kent: changes by file

review to branch (2009-11-17 to 2009-12-01) v220

• src/cdnaAli/cdnaOff/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/cdnaAli/findCdna/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/hg/hgTracks/bedTrack.c
  • 1.20 lines changed: 52, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/bigBedTrack.c
  • 1.1 lines changed: 123, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/bigWigTrack.c
  • 1.8 lines changed: 3, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/hgTracks.c
  • 1.1609 lines changed: 8, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/hgTracks.h
  • 1.193 lines changed: 27, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/makefile
  • 1.89 lines changed: 2, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/simpleTracks.c
  • 1.114 lines changed: 21, context: html, text, full: html, text
    Moving a few bigBed-specific functions from bedTrack.c to new modulc bigBedTrack.c Making bigBeds in dense mode do drawing by querying summary rather than going through itemList. Making it so that it only loads maxItems+1 (251 by default) items before flipping to dense. Making it draw density plot in grayscale if denseCoverage is set. Net result should be reduced bigBed i/o when zoomed out.
• src/hg/hgTracks/wigTrack.c
  • 1.98 lines changed: 2, context: html, text, full: html, text
    Removing whiskers when got more pixels than bases in window.
  • 1.97 lines changed: 3, context: html, text, full: html, text
    Making autoScale no longer the default for wiggle and related tracks. Making wiggleWindowingWhiskers follow name conventions better.
• src/hg/inc/hui.h
  • 1.143 lines changed: 1, context: html, text, full: html, text
    Making autoScale no longer the default for wiggle and related tracks. Making wiggleWindowingWhiskers follow name conventions better.
• src/hg/lib/trackDbCustom.c
  • 1.72 lines changed: 3, context: html, text, full: html, text
    Expanding size of buffer that looks like it is too small and may overflow someday.
• src/hg/lib/wiggleCart.c
  • 1.34 lines changed: 8, context: html, text, full: html, text
    Making autoScale no longer the default for wiggle and related tracks. Making wiggleWindowingWhiskers follow name conventions better.
  • 1.33 lines changed: 1, context: html, text, full: html, text
    Experimental change-a-comment commit because CVS is being quirky.
• src/hg/makeDb/doc/hg19.txt
  • 1.62 lines changed: 15, context: html, text, full: html, text
    Adding allenBrainGene.
• src/hg/makeDb/doc/ucscGenes/hg19.ucscGenes12.csh
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Adding -ignoreStrand to knownToCdsSnp build.
• src/hg/makeDb/doc/ucscGenes/mm9.ucscGenes12.csh
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding -ignoreStrand to knownToCdsSnp build.
• src/hg/makeDb/trackDb/README
  • 1.94 lines changed: 6, context: html, text, full: html, text
    Adding bigBed-specific optional field denseCoverage to trackDb system. One example of it is in wgEncodeGisRnaSeq.
• src/hg/makeDb/trackDb/trackDb.ra
  • 1.538 lines changed: 10, context: html, text, full: html, text
    Moving altEvents up to root level so everyone can use it. SImplifying knownGene priorities.
• src/hg/makeDb/trackDb/human/trackDb.encode.ra
  • 1.96 lines changed: 3, context: html, text, full: html, text
    Adding a few viewLimits
• src/hg/makeDb/trackDb/human/hg18/trackDb.ra
  • 1.425 lines changed: 14, context: html, text, full: html, text
    Moving altEvents up to root level so everyone can use it. SImplifying knownGene priorities.
  • 1.424 lines changed: 1, context: html, text, full: html, text
    Adding missing 4 to type bedGraph line.
• src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
  • 1.691 lines changed: 1, context: html, text, full: html, text
    Adding bigBed-specific optional field denseCoverage to trackDb system. One example of it is in wgEncodeGisRnaSeq.
  • 1.681 lines changed: 1, context: html, text, full: html, text
    Adding a viewLimits
  • 1.680 lines changed: 1, context: html, text, full: html, text
    Correcting viewLimit to viewLimits
  • 1.677 lines changed: 1, context: html, text, full: html, text
    Moving altEvents up to root level so everyone can use it. SImplifying knownGene priorities.
• src/hg/makeDb/trackDb/human/hg19/trackDb.ra
  • 1.61 lines changed: 11, context: html, text, full: html, text
    Moving altEvents up to root level so everyone can use it. SImplifying knownGene priorities.
• src/hg/makeDb/trackDb/mouse/mm9/trackDb.ra
  • 1.70 lines changed: 9, context: html, text, full: html, text
    Moving altEvents up to root level so everyone can use it. SImplifying knownGene priorities.
