rhead: changes by commit

review to branch (2009-04-07 to 2009-04-14) v204

• Adjusted chromStart for the second chrX PAR region by one. The off-by-one was found by a user.
  • src/hg/makeDb/trackDb/human/hg18/description.html 1.20 - lines changed: 1, context: html, text, full: html, text
• Rearranged PAR section so it's easier to see. Thanks, b0b.
  • src/hg/makeDb/trackDb/human/hg18/description.html 1.21 - lines changed: 7, context: html, text, full: html, text
• Small edits to disclaimer section.
  • src/hg/makeDb/trackDb/human/omimGene.html 1.18 - lines changed: 2, context: html, text, full: html, text
• Adding hg19.
  • src/hg/makeDb/genbank/etc/hgwbeta.dbs 1.97 - lines changed: 1, context: html, text, full: html, text
• Added hg19 to hg set.
  • src/hg/makeDb/schema/all.joiner 1.702 - lines changed: 1, context: html, text, full: html, text
• Initial file. Script to run genePredCheck/pslCheck, joinerCheck, gbSanity, and featureBits on GenBank tables.
  • src/utils/qa/doGenbankTests 1.1 - lines changed: 159, context: html, text, full: html, text
• Added a date stamp at the end. Put cd in a subshell.
  • src/utils/qa/doGenbankTests 1.2 - lines changed: 7, context: html, text, full: html, text
• Added doGenbankTests.
  • src/utils/qa/makefile 1.103 - lines changed: 1, context: html, text, full: html, text
• Initial checkin. qaConfig.csh and qaConfig.bash are configuration files for the remaining scripts.
  • src/utils/qa/qaConfig.bash 1.1 - lines changed: 9, context: html, text, full: html, text
  • src/utils/qa/qaConfig.csh 1.1 - lines changed: 9, context: html, text, full: html, text
• Sourced new qaConfig file at the top. Changed -h hgwbeta lines to look for sql host stored in a variable, specified in the new qaConfig file.
  • src/utils/qa/GS1.csh 1.5 - lines changed: 8, context: html, text, full: html, text
  • src/utils/qa/PB.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/activeGenbank.csh 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/alertBqueue.csh 1.9 - lines changed: 3, context: html, text, full: html, text
  • src/utils/qa/allowTraffic.csh 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/backupCentral.csh 1.10 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/bigPush.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/blatPing.csh 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/browserUsage.csh 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/catchBot.csh 1.19 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/chain.csh 1.23 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/chain2.csh 1.9 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/chainNetTrio.csh 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkAllStaticLinks.csh 1.10 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkBOT.csh 1.12 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkCoverage.csh 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkEncodeRegions.csh 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkGbdb.csh 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/checkGbdbDiffs.csh 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkHitter.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkMachineName.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkMetaAday.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkMetaData.csh 1.16 - lines changed: 4, context: html, text, full: html, text
  • src/utils/qa/checkOffend.csh 1.10 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkScaffoldGaps.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkStaticLinks.csh 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkStoreUnits.csh 1.26 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkSync.csh 1.16 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/checkSyncAll.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkTableStatus.csh 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/checkTrackUiLinks.csh 1.10 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/check_grp.csh 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/chromInfo_file_test.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/compareHgFindSpecAll.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/compareHgFindSpecFast.csh 1.5 - lines changed: 5, context: html, text, full: html, text
  • src/utils/qa/compareHgFindSpecs.csh 1.9 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/compareTableLists.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/compareTrackDbAll.csh 1.20 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/compareTrackDbFast.csh 1.7 - lines changed: 5, context: html, text, full: html, text
  • src/utils/qa/compareTrackDbs.csh 1.27 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/compareWholeColumn.csh 1.9 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/compareWholeTable.csh 1.6 - lines changed: 3, context: html, text, full: html, text
  • src/utils/qa/copyExtSeqRows.csh 1.5 - lines changed: 18, context: html, text, full: html, text
  • src/utils/qa/countPerChrom.csh 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/countRows.csh 1.6 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/cronLinks.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/databaseAday.csh 1.9 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/dbUpdateTimes.csh 1.5 - lines changed: 5, context: html, text, full: html, text
  • src/utils/qa/doGenbankTests 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/doRLUpdate.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/dropUserTables.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/dumpEmpty.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/field_null_none_range_checker.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/findBigFiles.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/findBlatServer.csh 1.10 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/findColumn.csh 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/findDbPartners.csh 1.8 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/findLevel.csh 1.16 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/findMtNets.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/findNewTables.csh 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/findOrg.csh 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/findPushQLocks.csh 1.7 - lines changed: 4, context: html, text, full: html, text
  • src/utils/qa/full_joinerCheck.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/genbankRun.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/generic_range_check.csh 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getAssemblies.csh 1.21 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/getChromFieldName.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getChromlist.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getConservation.csh 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/getDbSize.csh 1.12 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/getField.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getGbdbBeta.csh 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/getLastMonth.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getLiftOver.csh 1.5 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/getMatrixLines.csh 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getMonthLastYear.csh 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getOrderKey.csh 1.5 - lines changed: 3, context: html, text, full: html, text
  • src/utils/qa/getRRdatabases.csh 1.10 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getRRdumpfile.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getRRtableStatus.csh 1.11 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getRRtables.csh 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getSplit.csh 1.7 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/getTableSize.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getTableStatus.csh 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getTrackName.csh 1.8 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getVersion.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/getYield.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/hgFindSpecGlobal.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/host.csh 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/igtc.csh 1.21 - lines changed: 13, context: html, text, full: html, text
  • src/utils/qa/knownGene.csh 1.12 - lines changed: 12, context: html, text, full: html, text
  • src/utils/qa/makeFilledBlockBed.csh 1.3 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/makefile 1.104 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/net.csh 1.18 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/proteins.csh 1.5 - lines changed: 6, context: html, text, full: html, text
  • src/utils/qa/qaEnsGenes.csh 1.22 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/realTime.csh 1.10 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/retirePushQ.csh 1.9 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/runBits.csh 1.14 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/runJoiner.csh 1.13 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/sessionStats.csh 1.5 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/showProcesslist.csh 1.4 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/showTracks 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/syncAday.csh 1.7 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/tableDumpDates.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/trackDbGlobal.csh 1.29 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/trackDb_compare.csh 1.4 - lines changed: 2, context: html, text, full: html, text
  • src/utils/qa/trackDb_compare_visibility.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/track_Db_compare_priority.csh 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/utils/qa/updateTimes.csh 1.23 - lines changed: 4, context: html, text, full: html, text
  • src/utils/qa/updateTimesDb.csh 1.7 - lines changed: 5, context: html, text, full: html, text
  • src/utils/qa/whoMadeIt.csh 1.4 - lines changed: 1, context: html, text, full: html, text
• Changed -h hgwbeta to variable host specified in qaConfig.csh.
  • src/utils/qa/retirePushQ.csh 1.10 - lines changed: 1, context: html, text, full: html, text
• Forgot to specify entire path to a file.
  • src/utils/qa/doGenbankTests 1.4 - lines changed: 2, context: html, text, full: html, text
• Removed a redundant set host command that was causing the script to choke when hgwbeta was explicitly specified as an argument.
  • src/utils/qa/getAssemblies.csh 1.22 - lines changed: 1, context: html, text, full: html, text
• Changing from which to dirname to find path of qaConfig.csh file.
  • src/utils/qa/tableDumpDates.csh 1.3 - lines changed: 2, context: html, text, full: html, text