Commits for max

v415_base to v416_preview (2021-05-24 to 2021-06-01) v416

86033e65a4fc49aa971526bfaa1778844c5a34da Wed May 26 02:05:19 2021 -0700

• adding a preliminary makedoc for revel on hg38, refs #27142, even though the hg38 revel track will not be released, as it is broken (emailed authors)
  • src/hg/makeDb/doc/hg38/revel.txt - lines changed 8, context: html, text, full: html, text
  • src/optimalLeaf/LICENSE - lines changed 4, context: html, text, full: html, text

d78441779ba20c7b455b086247fd4c35e5e24a7a Wed May 26 03:26:41 2021 -0700

• adding docs for tableList, refs #27390
  • src/product/ex.hg.conf - lines changed 12, context: html, text, full: html, text

fcfb73cd2dc944a0a10ef34699dcb0c185ea8e6a Wed May 26 05:12:50 2021 -0700

• Trying to give users a clearer idea how many licenses this repo contains, what is under which license and who to contact to get the license. refs #27614
  • LICENSE - lines changed 25, context: html, text, full: html, text
  • src/LICENSE - lines changed 25, context: html, text, full: html, text
  • src/blat/LICENSE - lines changed 3, context: html, text, full: html, text
  • src/hg/LICENSE - lines changed 11, context: html, text, full: html, text
  • src/hg/autoXml/LICENSE - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/makefile - lines changed 12, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/pslLiftSubrangeBlat.c - lines changed 133, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/expected/qSubRangeTest.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/expected/qtSubRangeTest.psl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/expected/tSubRangeTest.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/input/qSubrange.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/input/qSubrange.qsizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.psl - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.qsizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.sizes - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/input/tSubrange.psl - lines changed 4, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/input/tSubrange.tsizes - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/pslLiftSubrangeBlat/tests/makefile - lines changed 31, context: html, text, full: html, text
  • src/hg/utils/raSqlQuery/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/raSqlQuery/raRecord.c - lines changed 185, context: html, text, full: html, text
  • src/hg/utils/raSqlQuery/raRecord.h - lines changed 54, context: html, text, full: html, text
  • src/hg/utils/raSqlQuery/raSqlQuery.c - lines changed 622, context: html, text, full: html, text
  • src/hg/utils/raSqlQuery/test.ra - lines changed 14, context: html, text, full: html, text
  • src/hg/utils/raSqlQuery/test2.ra - lines changed 20, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/makefile - lines changed 7, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/scaffoldFaToAgp.c - lines changed 213, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/test/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/test/runtest - lines changed 15, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/test/test.agp.gold - lines changed 5, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/test/test.fa - lines changed 6, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/test/test.gap.gold - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/scaffoldFaToAgp/test/test.lft.gold - lines changed 5, context: html, text, full: html, text
  • src/jkOwnLib/LICENSE - lines changed 6, context: html, text, full: html, text
  • src/tabFile/LICENSE - lines changed 2, context: html, text, full: html, text
  • src/tagStorm/LICENSE - lines changed 2, context: html, text, full: html, text
  • src/utils/makefile - lines changed 3, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/makefile - lines changed 12, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/pslLiftSubrangeBlat.c - lines changed 133, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/expected/qSubRangeTest.psl - lines changed 4, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/expected/qtSubRangeTest.psl - lines changed 3, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/expected/tSubRangeTest.psl - lines changed 4, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/input/qSubrange.psl - lines changed 4, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/input/qSubrange.qsizes - lines changed 1, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.psl - lines changed 3, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.qsizes - lines changed 1, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/input/qtSubrange.sizes - lines changed 2, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/input/tSubrange.psl - lines changed 4, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/input/tSubrange.tsizes - lines changed 1, context: html, text, full: html, text
  • src/utils/pslLiftSubrangeBlat/tests/makefile - lines changed 31, context: html, text, full: html, text
  • src/utils/raSqlQuery/makefile - lines changed 7, context: html, text, full: html, text
  • src/utils/raSqlQuery/raRecord.c - lines changed 185, context: html, text, full: html, text
  • src/utils/raSqlQuery/raRecord.h - lines changed 54, context: html, text, full: html, text
  • src/utils/raSqlQuery/raSqlQuery.c - lines changed 622, context: html, text, full: html, text
  • src/utils/raSqlQuery/test.ra - lines changed 14, context: html, text, full: html, text
  • src/utils/raSqlQuery/test2.ra - lines changed 20, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/makefile - lines changed 7, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/scaffoldFaToAgp.c - lines changed 213, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/.gitignore - lines changed 1, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/runtest - lines changed 15, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/test.agp.gold - lines changed 5, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/test.fa - lines changed 6, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/test.gap.gold - lines changed 2, context: html, text, full: html, text
  • src/utils/scaffoldFaToAgp/test/test.lft.gold - lines changed 5, context: html, text, full: html, text

