File Changes for braney

v429_base to v430_preview (2022-04-04 to 2022-04-11) v430

• src/hg/hgConvert/hgConvert.c
  • lines changed 16, context: html, text, full: html, text
    eaa76b9f96a1509b9591a4492e7b363f11eb58c9 Mon Apr 4 16:22:40 2022 -0700
    support genark hubs in hgConvert
  • lines changed 3, context: html, text, full: html, text
    e2b7d2fa29f32948a664ef74a7dd30dcdfb949db Tue Apr 5 08:28:27 2022 -0700
    delete hub prefix on trackHubs before looking for them in the database
• src/hg/hgTables/vcf.c
  • lines changed 4, context: html, text, full: html, text
    ad18889898ae327c9c2787fea48ca371527dd41f Fri Apr 8 13:36:37 2022 -0700
    support vcfTabix schema display on track hubs
• src/hg/hgc/hgc.c
  • lines changed 5, context: html, text, full: html, text
    d26707fc96ea80bad241b19ccca7eb9b770b6b3c Wed Apr 6 14:14:02 2022 -0700
    missed a case for bigBeds in extended dna coloring
• src/hg/lib/hdb.c
  • lines changed 2, context: html, text, full: html, text
    4231bb41a4af90422596fcc33304a6a20e654dc6 Tue Apr 5 13:12:56 2022 -0700
    when grabbing liftOver chains, don't check for database base presence since the chains may be for a track hub
  • lines changed 2, context: html, text, full: html, text
    7f87f28f5603d0d1619c8421d0e4aa7e71e2cd79 Tue Apr 5 14:44:33 2022 -0700
    Revert "when grabbing liftOver chains, don't check for database base presence" This reverts commit 4231bb41a4af90422596fcc33304a6a20e654dc6.
  • lines changed 2, context: html, text, full: html, text
    2292f9dea942be082a90d741927df1ff18a51574 Tue Apr 5 15:49:22 2022 -0700
    get hgLiftOver and liftOver to work with genark hubs where the liftOver chain may be a URL
• src/hg/lib/liftOver.c
  • lines changed 2, context: html, text, full: html, text
    2292f9dea942be082a90d741927df1ff18a51574 Tue Apr 5 15:49:22 2022 -0700
    get hgLiftOver and liftOver to work with genark hubs where the liftOver chain may be a URL
• src/inc/bbiAlias.h
  • lines changed 3, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/inc/bbiFile.h
  • lines changed 9, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/lib/bbiAlias.c
  • lines changed 34, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/lib/bbiWrite.c
  • lines changed 48, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/bedGraphToBigWig.c
  • lines changed 18, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/expected/mixed.err
  • lines changed 1, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/expected/testBadChrom1.err
  • lines changed 1, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/input/chromAliasIndex.as
  • lines changed 12, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/input/human.chrom.sizes.txt
  • lines changed 639, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/input/human.chromAlias.bed
  • lines changed 638, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/input/mixed.bed
  • lines changed 3, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/input/test1.bed
  • lines changed 38735, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedGraphToBigWig/tests/makefile
  • lines changed 27, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/bedToBigBed.c
  • lines changed 27, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/expected/mixed.err
  • lines changed 1, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/expected/testBadChrom1.err
  • lines changed 1, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/input/bigGenePred.as
  • lines changed 25, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/input/chromAliasIndex.as
  • lines changed 12, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/input/colored.genbank.bed
  • lines changed 264, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/input/human.chrom.sizes.txt
  • lines changed 639, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/input/human.chromAlias.bed
  • lines changed 638, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/input/mixed.bed
  • lines changed 3, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed
• src/utils/bedToBigBed/tests/makefile
  • lines changed 17, context: html, text, full: html, text
    8fdef9e866ecc228bfe4ea54102d0079818f0366 Fri Apr 8 14:49:38 2022 -0700
    let bedGraphToBigWig use chromAlias.bb as chromSizes file. Add tests to both bedGraphToBigWig and bedToBigBed