• src/hg/makeDb/trackDbPatch/makefile
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Creating patched files in -test mode now. Works for adding new fields, keeping comments and indentation level. Haven't tested yet for modifying existing fields.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Starting to work on utility to patch trackDb files. Just reads one of two inputs at the moment, no output.
• src/hg/makeDb/trackDbPatch/trackDbPatch.c
  • 1.2 lines changed: 298, context: html, text, full: html, text
    Creating patched files in -test mode now. Works for adding new fields, keeping comments and indentation level. Haven't tested yet for modifying existing fields.
  • 1.1 lines changed: 126, context: html, text, full: html, text
    Starting to work on utility to patch trackDb files. Just reads one of two inputs at the moment, no output.
• src/hg/near/makeNear.doc
  • 1.43 lines changed: 1, context: html, text, full: html, text
    Adding -ignoreStrand to knownToCdsSnp build.
• src/hg/near/hgMapToGene/hgMapToGene.c
  • 1.16 lines changed: 11, context: html, text, full: html, text
    Adding ignoreStrand option.
• src/hg/oneShot/findToFixBedGraphLimits/findToFixBedGraphLimits.c
  • 1.1 lines changed: 114, context: html, text, full: html, text
    Utility to figure out missing bedGraph limits seems to work.
• src/hg/oneShot/findToFixBedGraphLimits/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Utility to figure out missing bedGraph limits seems to work.
• src/hg/oneShot/findToFixBedGraphViewLimits/findToFixBedGraphViewLimits.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Bumping up recommended view range by another std on each side of mean.
  • 1.1 lines changed: 134, context: html, text, full: html, text
    One shot program to help patch viewLimits of bedGraph here.
• src/hg/oneShot/findToFixBedGraphViewLimits/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    One shot program to help patch viewLimits of bedGraph here.
• src/hg/oneShot/freen/freen.c
  • 1.94 lines changed: 69, context: html, text, full: html, text
    Adding rangeRoundUp to obscure library and testing in freen.
  • 1.93 lines changed: 21, context: html, text, full: html, text
    Adding simplifyPathToDir
• src/hg/oneShot/roundNewViewLimitsInRa/makefile
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Seems to work.
• src/hg/oneShot/roundNewViewLimitsInRa/roundNewViewLimitsInRa.c
  • 1.1 lines changed: 73, context: html, text, full: html, text
    Seems to work.
• src/inc/bbiFile.h
  • 1.20 lines changed: 1, context: html, text, full: html, text
    Adding bbiSumStandardDeviation to the summary types.
• src/inc/common.h
  • 1.163 lines changed: 14, context: html, text, full: html, text
    Making a couple of little functions inline.
  • 1.162 lines changed: 4, context: html, text, full: html, text
    Adding simplifyPathToDir
  • 1.159 lines changed: 6, context: html, text, full: html, text
    Adding sqlMatchLike
• src/inc/localmem.h
  • 1.7 lines changed: 3, context: html, text, full: html, text
    Adding lmCloneStringZ
• src/inc/obscure.h
  • 1.35 lines changed: 5, context: html, text, full: html, text
    Adding rangeFromMinMaxMeanStd
  • 1.34 lines changed: 6, context: html, text, full: html, text
    Adding 'hashThisEqThatLine.'
  • 1.33 lines changed: 1, context: html, text, full: html, text
    Fixing missing commnt end.
  • 1.32 lines changed: 3, context: html, text, full: html, text
    Adding rangeRoundUp to obscure library and testing in freen.
• src/inc/portable.h
  • 1.28 lines changed: 3, context: html, text, full: html, text
    Adding simplifyPathToDir
• src/inc/ra.h
  • 1.7 lines changed: 12, context: html, text, full: html, text
    Adding a few new .ra parsing routines.
• src/inc/tokenizer.h
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Adding leadingSpaces field to tokenizer
• src/index/indexfa/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/indexgl/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/ixali/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/ixword1/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/ixword3/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/makepgo/makefile
  • 1.8 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/index/stToXao/makefile
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Adding (indirectly) -lm to link.
• src/lib/bbiRead.c
  • 1.17 lines changed: 8, context: html, text, full: html, text
    Adding bbiSumStandardDeviation to the summary types.
• src/lib/bigBed.c
  • 1.24 lines changed: 8, context: html, text, full: html, text
    Fixing bug in maxItem handling in bigBedIntervalQuery
• src/lib/bwgCreate.c
  • 1.22 lines changed: 80, context: html, text, full: html, text
    Getting rid of largely redundant bwgSectionWriteUnc
• src/lib/common.c
  • 1.140 lines changed: 20, context: html, text, full: html, text
    Making a couple of little functions inline.
