • lines changed 108, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeGencodeV4.md5sum.history
  • lines changed 10, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeGencodeV7.md5sum.history
  • lines changed 18, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeGisChiaPet.md5sum.history
  • lines changed 71, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeGisDnaPet.md5sum.history
  • lines changed 50, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeGisRnaPet.md5sum.history
  • lines changed 182, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeGisRnaSeq.md5sum.history
  • lines changed 32, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeHaibGenotype.md5sum.history
  • lines changed 94, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethyl450.md5sum.history
  • lines changed 14, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethylArray.md5sum.history
  • lines changed 76, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethylRrbs.md5sum.history
  • lines changed 408, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethylSeq.md5sum.history
  • lines changed 147, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeHaibRnaSeq.md5sum.history
  • lines changed 212, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeHaibTfbs.md5sum.history
  • lines changed 2192, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeMapability.md5sum.history
  • lines changed 13, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromChip.md5sum.history
  • lines changed 368, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromDnase.md5sum.history
  • lines changed 462, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromFaire.md5sum.history
  • lines changed 244, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromSynth.md5sum.history
  • lines changed 20, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeRegDnaseClustered.md5sum.history
  • lines changed 7, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeRegMarkH3k27ac.md5sum.history
  • lines changed 12, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeRegMarkH3k4me1.md5sum.history
  • lines changed 12, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeRegMarkH3k4me3.md5sum.history
  • lines changed 12, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeRegTfbsClustered.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeRegTxn.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeRikenCage.md5sum.history
  • lines changed 441, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSunyAlbanyGeneSt.md5sum.history
  • lines changed 28, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSunyAlbanyTiling.md5sum.history
  • lines changed 12, context: html, text, full: html, text
    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSunyRipSeq.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSunySwitchgear.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSydhHistone.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSydhNsome.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSydhRnaSeq.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeSydhTfbs.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeUMassWengTfbsValid.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUchicagoTfbs.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/md5sumhistory/hg19/wgEncodeUmassDekker5C.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUncBsuProt.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUw5C.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUwAffyExonArray.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUwDgf.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUwDnase.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUwHistone.md5sum.history
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• src/hg/encode/md5sumhistory/hg19/wgEncodeUwTfbs.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeBetaTest.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeCaltechHistone.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeCaltechTfbs.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeLicrHistone.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeLicrRnaSeq.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeLicrTfbs.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeMapability.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodePsuHistone.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodePsuTfbs.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeSydhHist.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeSydhRnaSeq.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeSydhTfbs.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeTestChipSeq.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeUwDnase.md5sum.history
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• src/hg/encode/md5sumhistory/mm9/wgEncodeUwRnaSeq.md5sum.history
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    added in md5sums to source tree, not just my own
• src/hg/encode/metaCheck/README.txt
  • lines changed 20, context: html, text, full: html, text
    So the long awaited merge of metaTest into metaCheck is here. This is an arguments face lift because the original metaCheck was meant to be used in code not as a command line, so now there are defaults for all of the locations of the trackDb, metaDb, downloads dir but you can specify a different location.
• src/hg/encode/metaCheck/metaCheck.c
  • lines changed 95, context: html, text, full: html, text
    So the long awaited merge of metaTest into metaCheck is here. This is an arguments face lift because the original metaCheck was meant to be used in code not as a command line, so now there are defaults for all of the locations of the trackDb, metaDb, downloads dir but you can specify a different location.
• src/hg/hgApi/hgApi.c
  • lines changed 147, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/hgGene/synonym.c
  • lines changed 2, context: html, text, full: html, text
    Minor edit for <BR> placement.
• src/hg/hgHubConnect/hgHubConnect.c
  • lines changed 0, context: html, text, full: html, text
    move a space around for Greg
  • lines changed 1, context: html, text, full: html, text
    change page title per greg
• src/hg/hgTracks/hgTracks.c
  • lines changed 21, context: html, text, full: html, text
    more work on return image via URL (redmine 4888)
  • lines changed 82, context: html, text, full: html, text
    refactor blue bar hotLinks code so we build up a list which can be printed or sent to the javascript client code (see redmine #5245)
  • lines changed 33, context: html, text, full: html, text
    restore order of session and pdf/ps links
  • lines changed 11, context: html, text, full: html, text
    Removing open hand cursor and adding toggle clicking back into image as per Angie and Jim's desires.
