File Changes for markd

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

• src/hg/makeDb/genbank/common.mk
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    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, 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/src/align/gbAlignSetup
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    add hash table stats dump
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    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 1, 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/src/dbload/gbBuildState.c
  • lines changed 6, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 6, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 6, 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/src/dbload/gbIgnoreDelete.c
  • lines changed 1, 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/src/dbload/gbMDParse.c
  • lines changed 6, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 6, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 6, 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/src/extFileUpdate/raInfoTbl.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, 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/src/gbConf/gbConf.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, 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/src/inc/gbIgnore.h
  • lines changed 8, 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/src/inc/gbRelease.h
  • lines changed 14, 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/src/inc/gbUpdate.h
  • lines changed 3, 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/src/lib/extFileTbl.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • 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
  • lines changed 4, 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/src/lib/gbConf.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, 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/src/lib/gbIgnore.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • 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
  • lines changed 42, 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/src/lib/gbLoadedTbl.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • 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
  • lines changed 4, 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/src/lib/gbProcessed.c
  • lines changed 1, 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/src/lib/gbRelease.c
  • lines changed 18, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 18, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 37, 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/src/lib/gbStatusTbl.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • 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
  • lines changed 4, 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/src/lib/gbUpdate.c
  • lines changed 16, 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/src/lib/uniqueStrTbl.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, 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/src/orfeome/orfeomeDbLoad.c
  • lines changed 3, context: html, text, full: html, text
    add hash table stats dump
  • lines changed 3, context: html, text, full: html, text
    Revert "add hash table stats dump" This reverts commit 58672666e0eb7000c5bf20dd34c86728e3e243d3. didn't want this just yet
  • lines changed 3, 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/src/repair/refPepRepair.c
  • lines changed 4, context: html, text, full: html, text
    add hash table stats dump
  • 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
  • lines changed 4, 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/trackDb/human/hg19/wgEncodeGencode.html
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    updated GENCODE credits and references
• src/hg/utils/bedToPsl/bedToPsl.c
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    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/makefile
  • lines changed 28, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
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    fixed library path issues
• src/hg/utils/bedToPsl/tests/expected/basicTest.psl
  • lines changed 5, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/tests/input/basic.bed
  • lines changed 5, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/tests/input/chrom.sizes
  • lines changed 2, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/bedToPsl/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    added utility to convert BEDs to pseudo-psls
• src/hg/utils/makefile
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    added utility to convert BEDs to pseudo-psls
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    used inline function and memset for zeroing memory to give optimizer a chance
• src/inc/hash.h
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    added method to print out stats for hash usage
• src/lib/common.c
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    used inline function and memset for zeroing memory to give optimizer a chance
• src/lib/hash.c
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    added method to print out stats for hash usage
• src/lib/maf.c
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    fixed indent