Commits for max

v356_base to v357_preview (2017-10-09 to 2017-10-16) v357

c8d8db67358f26a4150328fdc1d3e6849eaa01ee Thu Oct 5 16:13:34 2017 -0700

• changing pslSelect for uniprot track, refs #20174
  • src/hg/pslSelect/pslSelect.c - lines changed 47, context: html, text, full: html, text
  • src/hg/pslSelect/tests/expected/queryPairs2.out.psl - lines changed 3, context: html, text, full: html, text
  • src/hg/pslSelect/tests/input/queryPairs2.in.psl - lines changed 5, context: html, text, full: html, text
  • src/hg/pslSelect/tests/input/queryPairs2.queries - lines changed 3, context: html, text, full: html, text
  • src/hg/pslSelect/tests/makefile - lines changed 7, context: html, text, full: html, text

1ac3db7f3d267c2852d42da712976fe2d962809a Mon Oct 9 13:03:50 2017 -0700

• CIRM: allowing symlinks in the little webSync tool
  • src/utils/webSync - lines changed 4, context: html, text, full: html, text

cb3f1b0b44201216b5cdb2b89b6da201dc1c1f48 Tue Oct 10 09:20:47 2017 -0700

• fixing the UniProt parser for Regeneron, refs #20174
  • src/utils/uniprotToTab - lines changed 257, context: html, text, full: html, text

a5eeaf99743492594b017b6d289d578cd9f1c9cd Tue Oct 10 14:57:34 2017 -0700

• fixing stray files in uniprot, refs #20174
  • src/hg/utils/otto/README.md - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/otto/uniprot/README.txt - lines changed 1, context: html, text, full: html, text
  • src/hg/utils/otto/uniprot/doUniprot - lines changed 680, context: html, text, full: html, text
  • src/hg/utils/otto/uniprot/makeUniProtPsl.sh - lines changed 127, context: html, text, full: html, text
  • src/hg/utils/otto/uniprot/makefile - lines changed 2, context: html, text, full: html, text

b36c36e95e76f131b6fc05719fd3d39df585cfed Tue Oct 10 14:58:58 2017 -0700

• fixing features with names that are just a number, refs #20268
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 13, context: html, text, full: html, text

c643ac79e685df447f830a72d6a4bda6cb57014c Tue Oct 10 15:29:07 2017 -0700

• removing the old clinvar pipeline, refs #20268
  • src/hg/utils/uniprotMutations/README.txt - lines changed 31, context: html, text, full: html, text
  • src/hg/utils/uniprotMutations/liftUniprotMut.py - lines changed 246, context: html, text, full: html, text
  • src/hg/utils/uniprotMutations/load.sh - lines changed 8, context: html, text, full: html, text

c023499db31b1b6f72eb83f3ccb76b239d81d0c0 Tue Oct 10 16:08:27 2017 -0700

• creating uniprot version file for Jorges auto archiver now at the very very end of the pipeline, refs #20268
  • src/hg/utils/otto/uniprot/doUniprot - lines changed 39, context: html, text, full: html, text

a409e830ae5c049aae9015e98aba82b186000cc0 Wed Oct 11 11:05:15 2017 -0700

• now that uniprot track is released, add back the temp file remove commands, and adding Chris to the track desc page, refs #20174
  • src/hg/makeDb/trackDb/uniprot.html - lines changed 37, context: html, text, full: html, text
  • src/hg/utils/otto/uniprot/doUniprot - lines changed 2, context: html, text, full: html, text
  • src/hg/utils/otto/uniprot/makeUniProtPsl.sh - lines changed 1, context: html, text, full: html, text

5fc4e4b808fce37ff781fd27d6782808ebbb5e92 Wed Oct 11 14:06:15 2017 -0700

• allowing trackDb statement dataVersion to be a file name, refs #20174
  • src/hg/hgc/hgc.c - lines changed 9, context: html, text, full: html, text
  • src/hg/utils/otto/uniprot/doUniprot - lines changed 2, context: html, text, full: html, text

379ae9b004b804fac2cb1681934c9c33d7250a2c Wed Oct 11 17:37:18 2017 -0700

• fixing number-only names in clinvar, refs #20268
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 13, context: html, text, full: html, text

5d06774aa3598b4b5cba29ba426c9b79f6967c28 Thu Oct 12 11:08:56 2017 -0700

• another fix for clinvar again, refs #20268
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 8, context: html, text, full: html, text

23f219ade6005831496b8e31507cdeab988dd8ae Thu Oct 12 12:44:21 2017 -0700

• shortening a few very long labels in clinvar, refs #20268
  • src/hg/utils/otto/clinvar/clinVarToBed - lines changed 8, context: html, text, full: html, text

c80ad337d8e24c79da3a927a6c2a5f40c9251075 Fri Oct 13 16:44:15 2017 -0700

• CIRM: fixing missing extensions for tarballs submitted as unknown filetype
  • src/hg/cirm/cdw/cdwGetFile/cdwGetFile.c - lines changed 3, context: html, text, full: html, text