File Changes for galt

v446_preview2 to v446_base (2023-03-27 to 2023-04-03) v446

• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 64, context: html, text, full: html, text
    61946925ad5049ff822bd5e4e76d00c3106797ee Tue Mar 28 16:45:14 2023 -0700
    re-ran dbsnp155 build after fixing bug rm30617. refs #30617.
• src/hg/snp/dbSnpJsonToTab/dbSnpJsonToTab.c
  • lines changed 71, context: html, text, full: html, text
    e9401d3358499d9ffa04eb076dfe18a12769d959 Tue Mar 28 16:43:15 2023 -0700
    fixing dbSnpJsonToTab part of the dbSnp pipeline, our code was not handling clinvar records that had multiple significances, even though the json clearly shows it can be a list. Also the jsonQuery code is great at fetching a list of elements that match your query, but it just sticks them all together, and has no idea which came from which so maintaining the grouping and order was tricky. Used Angies suggestion to html-encode the commas so the rest of the code just things it is a single string without any commas in it so it can work properly inside the comma-separated list. It also reports in Warnings.tab the comma-separated ones re-encoded so you can double check those RS ids worked correctly in the browser, it also lists the multiple-sigs list for easy viewing for the pipeline-runner. fixes #30617
• src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
  • lines changed 21, context: html, text, full: html, text
    eeda64a71cfc7fe13b91130dcf6e6cdc22767059 Thu Mar 30 17:19:13 2023 -0700
    Make test was failing for utility vcfToHgvs. The stopLoss for the test NM_005572.3 just picked up more alignments from hg38. Added these to the expected list.