• src/hg/hgTracks/hgTracks.h
  • lines changed 9, context: html, text, full: html, text
    refactor blue bar hotLinks code so we build up a list which can be printed or sent to the javascript client code (see redmine #5245)
• src/hg/hgTracks/imageV2.h
  • lines changed 4, context: html, text, full: html, text
    Removing open hand cursor and adding toggle clicking back into image as per Angie and Jim's desires.
• src/hg/hgTracks/renderMain.c
  • lines changed 13, context: html, text, full: html, text
    more work on return image via URL (redmine 4888)
• src/hg/hgTracks/simpleTracks.c
  • lines changed 12, context: html, text, full: html, text
    need to hard-code track handler for each gencode version. Also delete no long used MGC handler registration
  • lines changed 3, context: html, text, full: html, text
    Updated query to decide DECIPHER entry color.
• src/hg/hgc/hgc.c
  • lines changed 11, context: html, text, full: html, text
    Disabled OMIM NCBI links, and replaced mim2gene table to omim2gene table.
• src/hg/hgc/rnaFoldClick.c
  • lines changed 6, context: html, text, full: html, text
    added NOTE about needing the latest Java to run VARNA in some OS/browser combos
• src/hg/htdocs/ENCODE/dataMatrix/chipMatrix.css
  • lines changed 11, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/dataMatrix.css
  • lines changed 104, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixHuman.html
  • lines changed 14, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixInclude.html
  • lines changed 26, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeChipMatrixMouse.html
  • lines changed 13, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixHuman.html
  • lines changed 14, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixInclude.html
  • lines changed 25, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataMatrixMouse.html
  • lines changed 13, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryHuman.html
  • lines changed 14, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryInclude.html
  • lines changed 49, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataMatrix/encodeDataSummaryMouse.html
  • lines changed 13, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/ENCODE/dataStandards.html
  • lines changed 94, context: html, text, full: html, text
    checking in the files for the new encode data standards pages, Redmine #5135
  • lines changed 2, context: html, text, full: html, text
    add title to dataStandards, removed bad link from platform page, redmine# 5135
• src/hg/htdocs/ENCODE/downloads.html
  • lines changed 5, context: html, text, full: html, text
    added SYDH RNA-sew, redmine #383
• src/hg/htdocs/ENCODE/experiment_guidelines.html
  • lines changed 30, context: html, text, full: html, text
    checking in the files for the new encode data standards pages, Redmine #5135
• src/hg/htdocs/ENCODE/platform_characterization.html
  • lines changed 28, context: html, text, full: html, text
    checking in the files for the new encode data standards pages, Redmine #5135
  • lines changed 15, context: html, text, full: html, text
    Made changes as suggested by Katrina, redmine# 5135, note# 26
  • lines changed 2, context: html, text, full: html, text
    added italics to et al, redmine# 5135, note# 29
  • lines changed 2, context: html, text, full: html, text
    add title to dataStandards, removed bad link from platform page, redmine# 5135
• src/hg/htdocs/ENCODE/template.html
  • lines changed 7, context: html, text, full: html, text
    checking in the files for the new encode data standards pages, Redmine #5135
• src/hg/htdocs/FAQ/FAQformat.html
  • lines changed 1, context: html, text, full: html, text
    Fixing link and adding deprecated notes for tagAlign formats
• src/hg/htdocs/goldenPath/help/hgTracksHelp.html
  • lines changed 16, context: html, text, full: html, text
    Added doc for shift-drag-zoom, drag-scroll, and track group reorder.
  • lines changed 8, context: html, text, full: html, text
    Changed info about resetting image size.
  • lines changed 6, context: html, text, full: html, text
    Corrected some info about drag-scroll, per Mary's input.
  • lines changed 2, context: html, text, full: html, text
    Minor correction to zoom-drag description.
• src/hg/htdocs/goldenPath/newsarch.html
  • lines changed 57, context: html, text, full: html, text
    Added news about new javascript features, archived some items.
