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
- 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
- lines changed 12, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg18/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/hg18/wgEncodeCaltechRnaSeq.md5sum.history
- lines changed 297, context: html, text, full: html, text
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
- lines changed 43, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg18/wgEncodeGisPet.md5sum.history
- lines changed 83, context: html, text, full: html, text
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
- lines changed 8, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeRegTxn.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/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
- lines changed 73, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeSunySwitchgear.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/wgEncodeSydhHistone.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/wgEncodeSydhNsome.md5sum.history
- lines changed 85, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeSydhRnaSeq.md5sum.history
- lines changed 19, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeSydhTfbs.md5sum.history
- lines changed 2503, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUMassWengTfbsValid.md5sum.history
- lines changed 3, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUchicagoTfbs.md5sum.history
- lines changed 100, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUmassDekker5C.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/wgEncodeUncBsuProt.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/wgEncodeUw5C.md5sum.history
- lines changed 42, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUwAffyExonArray.md5sum.history
- lines changed 138, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUwDgf.md5sum.history
- lines changed 136, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUwDnase.md5sum.history
- lines changed 983, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUwHistone.md5sum.history
- lines changed 1154, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/hg19/wgEncodeUwTfbs.md5sum.history
- lines changed 831, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeBetaTest.md5sum.history
- lines changed 3, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeCaltechHistone.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/mm9/wgEncodeCaltechTfbs.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/mm9/wgEncodeLicrHistone.md5sum.history
- lines changed 233, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeLicrRnaSeq.md5sum.history
- lines changed 83, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeLicrTfbs.md5sum.history
- lines changed 263, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeMapability.md5sum.history
- lines changed 4, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodePsuHistone.md5sum.history
- lines changed 3, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodePsuTfbs.md5sum.history
- lines changed 48, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeSydhHist.md5sum.history
- lines changed 39, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeSydhRnaSeq.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/mm9/wgEncodeSydhTfbs.md5sum.history
- lines changed 347, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeTestChipSeq.md5sum.history
- lines changed 17, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeUwDnase.md5sum.history
- lines changed 411, context: html, text, full: html, text
added in md5sums to source tree, not just my own
- src/hg/encode/md5sumhistory/mm9/wgEncodeUwRnaSeq.md5sum.history
- lines changed 140, context: html, text, full: html, text
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).
- 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).
- 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).
- 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).
- 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
- src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes
- 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 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 51, context: html, text, full: html, text
fix genbank settings and add ctgPos2
- src/hg/makeDb/genbank/etc/genbank.conf
- 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 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 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 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
- 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
- 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
- src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra
- 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
- src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra
- 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 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
- 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 134, context: html, text, full: html, text
Adding the 4 new cell lines that would be Release 3
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibRnaSeq.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra
- src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html
- 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
- 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 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 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
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html
- src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra
- 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
- 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
- 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
- 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