Commits for hiram

v431_base to v432_preview (2022-05-16 to 2022-05-23) v432

6d1528f371ec8c7bfe19d0fe3f5a154a1ac82603 Tue May 17 09:50:20 2022 -0700

• images for new style repeat masker description page in place of the base64 encoding no redmine
  • src/hg/htdocs/images/rmskClassicPack.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/images/rmskDense.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/images/rmskFull.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/images/rmskPack.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

b4433df297256fc1e9d5d797aa8acc9a4ac732f5 Tue May 17 10:04:32 2022 -0700

• replace the base64 encoded png with reference to jpg images no redmine
  • src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker.html - lines changed 10425, context: html, text, full: html, text

7c934496e3650521dc129b65658326d542cbd20b Tue May 17 12:52:51 2022 -0700

• trying out new rmsk format bigBed joined display no redmine
  • src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 33, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubRmskJoinAlign.pl - lines changed 571, context: html, text, full: html, text
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 29, context: html, text, full: html, text
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/automation/doRepeatMasker.pl - lines changed 26, context: html, text, full: html, text

0aa6ca4913057168625becbe9dde31c55116272e Tue May 17 16:21:57 2022 -0700

• better use of sizesIsBb for alias.bb test generation no redmine
  • src/hg/utils/automation/aliasBedToCt.pl - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/automation/doAssemblyHub.pl - lines changed 1, context: html, text, full: html, text

1386b5f91d8d635cd76b984482e460dd05464237 Tue May 17 17:06:35 2022 -0700

• correctly sorting bed file output no redmine
  • src/hg/utils/automation/aliasTextToBed.pl - lines changed 1, context: html, text, full: html, text

f1b5eb49959cc16f05675a7f5e254bc787b99409 Wed May 18 09:08:32 2022 -0700

• better recognition of the align file presence no redmine
  • src/hg/utils/automation/asmHubRepeatMasker.sh - lines changed 3, context: html, text, full: html, text

b0838670c54b6a17b3971c11e41e84bacc89b6f7 Wed May 18 12:35:25 2022 -0700

• adding GCA_000297895.2_ASM29789v2 Pacific oyster per user request no redmine
  • src/hg/makeDb/doc/asmHubs/master.run.list - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/doc/invertebrateAsmHub/invertebrate.orderList.tsv - lines changed 2, context: html, text, full: html, text

463d8ccfcc27e9ea403fbf2ed74c344bfbf3897c Wed May 18 13:10:50 2022 -0700

• correct if statements to separate the two types of RM tracks no redmine
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 8, context: html, text, full: html, text

bfb5934c86c6e897da243f2b9277987dc8392ce3 Wed May 18 14:01:59 2022 -0700

• the new repeat masker track has lowered the minimum amount of tracks for a valid hub no redmine
  • src/hg/makeDb/doc/asmHubs/verifyOnDownload.sh - lines changed 6, context: html, text, full: html, text

1268543255ec6202fedc7d12bf2054d031f2fb89 Thu May 19 15:44:49 2022 -0700

• the new rmsk track can be done without the align file refs #29464
  • src/hg/utils/automation/asmHubTrackDb.sh - lines changed 11, context: html, text, full: html, text

5f4b98797c27ade66a4c599dcc5f46f1cd4458fb Thu May 19 17:18:33 2022 -0700

• more images for rmsk description page refs #29464
  • src/hg/htdocs/images/rmskLine2fragments.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/images/rmskLine2overlap.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/images/rmskLine2unaligned.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)
  • src/hg/htdocs/images/rmskSine384.jpg - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

ea93bef09b508ad550f5cd2f24357025ef939a31 Thu May 19 17:29:03 2022 -0700

• element drawing examples now replaced with URLs to jpg images refs #29464
  • src/hg/makeDb/doc/chm13v2.0userData/html/t2tRepeatMasker.html - lines changed 264, context: html, text, full: html, text

a8b96119d44c0455a215ea0000c001bc4a7b9074 Thu May 19 17:34:51 2022 -0700

• element drawing examples now replaced with URLs to jpg images refs #29464
  • src/hg/utils/automation/asmHubRmskJoinAlign.pl - lines changed 264, context: html, text, full: html, text

b24e3fe29bf4118ec0dd5804d363499a11db4311 Fri May 20 11:52:39 2022 -0700

• correctly display all items while in dense mode or original pack mode refs #29464
  • src/hg/hgTracks/bigRmskTrack.c - lines changed 2, context: html, text, full: html, text

33f285063b852a8a7b9d44e36585fb77a852c677 Fri May 20 13:35:16 2022 -0700

• fix broken interpretation of the palette colors for drawing refs #29464
  • src/hg/hgTracks/bigRmskTrack.c - lines changed 3, context: html, text, full: html, text

0faea16954ed530c537f5aa5d0cf8e0e33441b8a Fri May 20 17:21:22 2022 -0700

• now correctly show alias names on hgTracks chromInfoPage when using chromAliasBb file refs #26360
  • src/hg/hgTracks/hgTracks.c - lines changed 20, context: html, text, full: html, text