• src/hg/htdocs/inc/encodeProject.topbar.html
  • lines changed 3, context: html, text, full: html, text
    checking in the files for the new encode data standards pages, Redmine #5135
  • lines changed 0, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/htdocs/indexNews.html
  • lines changed 97, context: html, text, full: html, text
    Added news about new javascript features, archived some items.
  • lines changed 1, context: html, text, full: html, text
    Fixed date format for news item.
• src/hg/htdocs/style/encodeProject.css
  • lines changed 52, context: html, text, full: html, text
    checking in the files for the new encode data standards pages, Redmine #5135
  • lines changed 104, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/inc/cv.h
  • lines changed 6, context: html, text, full: html, text
    Further work to have cv label appear instead of term in file search, fileUi and metadata dropdown
• src/hg/inc/mdb.h
  • lines changed 1, context: html, text, full: html, text
    Using cvLabels in the overflow metadata in fileUi and file sort. However, this choice may be reversed when QA and Cricket actually see it.
• src/hg/js/encodeChipMatrix.js
  • lines changed 175, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
  • lines changed 1, context: html, text, full: html, text
    Remove dev browser refs
• src/hg/js/encodeDataMatrix.js
  • lines changed 176, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
  • lines changed 1, context: html, text, full: html, text
    Remove dev browser refs
• src/hg/js/encodeDataSummary.js
  • lines changed 171, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
  • lines changed 1, context: html, text, full: html, text
    Remove dev browser refs
• src/hg/js/encodeProject.js
  • lines changed 214, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
  • lines changed 1, context: html, text, full: html, text
    Fix sorting problem on cell tiers
• src/hg/js/hgTracks.js
  • lines changed 2, context: html, text, full: html, text
    fix code that was broken when I moved stuff from hiddens to hgTracks object (see redmine #5268)
  • lines changed 2, context: html, text, full: html, text
    Removing open hand cursor and adding toggle clicking back into image as per Angie and Jim's desires.
• src/hg/js/makefile
  • lines changed 3, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
  • lines changed 1, context: html, text, full: html, text
    remove unused js file
• src/hg/js/test/JsTestDriver-1.3.2.jar
  • lines changed 0, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/js/test/README
  • lines changed 130, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/js/test/coverage-1.3.2.jar
  • lines changed 0, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/js/test/jsTestCov
  • lines changed 3, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/js/test/jsTestDriver.conf
  • lines changed 12, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/js/test/jsTestRun
  • lines changed 3, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/js/test/jsTestServer
  • lines changed 3, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/js/test/testEncodeProject.js
  • lines changed 49, context: html, text, full: html, text
    ENCODE data matrix web app. First cut with most functionality in place, for internal feature review. There are 3 web pages -- a Data Summary, Data Matrix, and Chip Matrix -- for both human and mouse. This version doesn't have proper Mouse support. The Chip Matrix is missing some features present in the Data Matrix. There are performance improvements needed (notably, additional features in hgApi to limit data transferred by organism or other filters).
• src/hg/lib/cv.c
  • lines changed 24, context: html, text, full: html, text
    Further work to have cv label appear instead of term in file search, fileUi and metadata dropdown
  • lines changed 3, context: html, text, full: html, text
    Validation of cv terms should treat 'deprecated' terms similar to terms not found.
• src/hg/lib/fileUi.c
  • lines changed 7, context: html, text, full: html, text
    Further work to have cv label appear instead of term in file search, fileUi and metadata dropdown
  • lines changed 1, context: html, text, full: html, text
    Using cvLabels in the overflow metadata in fileUi and file sort. However, this choice may be reversed when QA and Cricket actually see it.
• src/hg/lib/hui.c
  • lines changed 17, context: html, text, full: html, text
    Use cv labels for vals in metadata drop down.
  • lines changed 15, context: html, text, full: html, text
    Further work to have cv label appear instead of term in file search, fileUi and metadata dropdown
• src/hg/lib/jsHelper.c
  • lines changed 2, context: html, text, full: html, text
    tolerate NULL name in jsonPrint (e.g. if printing jsonp)
• src/hg/lib/mdb.c
  • lines changed 1, context: html, text, full: html, text
    Wow, a stray ';' bug. Took awhile to notice that.
  • lines changed 10, context: html, text, full: html, text
    Using cvLabels in the overflow metadata in fileUi and file sort. However, this choice may be reversed when QA and Cricket actually see it.
