Commits for wong

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

• streamlined and rewrote some parts that I felt were inefficient
  • python/programs/DateCheck/dateCheck.py - lines changed 43, context: html, text, full: html, text
• added new tracks to haib methyl rrbs
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 82, context: html, text, full: html, text
• merge conflict resolved
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibMethylRrbs.new.ra - lines changed 3, context: html, text, full: html, text
• hope this resolves merge
• fixed short and long labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.ra - lines changed 333, context: html, text, full: html, text
• fixed some html stuff
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.html - lines changed 5, context: html, text, full: html, text
• revoked SL1511
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 5, context: html, text, full: html, text
• revoked SL1511
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeHaibTfbs.ra - lines changed 16, context: html, text, full: html, text
• added in md5sums to source tree, not just my own
  • src/hg/encode/md5sumhistory/hg18/wgEncodeAffyRnaChip.md5sum.history - lines changed 111, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeBroadChipSeq.md5sum.history - lines changed 552, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeBroadHmm.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeBuOrchid.md5sum.history - lines changed 5, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeCaltechRnaSeq.md5sum.history - lines changed 297, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeChromatinMap.md5sum.history - lines changed 534, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeCshlLoRnaSeq.md5sum.history - lines changed 9, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeCshlLongRnaSeq.md5sum.history - lines changed 20, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeCshlRnaSeq.md5sum.history - lines changed 54, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeCshlShortRnaSeq.md5sum.history - lines changed 43, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeDukeAffyExonArray.md5sum.history - lines changed 60, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeDukeDNaseSeq.md5sum.history - lines changed 8, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeGisDnaPet.md5sum.history - lines changed 43, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeGisPet.md5sum.history - lines changed 83, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeGisRnaSeq.md5sum.history - lines changed 20, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeHelicosRnaSeq.md5sum.history - lines changed 11, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaChipSeq.md5sum.history - lines changed 429, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaCnv.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaMethyl27.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaMethylSeq.md5sum.history - lines changed 93, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeHudsonalphaRnaSeq.md5sum.history - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeMapability.md5sum.history - lines changed 20, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeMarguliesChai.md5sum.history - lines changed 5, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeNhgriBip.md5sum.history - lines changed 15, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeNhgriNre.md5sum.history - lines changed 11, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeRikenCage.md5sum.history - lines changed 92, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeSangerGencode.md5sum.history - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeSunyalbanyRnaGeneChip.md5sum.history - lines changed 16, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUc.md5sum.history - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUmassdekker5C.md5sum.history - lines changed 11, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUmasshaTfbsValid.md5sum.history - lines changed 10, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUncFAIREseq.md5sum.history - lines changed 10, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUwAffyExonArray.md5sum.history - lines changed 75, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUwChIPSeq.md5sum.history - lines changed 554, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUwDGF.md5sum.history - lines changed 45, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeUwDnaseSeq.md5sum.history - lines changed 386, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg18/wgEncodeYaleChIPseq.md5sum.history - lines changed 1133, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeAffyRnaChip.md5sum.history - lines changed 56, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeBetaTest.md5sum.history - lines changed 6, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeBroadHistone.md5sum.history - lines changed 1274, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeBroadHmm.md5sum.history - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeBuOrchid.md5sum.history - lines changed 5, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeCaltechRnaSeq.md5sum.history - lines changed 573, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeCshlLongRnaSeq.md5sum.history - lines changed 1369, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeCshlShortRnaSeq.md5sum.history - lines changed 408, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeDukeAffyExon.md5sum.history - lines changed 108, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeGencodeV4.md5sum.history - lines changed 10, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeGencodeV7.md5sum.history - lines changed 18, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeGisChiaPet.md5sum.history - lines changed 71, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeGisDnaPet.md5sum.history - lines changed 50, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeGisRnaPet.md5sum.history - lines changed 182, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeGisRnaSeq.md5sum.history - lines changed 32, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeHaibGenotype.md5sum.history - lines changed 94, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethyl450.md5sum.history - lines changed 14, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethylArray.md5sum.history - lines changed 76, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethylRrbs.md5sum.history - lines changed 408, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeHaibMethylSeq.md5sum.history - lines changed 147, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeHaibRnaSeq.md5sum.history - lines changed 212, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeHaibTfbs.md5sum.history - lines changed 2192, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeMapability.md5sum.history - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromChip.md5sum.history - lines changed 368, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromDnase.md5sum.history - lines changed 462, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromFaire.md5sum.history - lines changed 244, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeOpenChromSynth.md5sum.history - lines changed 20, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeRegDnaseClustered.md5sum.history - lines changed 7, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeRegMarkH3k27ac.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeRegMarkH3k4me1.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeRegMarkH3k4me3.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeRegTfbsClustered.md5sum.history - lines changed 8, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeRegTxn.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeRikenCage.md5sum.history - lines changed 441, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSunyAlbanyGeneSt.md5sum.history - lines changed 28, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSunyAlbanyTiling.