Commits for braney

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

eaa76b9f96a1509b9591a4492e7b363f11eb58c9 Mon Apr 4 16:22:40 2022 -0700

• support genark hubs in hgConvert
  • src/hg/hgConvert/hgConvert.c - lines changed 16, 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/hgConvert/hgConvert.c - lines changed 3, 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
  • src/hg/lib/hdb.c - 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.
  • src/hg/lib/hdb.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/hg/lib/hdb.c - lines changed 2, context: html, text, full: html, text
  • src/hg/lib/liftOver.c - lines changed 2, 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/hgc/hgc.c - lines changed 5, context: html, text, full: html, text

ad18889898ae327c9c2787fea48ca371527dd41f Fri Apr 8 13:36:37 2022 -0700

• support vcfTabix schema display on track hubs
  • src/hg/hgTables/vcf.c - lines changed 4, 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/bbiAlias.h - lines changed 3, context: html, text, full: html, text
  • src/inc/bbiFile.h - lines changed 9, context: html, text, full: html, text
  • src/lib/bbiAlias.c - lines changed 34, context: html, text, full: html, text
  • src/lib/bbiWrite.c - lines changed 48, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/bedGraphToBigWig.c - lines changed 18, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/expected/mixed.err - lines changed 1, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/expected/testBadChrom1.err - lines changed 1, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/input/chromAliasIndex.as - lines changed 12, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/input/human.chrom.sizes.txt - lines changed 639, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/input/human.chromAlias.bed - lines changed 638, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/input/mixed.bed - lines changed 3, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/input/test1.bed - lines changed 38735, context: html, text, full: html, text
  • src/utils/bedGraphToBigWig/tests/makefile - lines changed 27, context: html, text, full: html, text
  • src/utils/bedToBigBed/bedToBigBed.c - lines changed 27, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/expected/mixed.err - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/expected/testBadChrom1.err - lines changed 1, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/bigGenePred.as - lines changed 25, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/chromAliasIndex.as - lines changed 12, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/colored.genbank.bed - lines changed 264, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/human.chrom.sizes.txt - lines changed 639, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/human.chromAlias.bed - lines changed 638, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/input/mixed.bed - lines changed 3, context: html, text, full: html, text
  • src/utils/bedToBigBed/tests/makefile - lines changed 17, context: html, text, full: html, text