Commits for angie

v398_base to v399_preview (2020-05-11 to 2020-05-18) v399

f6bebb8752bbd5f6f40713cc4ee93ed6c0804325 Mon May 11 16:06:38 2020 -0700

• Removed the warning about amino acid changes that don't match regex because they have added changes to '-' (as they did before for SNVs). refs #25188
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 2, context: html, text, full: html, text

a90606c0cc1d4650334172bdc0b193b2c19c1dbe Mon May 11 17:38:27 2020 -0700

• With Max's approval, convert the bedGraph Counts track to alt allele frequency (easier to explain, normalized to [0, 1]). Also, don't include ncov.json in the archive directories -- Trevor Bedford of Nextstrain said that GISAID doesn't want it available for public download. :( refs #25481, #25188
  • src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 8, context: html, text, full: html, text

db96d28dd92f6ad538d7f07ef1ee600bbd599fa7 Tue May 12 09:47:32 2020 -0700

• Use more force when downloading latest ncov.json so the script doesn't die if there's a read-only ncov.json file in the way. refs #25188
  • src/hg/utils/otto/nextstrainNcov/doUpdate.sh - lines changed 2, context: html, text, full: html, text

54f7a5994a7093acf25a912e1348ca1ef181a08c Tue May 12 10:07:04 2020 -0700

• Changing Nextstrain Counts to Nextstrain Frequency and adding description. refs #25481
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html - lines changed 73, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 70, context: html, text, full: html, text

7320e440fe5c1e94770d5fbc5ec30ea9242864c5 Tue May 12 10:18:52 2020 -0700

• Unfortunately GISAID has prevented Nextstrain from offering its latest ncov.json file for public download, so remove mentions of JSON from track descriptions. refs #25188, #25481
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html - lines changed 11, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html - lines changed 8, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html - lines changed 11, context: html, text, full: html, text

59749d287fb04a329cf873d4206d6657cb73fa76 Tue May 12 10:23:21 2020 -0700

• Update references to 'Nextstrain Vars' to 'Nextstrain Variants' now that 20-character shortLabels are in, yay. :) refs #25188
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainClade.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainFreq.html - lines changed 1, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainGene.html - lines changed 1, context: html, text, full: html, text

1c4981bf11687b15ff48044ccf434f0157410a43 Tue May 12 10:45:56 2020 -0700

• Turning off autoScale for Nextstrain Frequency because it has a natural range of 0.0 to 1.0. refs #25481
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 3, context: html, text, full: html, text

1f03198645ea9c851e031b83832e6412439c8130 Wed May 13 11:41:01 2020 -0700

• Nextstrain Variants description edits suggested by David with some clarifications/updates mixed in. refs #25409
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html - lines changed 68, context: html, text, full: html, text

e8405a958dae40b261b2eadcd59a20edc64761f1 Wed May 13 15:25:04 2020 -0700

• VCF details and track controls: use "sample" instead of "haplotype" when displaying SARS-CoV-2 data because viruses are not diploid. refs #25409 Also don't display "leaf cluster" shape option, which applies only to the center-weighted haplotype clustering, unless that method is selected.
  • src/hg/hgc/vcfClick.c - lines changed 5, context: html, text, full: html, text
  • src/hg/inc/vcfUi.h - lines changed 3, context: html, text, full: html, text
  • src/hg/lib/vcfUi.c - lines changed 74, context: html, text, full: html, text

39df62e630e31c0f8019bb350d64736ebe44220d Wed May 13 15:40:48 2020 -0700

• oops, forgot to call hReplaceGbdb on new tree file for VCF (and on .vcf.gz file for that matter). refs #25554
  • src/hg/hgTracks/vcfTrack.c - lines changed 2, context: html, text, full: html, text

5c4910deb5cbe427a10a75dd62f1912ae8a98a7b Thu May 14 10:19:02 2020 -0700

• Added Recurrent Bi-allelic subtrack and per-clade subtracks to Description section. refs #25409
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html - lines changed 26, context: html, text, full: html, text

f9d1e6b0d008cc1bb0265c59b2cdafd14dfed362 Thu May 14 10:50:44 2020 -0700

• Add a separate nextstrainSamplesDevOnly.html so that Recurrent Bi-allelic is described only on hgwdev. refs #25409
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamples.html - lines changed 4, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/nextstrainSamplesDevOnly.html - lines changed 154, context: html, text, full: html, text
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 13, context: html, text, full: html, text

0b18ad3971852efb98daabd60d55ec1cc1711612 Thu May 14 13:46:59 2020 -0700

• Python learning: the whole point of 'with open(...) as f' is that you don't have to remember to close f.
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 15, context: html, text, full: html, text

1395e00347b5e2aa8cdd2ad8039febd174fe951f Thu May 14 14:39:34 2020 -0700

• Fixing FORMAT column in per-clade and recurrent bi-allelic VCF output. (was causing about a million silent calls to vcfFileErr). refs #25188
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 2, context: html, text, full: html, text

5e880d2ed96fe5ad464fc9b98b07ea8dab70d7f6 Fri May 15 10:29:11 2020 -0700

• Back-mutations on the path to clade nodes cause duplicate blocks in the nextstrainClade bed, which causes sporadic bedToBigBed errors. Handle those by removing both the forward and back mutations because they cancel each other out in terms of the alleles at the clade node. Leave them in the variant string as a reminder that the tree has funky back-mutations. refs #25188
  • src/hg/utils/otto/nextstrainNcov/nextstrain.py - lines changed 28, context: html, text, full: html, text

4fb9760710c1a7398a72b491975c862e4704f594 Fri May 15 11:34:36 2020 -0700

• Removing extra space between beta and public that caused tdbQuery cron check failure.
  • src/hg/makeDb/trackDb/virus/wuhCor1/trackDb.nextstrain.ra - lines changed 0, context: html, text, full: html, text (a binary file or whitespace-only change or file-permission change shows no diff)

cf6c86d4ab35eecaebbaca76640393fd060af845 Fri May 15 14:35:22 2020 -0700

• Changed compatibleReleases to use recordMatchesRelease instead of sameString so that whitespace differences won't throw it off (and one record listing more releases than the other won't be a problem). Also changed buildReleaseBits to copy and clobber instead of clobbering and fixing (which could fail if there is a space before a comma). Also removed some logic for inheriting release from a parent because hgTrackDb doesn't do that.
  • src/hg/utils/tdbQuery/tdbQuery.c - lines changed 67, context: html, text, full: html, text

888f7654e2cd538922ffea023abf83f9db522b88 Fri May 15 14:51:34 2020 -0700

• Added test target to trackDb/makefile that invokes tdbQuery -check -release={alpha,beta,public} -strict.
  • src/hg/makeDb/trackDb/makefile - lines changed 5, context: html, text, full: html, text