  • 1.138 lines changed: 10, context: html, text, full: html, text
    Adding simplifyPathToDir
• src/lib/localmem.c
  • 1.11 lines changed: 12, context: html, text, full: html, text
    Adding lmCloneStringZ
• src/lib/makefile
  • 1.156 lines changed: 1, context: html, text, full: html, text
    Pulled rangeRoundUp into a new numObscure file so as not to force all obscure users to drag in mlib.
• src/lib/numObscure.c
  • 1.3 lines changed: 42, context: html, text, full: html, text
    Adding rangeIncludingZero logic to rangeFromMinMaxMeanStd in case when min/max/mean are the same.
  • 1.2 lines changed: 22, context: html, text, full: html, text
    Adding rangeFromMinMaxMeanStd
  • 1.1 lines changed: 65, context: html, text, full: html, text
    Pulled rangeRoundUp into a new numObscure file so as not to force all obscure users to drag in mlib.
• src/lib/obscure.c
  • 1.52 lines changed: 61, context: html, text, full: html, text
    Pulled rangeRoundUp into a new numObscure file so as not to force all obscure users to drag in mlib.
  • 1.51 lines changed: 12, context: html, text, full: html, text
    Adding 'hashThisEqThatLine.'
  • 1.50 lines changed: 4, context: html, text, full: html, text
    Polishing routine that rounds ranges.
  • 1.49 lines changed: 59, context: html, text, full: html, text
    Adding rangeRoundUp to obscure library and testing in freen.
• src/lib/osunix.c
  • 1.44 lines changed: 140, context: html, text, full: html, text
    Adding simplifyPathToDir
• src/lib/ra.c
  • 1.14 lines changed: 60, context: html, text, full: html, text
    Adding a few new .ra parsing routines.
• src/lib/tokenizer.c
  • 1.4 lines changed: 9, context: html, text, full: html, text
    Adding leadingSpaces field to tokenizer
• src/lib/wildcmp.c
  • 1.6 lines changed: 44, context: html, text, full: html, text
    Adding sqlMatchLike
• src/shortReads/bwtMake/bananas.suffix
  • 1.2 lines changed: 52, context: html, text, full: html, text
    Commenting on bananas example.
• src/shortReads/bwtMake/bwtMake.c
  • 1.4 lines changed: 3, context: html, text, full: html, text
    Tweaking size check to compile under 32 bit Mac OS.
• src/shortReads/itsaFind/itsaFind.c
  • 1.5 lines changed: 2, context: html, text, full: html, text
    Commenting out some debugging statements.
• src/shortReads/itsaMake/itsaMake.c
  • 1.5 lines changed: 3, context: html, text, full: html, text
    Improving comment.
• src/utils/makefile
  • 1.76 lines changed: 1, context: html, text, full: html, text
    Adding bedClip to utilities build.
  • 1.75 lines changed: 1, context: html, text, full: html, text
    Adding raSqlQuery to makefile of parent.
• src/utils/bedClip/makefile
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding required -lz to link line.
• src/utils/bigWigSummary/bigWigSummary.c
  • 1.13 lines changed: 1, context: html, text, full: html, text
    Adding bbiSumStandardDeviation to the summary types.
• src/utils/raMerge/raMerge.c
  • 1.3 lines changed: 9, context: html, text, full: html, text
    Adding -firstOnly option.
• src/utils/raSqlQuery/makefile
  • 1.5 lines changed: 1, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.4 lines changed: 1, context: html, text, full: html, text
    Adding 'strict' option, to only put in ones where database table exists.
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
  • 1.1 lines changed: 18, context: html, text, full: html, text
    Starting work on raSqlQuery.
• src/utils/raSqlQuery/raRecord.c
  • 1.8 lines changed: 80, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.7 lines changed: 1, context: html, text, full: html, text
    Skipping over things inside parenthesis in count(*). Trimming spaces.
  • 1.6 lines changed: 2, context: html, text, full: html, text
    Adding rcsid strings.
  • 1.5 lines changed: 17, context: html, text, full: html, text
    Implementing arbitrary databases in db= option. Adding db=all option.
  • 1.4 lines changed: 40, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.3 lines changed: 10, context: html, text, full: html, text
    Adding -addFile option.
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Fixes to get to compile under Linux unstead of my laptop.
  • 1.1 lines changed: 61, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/raRecord.h
  • 1.5 lines changed: 8, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.4 lines changed: 4, context: html, text, full: html, text
    Implementing arbitrary databases in db= option. Adding db=all option.
  • 1.3 lines changed: 3, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.2 lines changed: 12, context: html, text, full: html, text
    Adding -addFile option.