  • lines changed 1, context: html, text, full: html, text
    Spaces in freeText search were not safe. Redmine 5250.
• src/hg/makeDb/doc/danRer7.txt
  • lines changed 14, context: html, text, full: html, text
    adding liftOver 7 to 6
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
  • lines changed 22, context: html, text, full: html, text
    renamed Diff7d to Myc7d
  • lines changed 10, context: html, text, full: html, text
    Replacing the 1x75-Directional-HepG2-rep2 and rep1
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeHaibMethylRrbs.release2.notes
  • lines changed 917, context: html, text, full: html, text
    Adding the 4 new cell lines that would be Release 3
• src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes
  • lines changed 1297, context: html, text, full: html, text
    updated sydh tfbs notes to reflect the mnaseD experiment revocation
• src/hg/makeDb/doc/sacCer3.txt
  • lines changed 135, context: html, text, full: html, text
    regModule done, 32 alignments displayed, blat server on, and starting UW Footprints
  • lines changed 3, context: html, text, full: html, text
    noted some tweaks to growthCondition table
  • lines changed 14, context: html, text, full: html, text
    add iRow to maf
  • lines changed 32, context: html, text, full: html, text
    fixing some joinerCheck errors on oreganno track
• src/hg/makeDb/doc/xenTro3.txt
  • lines changed 268, context: html, text, full: html, text
    initial genome build and repeat masking
  • lines changed 69, context: html, text, full: html, text
    starting genbank run
  • lines changed 51, context: html, text, full: html, text
    fix genbank settings and add ctgPos2
• src/hg/makeDb/genbank/etc/genbank.conf
  • lines changed 33, context: html, text, full: html, text
    adding xenTro3
  • lines changed 2, context: html, text, full: html, text
    adjust alignments for xenTro3
  • lines changed 1, context: html, text, full: html, text
    fixup xenTro3 11.ooc location
• src/hg/makeDb/genbank/etc/hgwbeta.dbs
  • lines changed 1, context: html, text, full: html, text
    Added sacCer3 to list. QAing assembly and will be releasing soon. Turns on genbank updates.
• src/hg/makeDb/mdbUpdate/mdbPrint.c
  • lines changed 1, context: html, text, full: html, text
    Changing the invalids line to have the same behaviour as the other notices
• src/hg/makeDb/schema/all.joiner
  • lines changed 1, context: html, text, full: html, text
    Relaxed criteria for ikmcName a little bit.
  • lines changed 1, context: html, text, full: html, text
    Relaxed hgIkmcName a little.
• src/hg/makeDb/schema/joinerCheck/joinerCheck.c
  • lines changed 6, context: html, text, full: html, text
    indicate error for no operation specified
• src/hg/makeDb/schema/joinerCheck/makefile
  • lines changed 4, context: html, text, full: html, text
    add compile target and fix clean
• src/hg/makeDb/trackDb/README
  • lines changed 4, context: html, text, full: html, text
    add comment about ctgPos2 and url none
• src/hg/makeDb/trackDb/cv/alpha/cv.ra
  • lines changed 15, context: html, text, full: html, text
    Adding FOSL1 sc605
  • lines changed 17, context: html, text, full: html, text
    Commenting out CD20 generic stanza
  • lines changed 17, context: html, text, full: html, text
    Uncommenting out CD20+ since there are experiments that use. Redmine #5024.
  • lines changed 57, context: html, text, full: html, text
    Removing redundancies and cleaning up deprecated cell lines.
  • lines changed 6, context: html, text, full: html, text
    Removing old comment
  • lines changed 1, context: html, text, full: html, text
    MUNUS should be MINUS
  • lines changed 10, context: html, text, full: html, text
    Fixes for Katrina
  • lines changed 1, context: html, text, full: html, text
    Updating FibroP description to reflect pooled status
  • lines changed 9, context: html, text, full: html, text
    Few more changes for Katrina
  • lines changed 114, context: html, text, full: html, text
    Registering antibodies and fixing vendorId
  • lines changed 3, context: html, text, full: html, text
    filled out 5c's descriptions for it's files
• src/hg/makeDb/trackDb/cv/beta/cv.ra
  • lines changed 13, context: html, text, full: html, text
    Fixes from Katrina
  • lines changed 4, context: html, text, full: html, text
    More fixes for Katrina
  • lines changed 2, context: html, text, full: html, text
    Few more changes for Katrina
• src/hg/makeDb/trackDb/cv/public/cv.ra
  • lines changed 876, context: html, text, full: html, text
    releasing reviewed cv.ra changes, redmine #5188
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.html
  • lines changed 13, context: html, text, full: html, text
    Updated configuration of window function for Raw Signal to be mean+whiskers. Also updated References to follow standards (alphabetical etc). Redmine #236. Note #36.
