kent: changes by commit

branch to review (2009-03-10 to 2009-03-17) v202

• Making filter and non-base-pair intersections work with bigWig. (Base-by-base intersections work 80%, but going to have to change design to get last 20% working.) Fixed bug I introduced in correlation of regular wig that Kayla spotted. Moving bigWig stuff to it's own module.
  • src/hg/hgTables/bigWig.c 1.1 - lines changed: 266, context: html, text, full: html, text
  • src/hg/hgTables/correlate.c 1.72 - lines changed: 0, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c 1.64 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.125 - lines changed: 46, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c 1.45 - lines changed: 103, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c 1.137 - lines changed: 0, context: html, text, full: html, text
  • src/hg/hgTables/makefile 1.51 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/sumStats.c 1.24 - lines changed: 10, context: html, text, full: html, text
  • src/hg/hgTables/wiggle.c 1.68 - lines changed: 143, context: html, text, full: html, text
• Making correlations, and bed output work with bigWig. Possibly subtrack merge works too, but need to make a test case for it. Custom track bigWig output is still broken.
  • src/hg/hgTables/bedList.c 1.61 - lines changed: 18, context: html, text, full: html, text
  • src/hg/hgTables/bigWig.c 1.2 - lines changed: 66, context: html, text, full: html, text
  • src/hg/hgTables/correlate.c 1.73 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTables/correlate.h 1.15 - lines changed: 23, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.126 - lines changed: 0, context: html, text, full: html, text
  • src/hg/hgTables/wiggle.c 1.69 - lines changed: 4, context: html, text, full: html, text
• Adding wigCompareFromString and wigCompareValFilter.
  • src/hg/inc/wiggle.h 1.85 - lines changed: 6, context: html, text, full: html, text
  • src/hg/lib/wigDataStream.c 1.85 - lines changed: 82, context: html, text, full: html, text
• Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • src/hg/hgTables/compositeTrack.c 1.13 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/correlate.c 1.74 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTables/correlate.h 1.16 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/filterFields.c 1.65 - lines changed: 7, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c 1.46 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/wiggle.c 1.70 - lines changed: 2, context: html, text, full: html, text
• Fixing problem in bigWig custom track output. Testing (seems to work) with subtrack merge.
  • src/hg/hgTables/bedList.c 1.62 - lines changed: 2, context: html, text, full: html, text
• Putting up message about limits of subtrack merge in summary status page. Getting more extended intersection options back.
  • src/hg/hgTables/bigWig.c 1.3 - lines changed: 5, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c 1.47 - lines changed: 3, context: html, text, full: html, text
• Adding BIGDOUBLE constant.
  • src/inc/common.h 1.147 - lines changed: 1, context: html, text, full: html, text
• Adding udcReadStringAndZero
  • src/inc/udc.h 1.9 - lines changed: 3, context: html, text, full: html, text
  • src/lib/udc.c 1.15 - lines changed: 28, context: html, text, full: html, text
• Adding asFile to bigBed.
  • src/inc/bbiFile.h 1.7 - lines changed: 4, context: html, text, full: html, text
  • src/inc/bigBed.h 1.9 - lines changed: 6, context: html, text, full: html, text
  • src/lib/bbiRead.c 1.10 - lines changed: 2, context: html, text, full: html, text
  • src/lib/bigBed.c 1.11 - lines changed: 49, context: html, text, full: html, text
• Adding fields flag.
  • src/utils/bigBedSummary/bigBedSummary.c 1.4 - lines changed: 41, context: html, text, full: html, text
• Adding -as option.
  • src/utils/bedToBigBed/bedToBigBed.c 1.3 - lines changed: 6, context: html, text, full: html, text
• Adding bedAsDef.
  • src/hg/inc/bed.h 1.51 - lines changed: 3, context: html, text, full: html, text
  • src/hg/lib/bed.c 1.61 - lines changed: 42, context: html, text, full: html, text
• Testing bedAsDef.
  • src/hg/oneShot/freen/freen.c 1.87 - lines changed: 29, context: html, text, full: html, text
• Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
  • src/hg/hgTracks/bedTrack.c 1.6 - lines changed: 1, context: html, text, full: html, text
  • src/inc/bigBed.h 1.10 - lines changed: 4, context: html, text, full: html, text
  • src/lib/bigBed.c 1.12 - lines changed: 16, context: html, text, full: html, text
  • src/utils/bigBedToBed/bigBedToBed.c 1.5 - lines changed: 17, context: html, text, full: html, text
• Starting to add bigBed support. So far the schema button works at least.
  • src/hg/hgTables/bigBed.c 1.1 - lines changed: 127, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.173 - lines changed: 62, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.127 - lines changed: 16, context: html, text, full: html, text
  • src/hg/hgTables/makefile 1.52 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/schema.c 1.54 - lines changed: 55, context: html, text, full: html, text
• Adding parameter to bedAsDef.
  • src/hg/hgTables/bigBed.c 1.2 - lines changed: 1, context: html, text, full: html, text
  • src/hg/inc/bed.h 1.52 - lines changed: 4, context: html, text, full: html, text
  • src/hg/lib/bed.c 1.62 - lines changed: 21, context: html, text, full: html, text
• Adding bigBedItemCount
  • src/inc/bigBed.h 1.11 - lines changed: 3, context: html, text, full: html, text
  • src/lib/bigBed.c 1.13 - lines changed: 9, context: html, text, full: html, text
• Polishing bigBed status page a little.
  • src/hg/hgTables/bigBed.c 1.3 - lines changed: 6, context: html, text, full: html, text
• Removing function prototype for a nonexistant function.
  • src/hg/inc/hdb.h 1.165 - lines changed: 15, context: html, text, full: html, text
• Making hFindBed12FieldsAndBinWithConn static. Initializing empty strings a place where it might have been missed, and would certainly do no harm to add.
  • src/hg/lib/hdb.c 1.397 - lines changed: 3, context: html, text, full: html, text
• Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • src/hg/hgTables/bedList.c 1.63 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/bigBed.c 1.4 - lines changed: 57, context: html, text, full: html, text
  • src/hg/hgTables/gffOut.c 1.17 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.c 1.175 - lines changed: 30, context: html, text, full: html, text
  • src/hg/hgTables/hgTables.h 1.128 - lines changed: 11, context: html, text, full: html, text
  • src/hg/hgTables/identifiers.c 1.27 - lines changed: 3, context: html, text, full: html, text
  • src/hg/hgTables/intersect.c 1.48 - lines changed: 6, context: html, text, full: html, text
  • src/hg/hgTables/joining.c 1.52 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/mainPage.c 1.138 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/seqOut.c 1.20 - lines changed: 2, context: html, text, full: html, text
  • src/hg/hgTables/sumStats.c 1.25 - lines changed: 1, context: html, text, full: html, text
  • src/hg/hgTables/wiggle.c 1.71 - lines changed: 1, context: html, text, full: html, text