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSunyRipSeq.md5sum.history - lines changed 73, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSunySwitchgear.md5sum.history - lines changed 6, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSydhHistone.md5sum.history - lines changed 147, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSydhNsome.md5sum.history - lines changed 85, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSydhRnaSeq.md5sum.history - lines changed 19, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeSydhTfbs.md5sum.history - lines changed 2503, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUMassWengTfbsValid.md5sum.history - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUchicagoTfbs.md5sum.history - lines changed 100, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUmassDekker5C.md5sum.history - lines changed 12, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUncBsuProt.md5sum.history - lines changed 13, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUw5C.md5sum.history - lines changed 42, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUwAffyExonArray.md5sum.history - lines changed 138, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUwDgf.md5sum.history - lines changed 136, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUwDnase.md5sum.history - lines changed 983, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUwHistone.md5sum.history - lines changed 1154, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/hg19/wgEncodeUwTfbs.md5sum.history - lines changed 831, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeBetaTest.md5sum.history - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeCaltechHistone.md5sum.history - lines changed 6, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeCaltechTfbs.md5sum.history - lines changed 2, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeLicrHistone.md5sum.history - lines changed 233, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeLicrRnaSeq.md5sum.history - lines changed 83, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeLicrTfbs.md5sum.history - lines changed 263, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeMapability.md5sum.history - lines changed 4, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodePsuHistone.md5sum.history - lines changed 3, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodePsuTfbs.md5sum.history - lines changed 48, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeSydhHist.md5sum.history - lines changed 39, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeSydhRnaSeq.md5sum.history - lines changed 14, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeSydhTfbs.md5sum.history - lines changed 347, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeTestChipSeq.md5sum.history - lines changed 17, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeUwDnase.md5sum.history - lines changed 411, context: html, text, full: html, text
  • src/hg/encode/md5sumhistory/mm9/wgEncodeUwRnaSeq.md5sum.history - lines changed 140, context: html, text, full: html, text
• some QA requested html changes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.html - lines changed 63, context: html, text, full: html, text
• renamed Diff7d to Myc7d
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeCaltechRnaSeq.release2.notes - lines changed 22, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeCaltechRnaSeq.ra - lines changed 172, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCaltechRnaSeq.new.ra - lines changed 6, context: html, text, full: html, text
• replcaed incorrectly duplicated files
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 265, context: html, text, full: html, text
• merged with the R1 trackDb, as nothing is in release 2 now yet
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 333, context: html, text, full: html, text
• added in md5sums for new files
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 12, context: html, text, full: html, text
• incorrect trackDb settings for sydh tfbs
  • src/hg/makeDb/trackDb/human/hg19/trackDb.wgEncode.ra - lines changed 2, context: html, text, full: html, text
• changed how libraries are handles, and added usage statement
  • python/programs/DateCheck/dateCheck.py - lines changed 17, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhTfbs.new.ra - lines changed 5425, context: html, text, full: html, text
• updated sydh tfbs notes to reflect the mnaseD experiment revocation
  • python/programs/DateCheck/dateCheck.py - lines changed 110, context: html, text, full: html, text
  • python/programs/dateCheck/dateCheck - lines changed 110, context: html, text, full: html, text
  • src/hg/makeDb/doc/encodeDccHg19/wgEncodeSydhTfbs.release1.notes - lines changed 1297, context: html, text, full: html, text
• started release 2's html and added line in trackDb
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html - lines changed 157, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.ra - lines changed 1, context: html, text, full: html, text
• fixed some html stuff
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSydhHistone.new.html - lines changed 26, context: html, text, full: html, text
• fixed stuff per pre-QA requestwq
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwHistone.new.ra - lines changed 1, context: html, text, full: html, text
• fixed long labels and short labels
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra - lines changed 38, context: html, text, full: html, text
• odd error with wrong lab name in long label
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlShortRnaSeq.new.ra - lines changed 21, 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.
  • python/programs/dateCheck/dateCheck - lines changed 141, context: html, text, full: html, text
• QA changes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwTfbs.new.html - lines changed 3, context: html, text, full: html, text
• pre-QA changes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.html - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUwDnase.new.ra - lines changed 1, context: html, text, full: html, text
• pre-QA fixes
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeSunyAlbanyGeneSt.new.html - lines changed 16, context: html, text, full: html, text
• loaded 4 tracks for broad histone
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeBroadHistone.ra - lines changed 517, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeBroadHistone.new.ra - lines changed 81, context: html, text, full: html, text
• restored a missing subtrack
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 8, context: html, text, full: html, text
• corrected som trackDb errors
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 2, context: html, text, full: html, text
• revamped longlabels by script, tried to make them as consistent as possible.
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 130, context: html, text, full: html, text
• cleaned up short lavels a bit
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 3, context: html, text, full: html, text
• removed empty lines that broke trackDb
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 1, context: html, text, full: html, text
• git hack, ignore this one
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 58, context: html, text, full: html, text
• removed empty lines that broke trackDb
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeCshlLongRnaSeq.ra - lines changed 29, context: html, text, full: html, text
• renamed E2f6 to E2f4sc22832whatever
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeHaibTfbs.ra - lines changed 21, context: html, text, full: html, text
• added objstatus=replaced to the V1 data
  • src/hg/makeDb/trackDb/human/hg19/metaDb/alpha/wgEncodeSunyAlbanyGeneSt.ra - lines changed 25, context: html, text, full: html, text
• fix some pre-qa stuff
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeUw5C.html - lines changed 21, context: html, text, full: html, text
• filled out 5c's descriptions for it's files
  • src/hg/makeDb/trackDb/cv/alpha/cv.ra - lines changed 3, context: html, text, full: html, text