kent: changes by commit

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

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