Commits for markd

v248_preview2 to v248_base (2011-03-01 to 2011-03-08) v248

• updated GENCODE credits and references
  • src/hg/makeDb/trackDb/human/hg19/wgEncodeGencode.html - lines changed 51, context: html, text, full: html, text
• added utility to convert BEDs to pseudo-psls
  • src/hg/utils/bedToPsl/bedToPsl.c - lines changed 125, context: html, text, full: html, text
  • src/hg/utils/bedToPsl/makefile - lines changed 28, context: html, text, full: html, text
  • src/hg/utils/bedToPsl/tests/expected/basicTest.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/bedToPsl/tests/input/basic.bed - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/bedToPsl/tests/input/chrom.sizes - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/bedToPsl/tests/makefile - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/makefile - lines changed 1, context: html, text, full: html, text
• fixed indent
  • src/lib/maf.c - lines changed 0, context: html, text, full: html, text (whitespace-only change shows no diff)
• fixed library path issues
  • src/hg/utils/bedToPsl/makefile - lines changed 1, context: html, text, full: html, text
• used inline function and memset for zeroing memory to give optimizer a chance
  • src/inc/common.h - lines changed 4, context: html, text, full: html, text
  • src/lib/common.c - lines changed 8, context: html, text, full: html, text
• add hash table stats dump
  • src/hg/makeDb/genbank/common.mk - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignSetup - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbBuildState.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbMDParse.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/extFileUpdate/raInfoTbl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbConf/gbConf.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/extFileTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbConf.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbIgnore.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbLoadedTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbRelease.c - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbStatusTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/uniqueStrTbl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/orfeome/orfeomeDbLoad.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/repair/refPepRepair.c - lines changed 4, context: html, text, full: html, text
• Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • src/hg/makeDb/genbank/common.mk - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignSetup - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbBuildState.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbMDParse.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/extFileUpdate/raInfoTbl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbConf/gbConf.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/extFileTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbConf.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbIgnore.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbLoadedTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbRelease.c - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbStatusTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/uniqueStrTbl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/orfeome/orfeomeDbLoad.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/repair/refPepRepair.c - lines changed 4, context: html, text, full: html, text
• added method to print out stats for hash usage
  • src/inc/hash.h - lines changed 4, context: html, text, full: html, text
  • src/lib/hash.c - lines changed 23, context: html, text, full: html, text
• improve performance of genbank alignments by adjusting size of some hash tables and making some of them more specialized. Generally trading off initializing a large hash table for a short lived program with has collisions
  • src/hg/makeDb/genbank/common.mk - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/align/gbAlignSetup - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbBuildState.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbIgnoreDelete.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/dbload/gbMDParse.c - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/extFileUpdate/raInfoTbl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/gbConf/gbConf.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/inc/gbIgnore.h - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/inc/gbRelease.h - lines changed 14, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/inc/gbUpdate.h - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/extFileTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbConf.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbIgnore.c - lines changed 42, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbLoadedTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbProcessed.c - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbRelease.c - lines changed 37, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbStatusTbl.c - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/gbUpdate.c - lines changed 16, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/lib/uniqueStrTbl.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/orfeome/orfeomeDbLoad.c - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/genbank/src/repair/refPepRepair.c - lines changed 4, context: html, text, full: html, text