kent: changes by commit

review to branch (2009-09-22 to 2009-09-29) v216

• Fixing problem with bptTraverse on larger data sets. Causes problems in bigWig on scaffolded assemblies.
  • src/lib/bPlusTree.c 1.6 - lines changed: 7, context: html, text, full: html, text
• Making wigToBigWig creation check for overlaps in sections for a better error message rather than the internal error message.
  • src/lib/bwgCreate.c 1.16 - lines changed: 20, context: html, text, full: html, text
• Sped up 10 or 20x by using a hash table instead of repeated sql queries.
  • src/hg/protein/pfamXref/pfamXref.c 1.10 - lines changed: 12, context: html, text, full: html, text
• Simplified code. Reduced run time from 5 hours to 20 minutes.
  • src/hg/protein/pbCalPi/pbCalPi.c 1.8 - lines changed: 43, context: html, text, full: html, text
• Reduced a warn to a verbose 2 since it was complaining about 'U' which is common these days. Also took out a system call to speed it up about 2x.
  • src/hg/protein/pbCalDistGlobal/pbCalDistGlobal.c 1.9 - lines changed: 3, context: html, text, full: html, text
• Adding database parameter as now required for hAllocConn(). Changing a stderr message to verbose(2 since it was coming up a lot to no bad effect. Bumping up MAXN so can handle 20 million proteins in SwissProt since now up to 9.3 million and previous limit was 10 million. Changing biggest array to be dynamically allocated to avoid linkage error.
  • src/hg/protein/pbCalResStdGlobal/pbCalResStdGlobal.c 1.8 - lines changed: 10, context: html, text, full: html, text
• Adding pbCalResStdGlobal to parent makefile so we'll spot when it doesn't compile sooner.
  • src/hg/protein/makefile 1.24 - lines changed: 1, context: html, text, full: html, text
• Built new version of proteins database on top of corresponding swissProt database.
  • src/hg/makeDb/doc/proteins/090821.txt 1.1 - lines changed: 305, context: html, text, full: html, text
• Done with first pass of the build. Now for some testing....
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh 1.2 - lines changed: 29, context: html, text, full: html, text
• Adding some configuration so hg19 known genes details page works.
  • src/hg/hgGene/hgGeneData/Human/hg19/links.ra 1.1 - lines changed: 9, context: html, text, full: html, text
  • src/hg/hgGene/hgGeneData/Human/hg19/otherOrgs.ra 1.1 - lines changed: 17, context: html, text, full: html, text
• Working around mysql 5 bug.
  • src/hg/utils/automation/synBlastp.csh 1.4 - lines changed: 2, context: html, text, full: html, text
• Making directory for config files for hg19
  • src/hg/near/hgNear/hgNearData/Human/hg19/acc.html 1.1 - lines changed: 2, context: html, text, full: html, text
• Fixed bug in memory management Andy recently introduced where the geneId was freed after the microarray section leaving subsequent sections with garbage geneId.
  • src/hg/hgGene/microarray.c 1.17 - lines changed: 1, context: html, text, full: html, text
• Finishing up build and database integration. Will need to add more knownTo and XyzDistance tables as the hg19 database in general is built up.
  • src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh 1.3 - lines changed: 26, context: html, text, full: html, text
• Got rid of a test case that depended on a database being constant.
  • src/hg/sqlToXml/doTest 1.8 - lines changed: 1, context: html, text, full: html, text
• Making error message a little more informative, and not an 'internal error' since it is in response to erronious input, not software error.
  • src/hg/lib/customTrack.c 1.178 - lines changed: 1, context: html, text, full: html, text
• Making printf formating agree in signedness to avoid error on different compilers.
  • src/utils/bedToBigBed/bedToBigBed.c 1.11 - lines changed: 1, context: html, text, full: html, text
• Patching things to look for all_mrna when chr1_mrna doesn't exist and the like.
  • src/hg/lib/hdb.c 1.415 - lines changed: 10, context: html, text, full: html, text