Commits for hiram

v438_preview to v438_preview2 (2022-09-26 to 2022-10-03) v438

75892bebe2505e10302cb56e9e1050bd811351d9 Tue Sep 27 09:03:45 2022 -0700

• accomodate promoted hubs with db but no chromInfo refs #29819
  • src/hg/utils/automation/HgAutomate.pm - lines changed 16, context: html, text, full: html, text
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 17, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 11, context: html, text, full: html, text

b0b850bdc2557fed7f69594bc8fe013d478dbe85 Wed Sep 28 10:19:12 2022 -0700

• fixups for hs1 to database assemblies refs #29819
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/automation/doRecipBest.pl - lines changed 6, context: html, text, full: html, text

587c0ae924cde64738db226abbf1b0ef4ba86ff9 Wed Sep 28 11:12:52 2022 -0700

• fixups for hs1 to database assemblies refs #29819
  • src/hg/utils/automation/doBlastzChainNet.pl - lines changed 25, context: html, text, full: html, text

16db4fab0d0beacea2a743bde43856408a1847d1 Wed Sep 28 12:05:06 2022 -0700

• adding definitions for chainNetHs1 refs #29819
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 97, context: html, text, full: html, text

af7fd9fe9619c76334b32d4598ea54bb31d98d4b Wed Sep 28 16:33:16 2022 -0700

• better short long lables for hs1 refs #29819
  • src/hg/makeDb/trackDb/trackDb.chainNet.asmHub.ra - lines changed 14, context: html, text, full: html, text

f84f4de709143cb83d1478762b1556de255e157c Thu Sep 29 12:05:39 2022 -0700

• preparing to use reading of rmsk.out file into a library function refs #29819
  • src/hg/makeDb/hgLoadOut/tests/chrCp.expected.tab - lines changed 198, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadOut/tests/chrCp.fa.out.gz - 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/makeDb/hgLoadOut/tests/makefile - lines changed 10, context: html, text, full: html, text

dc4322ce21733176ef6b04f060f15c6a3c7c773a Thu Sep 29 12:09:25 2022 -0700

• moving the reading of rmsk .out files into library function refs #29819
  • src/hg/makeDb/hgLoadOut/hgLoadOut.c - lines changed 15, context: html, text, full: html, text
  • src/inc/repMask.h - lines changed 3, context: html, text, full: html, text
  • src/lib/repMask.c - lines changed 30, context: html, text, full: html, text

39b563455274f8e71dce53a9f8d9f8f5ad7d7832 Fri Sep 30 10:37:37 2022 -0700

• testing the URL input option refs #29819
  • src/hg/makeDb/hgLoadOut/tests/GCA_001708105.1.expected.tab.gz - 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/makeDb/hgLoadOut/tests/makefile - lines changed 21, context: html, text, full: html, text
  • src/hg/makeDb/hgLoadOut/tests/triCas2.expected.md5sum - lines changed 1, context: html, text, full: html, text

ff4077c982e6b7fc46830e9899120983065438d2 Fri Sep 30 10:38:37 2022 -0700

• testing the URL input option refs #29819
  • src/hg/makeDb/hgLoadOut/tests/makefile - lines changed 4, context: html, text, full: html, text

02b89750add031d61f9781126b261e412ef493da Fri Sep 30 10:47:20 2022 -0700

• use local copy of test when present refs #29819
  • src/hg/makeDb/hgLoadOut/tests/makefile - lines changed 10, context: html, text, full: html, text

1f903fb4d0e10487d6bb9305d74adf57fa3f3f52 Fri Sep 30 11:39:16 2022 -0700

• add files to dynamic blat server refs #29811
  • src/hg/makeDb/doc/mpxvRivers/dynamicBlat.txt - lines changed 28, context: html, text, full: html, text

1759ea445907a44278042b057685fa448325c845 Fri Sep 30 11:44:18 2022 -0700

• preparing to alter netClass to work with assembly hubs refs #29819
  • src/hg/mouseStuff/netClass/tests/dm6.apiMel4.expected.net.gz - 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/mouseStuff/netClass/tests/dm6.apiMel4.noClass.net.gz - 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/mouseStuff/netClass/tests/makefile - lines changed 13, context: html, text, full: html, text

3dce48f138f6d1e533c85911b29c19d1f719ac85 Fri Sep 30 13:55:10 2022 -0700

• indicate input file options in the usage message refs #29819
  • src/hg/makeDb/hgLoadOut/hgLoadOut.c - lines changed 3, context: html, text, full: html, text

aa6447741ae61479b43cbd2b02182aa405487dab Fri Sep 30 15:19:00 2022 -0700

• can now read qSizes from file or URL refs #29819
  • src/hg/mouseStuff/netClass/netClass.c - lines changed 30, context: html, text, full: html, text
  • src/hg/mouseStuff/netClass/tests/makefile - lines changed 12, context: html, text, full: html, text

6b2cab8abbdd64d0bf86e1d4cdbe35b41e717d59 Fri Sep 30 15:25:14 2022 -0700

• need to have bash pipefail to make it exit on a command error refs #29819
  • src/hg/mouseStuff/netClass/tests/makefile - lines changed 2, context: html, text, full: html, text

c8ca88c9c4552b413376e7cf2a5b84100793b88b Fri Sep 30 15:26:43 2022 -0700

• allow chromInfo to read from URL refs #29819
  • src/hg/lib/chromInfo.c - lines changed 6, context: html, text, full: html, text

ea09f3a92d57f23c6a26118009a34a18ec7f46fb Fri Sep 30 15:27:54 2022 -0700

• some functions had not been declared here refs #29819
  • src/hg/inc/chromInfo.h - lines changed 9, context: html, text, full: html, text