Commits for hiram

v398_preview2 to v398_base (2020-05-04 to 2020-05-11) v398

c254573e477c6da281ca8d4f041770cd06d417b3 Mon May 4 15:11:59 2020 -0700

• two genbank assemblies have become refseq assemblies refs #23734
  • src/hg/makeDb/doc/asmHubs/vgp.asmId.commonName.tsv - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/vgp.commonName.asmId.orderList.tsv - lines changed 2, context: html, text, full: html, text

5234cfcb4a8b7c971f749002bfa4c26ff6f05804 Tue May 5 11:33:58 2020 -0700

• fixup needLargeMem argument type to get this to work with SARS MERS alignment no redmine
  • src/lib/pairHmm.c - lines changed 2, context: html, text, full: html, text

dc6d6e4b842178bd00a20da9a03ddf6deeee9e94 Thu May 7 10:55:45 2020 -0700

• and fixup pointer arithmetic due to correct needLargeMem argument and hence much larger array sizes for difficult alignments no redmine
  • src/lib/pairHmm.c - lines changed 1, context: html, text, full: html, text

a6dd687f9d58da63c02a407d40d19b12ba38ec5c Fri May 8 16:53:27 2020 -0700

• small experiment with a 7-way refs #25090
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.7way.ra - lines changed 108, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 1, context: html, text, full: html, text

a3221ce060e8efe2e9ef46392625606896f64f96 Fri May 8 23:06:59 2020 -0700

• do not print links to other assembly hubs from VGP index pages refs #23734
  • src/hg/makeDb/doc/asmHubs/mkAsmStats.pl - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkGenomes.pl - lines changed 2, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/mkHubIndex.pl - lines changed 3, context: html, text, full: html, text
  • src/hg/makeDb/doc/asmHubs/trackData.pl - lines changed 13, context: html, text, full: html, text

6e49b6de0de742e4e8cb8057440a63ece6e7ec53 Sun May 10 12:27:57 2020 -0700

• updates to work with Mac OSX Catalina and brew install of mariadb and openssl no redmine
  • src/inc/common.mk - lines changed 17, context: html, text, full: html, text

a2e177597fbd6c1a6dc7f8ea5f4f45ec9b8f08ac Sun May 10 13:23:19 2020 -0700

• better time to select libmariadbclient.a for Mac OSX Catalina no redmine
  • src/inc/common.mk - lines changed 8, context: html, text, full: html, text

725a8349dd0337b68ba8bedf10cf9fe1ab7492d3 Mon May 11 09:48:12 2020 -0700

• fix calculation for protein blat on negative strand refs #25538
  • src/utils/pslScore/pslScore.pl - lines changed 5, context: html, text, full: html, text
  • src/utils/pslScore/tests/NP_149062.psl - lines changed 9, context: html, text, full: html, text
  • src/utils/pslScore/tests/expect.NP_149062.tab - lines changed 9, context: html, text, full: html, text
  • src/utils/pslScore/tests/makefile - lines changed 5, context: html, text, full: html, text