Commits for angie

v406_preview2 to v406_base (2020-10-19 to 2020-10-26) v406

d2b64fc2cb3878ce1c0a9b8512bc652e12994600 Mon Oct 19 10:13:58 2020 -0700

• Rename 'SARS-CoV-2 Phylo Pub' to 'Phylogeny: Public' and 'SARS-CoV-2 Phylogeny' to 'Phylogeny: GISAID' in order to make the difference between them more clear. Also hide the latter by default. refs #26364
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 52, context: html, text, full: html, text

5ccdd64cb512aba793f6a36676db6a69792bf923 Mon Oct 19 16:18:10 2020 -0700

• Removing 'tableBrowser off' setting from sarsCov2PhyloPub (copied by accident, thanks Daniel\!) refs #26364
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.ra - lines changed 2, context: html, text, full: html, text

b00557148488a34f1d4ba7ed2a2b37264b33ea23 Tue Oct 20 13:02:44 2020 -0700

• Raise VCF_MAX_COLUMNS yet again -- sarscov2phylo latest release has >100,000 sequences\!
  • src/lib/vcf.c - lines changed 1, context: html, text, full: html, text

376a3438b1a96761c019bbe128908fc69b5083df Thu Jul 30 18:04:05 2020 -0700

• Adding VCF_NUM_COLS_BEFORE_GENOTYPES to vcf.h to reduce the proliferation of magic number 9's in the code.
  • src/inc/vcf.h - lines changed 1, context: html, text, full: html, text

edd8fa03488ce1ee3fa7b12b64de39ad0e3fc216 Wed Oct 21 12:57:36 2020 -0700

• New utils for making the public-sequences-only version of the SARS-CoV-2 Phylogeny track. Forgot to add these back in commit 0901c8be. refs #26364
  • src/hg/utils/phyloRenameAndPrune/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/phyloRenameAndPrune/phyloRenameAndPrune.c - lines changed 84, context: html, text, full: html, text
  • src/hg/utils/vcfRenameAndPrune/makefile - lines changed 3, context: html, text, full: html, text
  • src/hg/utils/vcfRenameAndPrune/vcfRenameAndPrune.c - lines changed 166, context: html, text, full: html, text

358232fdd2fe9b78248b54fd38a9cd2f52ff4586 Wed Oct 21 12:49:05 2020 -0700

• lineFileUdcMayOpen automatically decompresses local files but not urls. netLineFileMayOpen does automatically decompress. For now, just use netLineFileMayOpen, although in the long term it would be better to ad support to lineFileUdcMayOpen to get the benefits of caching.
  • src/hg/hgTracks/vcfTrack.c - lines changed 5, context: html, text, full: html, text
  • src/lib/linefile.c - lines changed 7, context: html, text, full: html, text

bdb0cd1324dd7f96ab40203b2c9a031e9bd9d0cf Wed Oct 21 12:55:37 2020 -0700

• Adding note for next time about how a file mysteriously ended up with garbage at the end.
  • src/hg/makeDb/doc/wuhCor1/phylogenetics.txt - lines changed 5, context: html, text, full: html, text

7f2c8c7e74571f25d11da0dc618c95bc0bb5dd67 Wed Oct 21 13:03:00 2020 -0700

• Adding new utils phyloRenameAndPrune and vcfRenameAndPrune to top-level build target.
  • src/hg/utils/makefile - lines changed 2, context: html, text, full: html, text