• src/hg/makeDb/trackDb/human/hg18/wgEncodeUwDnaseSeq.new.ra
  • lines changed 1, context: html, text, full: html, text
    Updated configuration of window function for Raw Signal to be mean+whiskers. Also updated References to follow standards (alphabetical etc). Redmine #236. Note #36.
• src/hg/makeDb/trackDb/human/hg19/cosmic.html
  • lines changed 40, context: html, text, full: html, text
    Created cosmic.html
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra
  • lines changed 517, context: html, text, full: html, text
    loaded 4 tracks for broad histone
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra
  • lines changed 172, context: html, text, full: html, text
    renamed Diff7d to Myc7d
  • lines changed 58, context: html, text, full: html, text
    Replacing the 1x75-Directional-HepG2-rep2 and rep1
  • lines changed 61, context: html, text, full: html, text
    Adding the md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCshlLongRnaSeq.ra
  • lines changed 55, context: html, text, full: html, text
    Added table names for the Junctions
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeGisChiaPet.ra
  • lines changed 1475, context: html, text, full: html, text
    Removed the unloaded data for Chia Pet
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibMethylRrbs.ra
  • lines changed 487, context: html, text, full: html, text
    Adding the 4 new cell lines that would be Release 3
  • lines changed 21, context: html, text, full: html, text
    Adding md5sums
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
  • lines changed 5, context: html, text, full: html, text
    revoked SL1511
  • lines changed 265, context: html, text, full: html, text
    replcaed incorrectly duplicated files
  • lines changed 12, context: html, text, full: html, text
    added in md5sums for new files
  • lines changed 21, context: html, text, full: html, text
    renamed E2f6 to E2f4sc22832whatever
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 25, context: html, text, full: html, text
    added objstatus=replaced to the V1 data
• src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeYaleRnaSeq.ra
  • lines changed 258, context: html, text, full: html, text
    Remove the Yale mdb, it is SYDH
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/makefile
  • lines changed 1, context: html, text, full: html, text
    staging SYDH TFBS on beta, redmine# 69
• src/hg/makeDb/trackDb/human/hg19/metaDb/beta/wgEncodeSydhTfbs.ra
  • lines changed 47050, context: html, text, full: html, text
    staging SYDH TFBS on beta, redmine# 69
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/makefile
  • lines changed 1, context: html, text, full: html, text
    preparing metadata for release, redmine #383
• src/hg/makeDb/trackDb/human/hg19/metaDb/public/wgEncodeSydhRnaSeq.ra
  • lines changed 270, context: html, text, full: html, text
    preparing metadata for release, redmine #383
• src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra
  • lines changed 2, context: html, text, full: html, text
    incorrect trackDb settings for sydh tfbs
  • lines changed 1, context: html, text, full: html, text
    staging SYDH TFBS on beta, redmine# 69
• src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra
  • lines changed 81, context: html, text, full: html, text
    loaded 4 tracks for broad histone
  • lines changed 1, context: html, text, full: html, text
    Forgot to check in this mean+whiskers
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.html
  • lines changed 3, context: html, text, full: html, text
    Fixing references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
  • lines changed 6, context: html, text, full: html, text
    renamed Diff7d to Myc7d
  • lines changed 2, context: html, text, full: html, text
    Replacing the 1x75-Directional-HepG2-rep2 and rep1
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra
  • lines changed 8, context: html, text, full: html, text
    restored a missing subtrack
  • lines changed 2, context: html, text, full: html, text
    corrected som trackDb errors
  • lines changed 296, context: html, text, full: html, text
    Changing long labels to have no Strand and to have lowercase polyA
  • lines changed 130, context: html, text, full: html, text
    revamped longlabels by script, tried to make them as consistent as possible.