  • 1.1 lines changed: 27, context: html, text, full: html, text
    Adding raRecord.h
• src/utils/raSqlQuery/raSqlQuery.c
  • 1.24 lines changed: 5, context: html, text, full: html, text
    Fixing bug in track replacement by lower level tracks. Downgraded a verbose 2 to a verbose 3.
  • 1.23 lines changed: 66, context: html, text, full: html, text
    Hacking a lot of very trackDb-specific settings parsing into raSqlQuery with db= option on. This enables inherit-by-view.
  • 1.22 lines changed: 56, context: html, text, full: html, text
    Making count statement work better with db=all and with from clauses.
  • 1.21 lines changed: 39, context: html, text, full: html, text
    Implementing from as file list.
  • 1.20 lines changed: 13, context: html, text, full: html, text
    Improving usage statement.
  • 1.19 lines changed: 1, context: html, text, full: html, text
    Adding a little more error checking to command line.
  • 1.18 lines changed: 2, context: html, text, full: html, text
    Adding a little more error checking to command line.
  • 1.17 lines changed: 12, context: html, text, full: html, text
    Adding 'strict' option, to only put in ones where database table exists.
  • 1.16 lines changed: 102, context: html, text, full: html, text
    Implementing arbitrary databases in db= option. Adding db=all option.
  • 1.15 lines changed: 198, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.14 lines changed: 27, context: html, text, full: html, text
    Doing some stuff to cope with track names having additional fields after the first word.
  • 1.13 lines changed: 3, context: html, text, full: html, text
    Fixing it so only prints file field once.
  • 1.12 lines changed: 29, context: html, text, full: html, text
    Adding -addFile option.
  • 1.11 lines changed: 119, context: html, text, full: html, text
    Adding parent,key,noInherit options and implementing inheritance.
  • 1.10 lines changed: 948, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
  • 1.9 lines changed: 1, context: html, text, full: html, text
    Improving usage statement.
  • 1.8 lines changed: 41, context: html, text, full: html, text
    Adding parenthesis in expressions.
  • 1.7 lines changed: 115, context: html, text, full: html, text
    Adding 'or' and 'and'
  • 1.6 lines changed: 38, context: html, text, full: html, text
    Allowing like in where spec.
  • 1.5 lines changed: 44, context: html, text, full: html, text
    Making wildcards (other than the single ?) work in field specs.
  • 1.4 lines changed: 128, context: html, text, full: html, text
    Adding inequalities. Reducing debugging uglies to verboses.
  • 1.3 lines changed: 34, context: html, text, full: html, text
    Adding unary minus.
  • 1.2 lines changed: 221, context: html, text, full: html, text
    Adding casts to parse tree and evaluator so can have numeric as well as string types. Making floating point numbers parse.
  • 1.1 lines changed: 658, context: html, text, full: html, text
    Starting work on raSqlQuery.
• src/utils/raSqlQuery/rql.h
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Parsing out (and ignoring) optional from clause.
  • 1.1 lines changed: 98, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/rqlEval.c
  • 1.2 lines changed: 2, context: html, text, full: html, text
    Adding rcsid strings.
  • 1.1 lines changed: 286, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/rqlParse.c
  • 1.8 lines changed: 6, context: html, text, full: html, text
    Implementing from as file list.
  • 1.7 lines changed: 5, context: html, text, full: html, text
    Skipping over things inside parenthesis in count(*). Trimming spaces.
  • 1.6 lines changed: 20, context: html, text, full: html, text
    Parsing out (and ignoring) optional from clause.
  • 1.5 lines changed: 21, context: html, text, full: html, text
    Letting 'select count(*)' be a synonym for 'count'
  • 1.4 lines changed: 2, context: html, text, full: html, text
    Adding rcsid strings.
  • 1.3 lines changed: 1, context: html, text, full: html, text
    Fixes to get to compile under Linux unstead of my laptop.
  • 1.2 lines changed: 23, context: html, text, full: html, text
    Adding logical not
  • 1.1 lines changed: 572, context: html, text, full: html, text
    Adding in merge option. Supporting 'not like' operation. Splitting into modules.
• src/utils/raSqlQuery/test.ra
  • 1.1 lines changed: 11, context: html, text, full: html, text
    Adding test set.
• src/utils/raSqlQuery/test2.ra
  • 1.3 lines changed: 4, context: html, text, full: html, text
    Making it deal with overrides. Making it start to work with our usual trackDb directory structure when using -db= flag.
  • 1.2 lines changed: 8, context: html, text, full: html, text
    Adding parent,key,noInherit options and implementing inheritance.
  • 1.1 lines changed: 8, context: html, text, full: html, text
    Adding test set.