636a282f845f2264d0a8d767f039b573f70d22cb Wed May 26 05:30:44 2021 -0700

• clarifying license/index.html a little more, refs #27614
  • src/hg/htdocs/license/index.html - lines changed 31, context: html, text, full: html, text

d5ca45ddca96bf7a9756f5a250dd93d29e87103b Wed May 26 05:38:24 2021 -0700

• fixing conditions of use page, refs #27614
  • src/hg/htdocs/conditions.html - lines changed 1, context: html, text, full: html, text

2b135d602655887e43cae9ecd478d24c8fdf136c Thu May 27 05:33:50 2021 -0700

• centering error message box, refs #27460
  • src/hg/htdocs/style/HGStyle.css - lines changed 4, context: html, text, full: html, text

b5c7a5e272435eae70479a211b22626897e81edc Thu May 27 07:49:34 2021 -0700

• making cd8escape track, refs #27629
  • src/hg/makeDb/doc/wuhCor1/cd8Escape.txt - lines changed 6, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cd8Escape/escape_mutants.as - lines changed 18, context: html, text, full: html, text
  • src/hg/makeDb/scripts/cd8Escape/process_epitopes.py - lines changed 195, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 49, context: html, text, full: html, text

e4d6c24a36a8d98fc285930bb3b390b1f77a56d9 Mon May 31 06:42:38 2021 -0700

• update to GBIC docs page, refs #27636
  • src/hg/htdocs/goldenPath/help/gbic.html - lines changed 10, context: html, text, full: html, text

c84cc71e4df12de399ff9c00bc68faf5b711ed62 Mon May 31 06:54:06 2021 -0700

• another gbic docs update, refs #27636
  • src/hg/htdocs/goldenPath/help/gbic.html - lines changed 11, context: html, text, full: html, text

b8199c996bd6603e6f9e43c8661134532032f4fa Tue Jun 1 02:41:14 2021 -0700

• adding phylocsf track, refs #25946
  • src/hg/makeDb/trackDb/virus/wuhCor1/phyloGenes.html - lines changed 37, context: html, text, full: html, text

8afa5f78425ec225b329db5e1e204384ad0bdfc1 Tue Jun 1 05:06:00 2021 -0700

• adding revel track for hg38, refs #27142
  • src/hg/makeDb/doc/hg38/revel.txt - lines changed 9, context: html, text, full: html, text
  • src/hg/makeDb/revel/revelToWig-hg38.py - lines changed 115, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/revel.html - lines changed 19, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/human/revel.ra - lines changed 7, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 5, context: html, text, full: html, text

480b442228c96496bd399c8c63d7e23aebc4eb15 Tue Jun 1 05:18:42 2021 -0700

• adding pennanticon for revel track on hg38, refs #27142
  • src/hg/makeDb/trackDb/human/hg38/trackDb.ra - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/relatedTracks.ra - lines changed 1, context: html, text, full: html, text