  • lines changed 1, context: html, text, full: html, text
    One short label
  • lines changed 3, context: html, text, full: html, text
    cleaned up short lavels a bit
  • lines changed 1, context: html, text, full: html, text
    removed empty lines that broke trackDb
  • lines changed 58, context: html, text, full: html, text
    git hack, ignore this one
  • lines changed 29, context: html, text, full: html, text
    removed empty lines that broke trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html
  • lines changed 63, context: html, text, full: html, text
    some QA requested html changes
  • lines changed 22, context: html, text, full: html, text
    Making changes for Jacob on ticket 1634
• src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra
  • lines changed 20, context: html, text, full: html, text
    wgEncodeCshlShortRnaSeq.new.html
  • lines changed 38, context: html, text, full: html, text
    fixed long labels and short labels
  • lines changed 21, context: html, text, full: html, text
    odd error with wrong lab name in long label
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGencodeV7.ra
  • lines changed 3, context: html, text, full: html, text
    use 'like' instead of '=' for find specs, #5158
• src/hg/makeDb/trackDb/human/hg19/wgEncodeGisChiaPet.html
  • lines changed 12, context: html, text, full: html, text
    Fixing references
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.html
  • lines changed 11, context: html, text, full: html, text
    Adding the 4 new cell lines that would be Release 3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra
  • lines changed 82, context: html, text, full: html, text
    added new tracks to haib methyl rrbs
  • lines changed 3, context: html, text, full: html, text
    merge conflict resolved
  • lines changed 134, context: html, text, full: html, text
    Adding the 4 new cell lines that would be Release 3
  • lines changed 81, context: html, text, full: html, text
    Fixing merge conflict
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Typo in HELAS3
• src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
  • lines changed 16, context: html, text, full: html, text
    revoked SL1511
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html
  • lines changed 16, context: html, text, full: html, text
    pre-QA fixes
  • lines changed 10, context: html, text, full: html, text
    Removing the view, since it is a single view track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.ra
  • lines changed 5, context: html, text, full: html, text
    Trying to fix the Tier 1 and Tier 2 mistake that I put in the .ra instead of the .new.ra
  • lines changed 67, context: html, text, full: html, text
    Removing the view, since it is a single view track
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.ra
  • lines changed 9, context: html, text, full: html, text
    Trying to fix the Tier 1 and Tier 2 mistake that I put in the .ra instead of the .new.ra
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html
  • lines changed 157, context: html, text, full: html, text
    started release 2's html and added line in trackDb
  • lines changed 26, context: html, text, full: html, text
    fixed some html stuff
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    started release 2's html and added line in trackDb
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.html
  • lines changed 2, context: html, text, full: html, text
    made 'et al' italicized and changed 'RNA Seq' to 'RNA-seq' which is our convention, remdine #383
  • lines changed 2, context: html, text, full: html, text
    Change Peggy's link to USC
  • lines changed 8, context: html, text, full: html, text
    Ticket 383, changing the html and the view limits per Katrina requests
  • lines changed 4, context: html, text, full: html, text
    Resolving merge conflict
  • lines changed 2, context: html, text, full: html, text
    Fixed a broken link and changed Seq to seq and dropped orig assembly
  • lines changed 2, context: html, text, full: html, text
    fixed commenting out of polyA-/rRNA- info, redmine #383
  • lines changed 3, context: html, text, full: html, text
    commenting out broken link to SYDH TFBS and adding temporary link to the track on genome-preview; will revert back once SYDH TFBS is released, redmine #383
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhRnaSeq.ra
  • lines changed 1, context: html, text, full: html, text
    Ticket 383, changing the html and the view limits per Katrina requests
  • lines changed 12, context: html, text, full: html, text
    Fixed a broken link and changed Seq to seq and dropped orig assembly
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html
  • lines changed 5, context: html, text, full: html, text
    fixed some html stuff
  • lines changed 2, context: html, text, full: html, text
    removed non breaking spaces and added <p> tags, redmine# 69
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra
  • lines changed 333, context: html, text, full: html, text
    merged with the R1 trackDb, as nothing is in release 2 now yet
  • lines changed 5425, context: html, text, full: html, text
    changed how libraries are handles, and added usage statement
• src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra
  • lines changed 333, context: html, text, full: html, text
    fixed short and long labels
