kent: changes by file

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

• src/hg/hgTables/bedList.c
  • 1.63 lines changed: 2, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.62 lines changed: 2, context: html, text, full: html, text
    Fixing problem in bigWig custom track output. Testing (seems to work) with subtrack merge.
  • 1.61 lines changed: 18, 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/bigBed.c
  • 1.4 lines changed: 57, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Polishing bigBed status page a little.
  • 1.2 lines changed: 1, context: html, text, full: html, text
    Adding parameter to bedAsDef.
  • 1.1 lines changed: 127, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
• src/hg/hgTables/bigWig.c
  • 1.3 lines changed: 5, context: html, text, full: html, text
    Putting up message about limits of subtrack merge in summary status page. Getting more extended intersection options back.
  • 1.2 lines changed: 66, 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.
  • 1.1 lines changed: 266, context: html, text, full: html, text
    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/compositeTrack.c
  • 1.13 lines changed: 2, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
• src/hg/hgTables/correlate.c
  • 1.74 lines changed: 6, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.73 lines changed: 6, 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.
  • 1.72 lines changed: 0, context: html, text, full: html, text
    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/correlate.h
  • 1.16 lines changed: 1, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.15 lines changed: 23, 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/filterFields.c
  • 1.65 lines changed: 7, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.64 lines changed: 1, context: html, text, full: html, text
    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/gffOut.c
  • 1.17 lines changed: 1, 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/hgTables.c
  • 1.175 lines changed: 30, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.173 lines changed: 62, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
• src/hg/hgTables/hgTables.h
  • 1.128 lines changed: 11, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.127 lines changed: 16, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
  • 1.126 lines changed: 0, 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.
  • 1.125 lines changed: 46, context: html, text, full: html, text
    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/identifiers.c
  • 1.27 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/intersect.c
  • 1.48 lines changed: 6, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.47 lines changed: 3, context: html, text, full: html, text
    Putting up message about limits of subtrack merge in summary status page. Getting more extended intersection options back.
  • 1.46 lines changed: 1, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.45 lines changed: 103, context: html, text, full: html, text
    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/joining.c
  • 1.52 lines changed: 2, 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/mainPage.c
  • 1.138 lines changed: 1, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.137 lines changed: 0, context: html, text, full: html, text
    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/makefile
  • 1.52 lines changed: 1, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
  • 1.51 lines changed: 2, context: html, text, full: html, text
    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/schema.c
  • 1.54 lines changed: 55, context: html, text, full: html, text
    Starting to add bigBed support. So far the schema button works at least.
• src/hg/hgTables/seqOut.c
  • 1.20 lines changed: 2, 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/sumStats.c
  • 1.25 lines changed: 1, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.24 lines changed: 10, context: html, text, full: html, text
    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/wiggle.c
  • 1.71 lines changed: 1, context: html, text, full: html, text
    Adding parameter to getHti, and creating a hti object for bigBed tables out of the associated .as information.
  • 1.70 lines changed: 2, context: html, text, full: html, text
    Making a sweep to make sure that bigWig is addressed everywhere bedGraph is addressed.
  • 1.69 lines changed: 4, 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.
  • 1.68 lines changed: 143, context: html, text, full: html, text
    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/hgTracks/bedTrack.c
  • 1.6 lines changed: 1, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
• src/hg/inc/bed.h
  • 1.52 lines changed: 4, context: html, text, full: html, text
    Adding parameter to bedAsDef.
  • 1.51 lines changed: 3, context: html, text, full: html, text
    Adding bedAsDef.
• src/hg/inc/hdb.h
  • 1.165 lines changed: 15, context: html, text, full: html, text
    Removing function prototype for a nonexistant function.
• src/hg/inc/wiggle.h
  • 1.85 lines changed: 6, context: html, text, full: html, text
    Adding wigCompareFromString and wigCompareValFilter.
• src/hg/lib/bed.c
  • 1.62 lines changed: 21, context: html, text, full: html, text
    Adding parameter to bedAsDef.
  • 1.61 lines changed: 42, context: html, text, full: html, text
    Adding bedAsDef.
• src/hg/lib/hdb.c
  • 1.397 lines changed: 3, 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/wigDataStream.c
  • 1.85 lines changed: 82, context: html, text, full: html, text
    Adding wigCompareFromString and wigCompareValFilter.
• src/hg/oneShot/freen/freen.c
  • 1.87 lines changed: 29, context: html, text, full: html, text
    Testing bedAsDef.
• src/inc/bbiFile.h
  • 1.7 lines changed: 4, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/inc/bigBed.h
  • 1.11 lines changed: 3, context: html, text, full: html, text
    Adding bigBedItemCount
  • 1.10 lines changed: 4, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
  • 1.9 lines changed: 6, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/inc/common.h
  • 1.147 lines changed: 1, context: html, text, full: html, text
    Adding BIGDOUBLE constant.
• src/inc/udc.h
  • 1.9 lines changed: 3, context: html, text, full: html, text
    Adding udcReadStringAndZero
• src/lib/bbiRead.c
  • 1.10 lines changed: 2, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/lib/bigBed.c
  • 1.13 lines changed: 9, context: html, text, full: html, text
    Adding bigBedItemCount
  • 1.12 lines changed: 16, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.
  • 1.11 lines changed: 49, context: html, text, full: html, text
    Adding asFile to bigBed.
• src/lib/udc.c
  • 1.15 lines changed: 28, context: html, text, full: html, text
    Adding udcReadStringAndZero
• src/utils/bedToBigBed/bedToBigBed.c
  • 1.3 lines changed: 6, context: html, text, full: html, text
    Adding -as option.
• src/utils/bigBedSummary/bigBedSummary.c
  • 1.4 lines changed: 41, context: html, text, full: html, text
    Adding fields flag.
• src/utils/bigBedToBed/bigBedToBed.c
  • 1.5 lines changed: 17, context: html, text, full: html, text
    Adding maxItems parameter to bigBedIntervalQuery. Checking that asFile field count matches tab-file field count.