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUncBsuProt.html
  • lines changed 79, context: html, text, full: html, text
    Somehow when I cleared up a [to appear] reference, I lost some previous modifications on this file, such as sanitizing an email address. So, I'm re-doing those modifications after reverting to the previous version. If I did it right, this check-in should affect four lines relative to commit 0136ebcca4eacb7763114281cfba8990b6839d48, not 80
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html
  • lines changed 21, context: html, text, full: html, text
    fix some pre-qa stuff
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
  • lines changed 14, context: html, text, full: html, text
    pre-QA changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
  • lines changed 1, context: html, text, full: html, text
    pre-QA changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html
  • lines changed 4, context: html, text, full: html, text
    fixed stuff per pre-QA requestwq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra
  • lines changed 1, context: html, text, full: html, text
    fixed stuff per pre-QA requestwq
• src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html
  • lines changed 3, context: html, text, full: html, text
    QA changes
• src/hg/makeDb/trackDb/human/hg19/wgEncodeYaleRnaSeq.html
  • lines changed 147, context: html, text, full: html, text
    Removed the html that goes with the deprecated track
• src/hg/makeDb/trackDb/human/omimLocation.html
  • lines changed 3, context: html, text, full: html, text
    Added step to Methods section about phenotype map keys. Redmine #4456, note-60.
• src/hg/makeDb/trackDb/makefile
  • lines changed 1, context: html, text, full: html, text
    adding xenTro3 to the build
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechHist.ra
  • lines changed 37, context: html, text, full: html, text
    Updated the md5sum in the metaData with the md5sum's of the files found in the downloads directory. Some of the md5sum's given by the lab were incorrect because we gz some of the files which changes the md5sum. Also since the fastq's are tar'd there is only 1 md5sum rather than mutliple individual md5sum's.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodeCaltechTfbs.ra
  • lines changed 86, context: html, text, full: html, text
    Updated the md5sum in the metaData with the md5sum's of the files found in the downloads directory. Some of the md5sum's given by the lab were incorrect because we gz some of the files which changes the md5sum. Also since the fastq's are tar'd there is only 1 md5sum rather than mutliple individual md5sum's.
• src/hg/makeDb/trackDb/mouse/mm9/metaDb/alpha/wgEncodePsuTfbs.ra
  • lines changed 113, context: html, text, full: html, text
    Replaced submission 3044 with 4817.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodePsuTfbs.ra
  • lines changed 36, context: html, text, full: html, text
    Replaced submission 3044 with 4817.
• src/hg/makeDb/trackDb/mouse/mm9/wgEncodeSydhTfbs.new.html
  • lines changed 2, context: html, text, full: html, text
    Removed spaces in references for journal with name USA. Also added period after journal for 5 reference. Removed period in abbreviation for Journal Nat. Methods. Redmine #2726.
• src/hg/makeDb/trackDb/sacCer/sacCer2/trackDb.ra
  • lines changed 1, context: html, text, full: html, text
    added chromosomes none to gap track as demo for steve
• src/hg/makeDb/trackDb/sacCer/sacCer3/gold.html
  • lines changed 3, context: html, text, full: html, text
    made all species names italic. thanks, steve
• src/hg/makeDb/trackDb/sacCer/sacCer3/strainAlignments.html
  • lines changed 129, context: html, text, full: html, text
    initial contents for this alignment track
• src/hg/makeDb/trackDb/sacCer/sacCer3/strainAlignments.ra
  • lines changed 242, context: html, text, full: html, text
    initial contents for this alignment track
  • lines changed 32, context: html, text, full: html, text
    change to psl from the mafNet files
• src/hg/makeDb/trackDb/sacCer/sacCer3/trackDb.ra
  • lines changed 3, context: html, text, full: html, text
    including the strainAlignments
• src/hg/makeDb/trackDb/xenTro/xenTro3/ctgPos2.html
  • lines changed 10, context: html, text, full: html, text
    initial contents for ctgPos2 track
  • lines changed 1, context: html, text, full: html, text
    better to open the directory at NCBI instead of downloading the file
• src/hg/makeDb/trackDb/xenTro/xenTro3/description.html
  • lines changed 131, context: html, text, full: html, text
    initial contents for xenTro3
• src/hg/makeDb/trackDb/xenTro/xenTro3/gap.html
  • lines changed 31, context: html, text, full: html, text
    initial contents for xenTro3
• src/hg/makeDb/trackDb/xenTro/xenTro3/gold.html
  • lines changed 23, context: html, text, full: html, text
    initial contents for xenTro3
• src/hg/makeDb/trackDb/xenTro/xenTro3/trackDb.ra
  • lines changed 7, context: html, text, full: html, text
    initial contents for xenTro3
  • lines changed 15, context: html, text, full: html, text
    adding ctgPos2 table and search spec
  • lines changed 1, context: html, text, full: html, text
    turn off the url for ctgPos2
• src/hg/oneShot/doOmimAv/doOmimAv.c
  • lines changed 12, context: html, text, full: html, text
    Fixed a bug that generate 'rsrs...'.
  • lines changed 6, context: html, text, full: html, text
    Disabled logic that process subsequent entries if a line has multiple replacement AA strings or multiple dbSnpId.
• src/hg/protein/pbCalDist/pbCalDist.c
  • lines changed 14, context: html, text, full: html, text
    Reinstating various proteome browser files to their previous versions, before I got this wild idea of doing a 'quick bug fix' to stop error messages from appearing relating to selenocysteines
• src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c
  • lines changed 14, context: html, text, full: html, text
    Reinstating various proteome browser files to their previous versions, before I got this wild idea of doing a 'quick bug fix' to stop error messages from appearing relating to selenocysteines
• src/hg/protein/pbCalResStd/pbCalResStd.c
  • lines changed 22, context: html, text, full: html, text
    Reinstating various proteome browser files to their previous versions, before I got this wild idea of doing a 'quick bug fix' to stop error messages from appearing relating to selenocysteines
• src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c
  • lines changed 8, context: html, text, full: html, text
    Reinstating various proteome browser files to their previous versions, before I got this wild idea of doing a 'quick bug fix' to stop error messages from appearing relating to selenocysteines
• src/hg/protein/pbGlobal/pbGlobal.c
  • lines changed 2, context: html, text, full: html, text
    Reinstating various proteome browser files to their previous versions, before I got this wild idea of doing a 'quick bug fix' to stop error messages from appearing relating to selenocysteines
• src/hg/protein/pbTracks/pbTracks.c
  • lines changed 5, context: html, text, full: html, text
    Reinstating various proteome browser files to their previous versions, before I got this wild idea of doing a 'quick bug fix' to stop error messages from appearing relating to selenocysteines
• src/hg/utils/automation/makefile
  • lines changed 2, context: html, text, full: html, text
    Added unigene.csh.
• src/hg/utils/automation/unigene.csh
  • lines changed 12, context: html, text, full: html, text
    Took out the $myPath variable and made everything run from $localRepos. (Redmine 2047#note-3).
• src/hg/utils/cpAndLinkToResourceFiles.pl
  • lines changed 33, context: html, text, full: html, text
    skip duplicate files; add experimental minify code (not currently used; see redmine #5145)
• src/lib/oldGff.c
  • lines changed 55, context: html, text, full: html, text
    rearrange static function definitions to avoid compiler problems on Suse linux
• src/lib/tests/udcTest.c
  • lines changed 74, context: html, text, full: html, text
    added read-ahead buffer testing
• src/lib/tests/udcTrials.csh
  • lines changed 19, context: html, text, full: html, text
    added read-ahead buffer testing
• src/utils/qa/weeklybld/buildEnv.csh
  • lines changed 2, context: html, text, full: html, text
    v257 preview2
• src/utils/qa/weeklybld/doHgTablesTestRobot.csh
  • lines changed 1, context: html, text, full: html, text
    add Luvina, the future push shepherd!!
• src/utils/qa/weeklybld/doNewBranch.csh
  • lines changed 1, context: html, text, full: html, text
    add Luvina, the future push shepherd!!
• src/utils/qa/weeklybld/doNewReview.csh
  • lines changed 1, context: html, text, full: html, text
    add Luvina, the future push shepherd!!
• src/utils/qa/weeklybld/doNewReview2.csh
  • lines changed 1, context: html, text, full: html, text
    add Luvina, the future push shepherd!!

• lines changed: 88794
• files changed: 355