File Changes for angie

switch to commits view, user index

v436_preview2 to v436_base (2022-08-22 to 2022-08-29) v436

Show details

src/hg/cgilib/tests/expected/annoGrator/insertions.txt
- lines changed 0, context: html, text, full: html, text
  ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
  Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
src/hg/cgilib/tests/input/annoGrator/insertionsPrimary.vcf
- lines changed 0, context: html, text, full: html, text
  ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
  Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
src/hg/cgilib/tests/input/annoGrator/insertionsPrimary.vcf.gz
- lines changed 0, context: html, text, full: html, text
  ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
  Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
src/hg/cgilib/tests/input/annoGrator/insertionsPrimary.vcf.gz.tbi
- lines changed 0, context: html, text, full: html, text
  ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
  Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
src/hg/cgilib/tests/input/annoGrator/insertionsSecondary.vcf
- lines changed 0, context: html, text, full: html, text
  ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
  Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
src/hg/cgilib/tests/input/annoGrator/insertionsSecondary.vcf.gz
- lines changed 0, context: html, text, full: html, text
  ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
  Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
src/hg/cgilib/tests/input/annoGrator/insertionsSecondary.vcf.gz.tbi
- lines changed 0, context: html, text, full: html, text
  ae5fa46665b19315211b621745d925fb94aa65a0 Wed Aug 24 15:16:45 2022 -0700
  Replacing spaces in some VCF header #CHROM lines with tabs -- this was overlooked when vcf.c was using chopLine instead of chopTabs as it should.
src/hg/hgPhyloPlace/hgPhyloPlace.c
- lines changed 103, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/hgPhyloPlace/phyloPlace.c
- lines changed 207, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/hgPhyloPlace/phyloPlace.h
- lines changed 13, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/hgPhyloPlace/runUsher.c
- lines changed 62, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/hgPhyloPlace/treeToAuspiceJson.c
- lines changed 8, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/hgPhyloPlace/vcfFromFasta.c
- lines changed 24, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/hgPhyloPlace/writeCustomTracks.c
- lines changed 41, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/inc/trackHub.h
- lines changed 3, context: html, text, full: html, text
  afafa0301ea4b14fbe1fbd5aa379c5351ecd640d Tue Aug 2 19:41:44 2022 -0700
  Add support for non-wuhCor1 genomes (e.g. monkeypox GenArk hub). * Search in hgPhyloPlaceData for config.ra files, taking assembly name (minus hub prefix) from directory name. * Add a menu input to the main page for switching between supported genomes if there are more than one. * Replace hardcoded values or global vars with dnaSeq attributes, assembly metadata queries or new config.ra settings. * Separate out SARS-CoV-2-specific help text like GISAID/CNCB descriptions. * Support metadata columns for GenBank-specific stuff & Nextstrain lineages (for MPXV). * also a little refactoring in runUsher in preparation for supporting usher server mode: parse new placement info file so we don't have to parse that data form usher stderr output. TODO: update Nextstrain/Auspice JSON output to use appropriate metadata columns and support monkeypox genes.
src/hg/lib/tests/expected/hgvs/validTerms.txt
- lines changed 1, context: html, text, full: html, text
  fec32cc187d7b42cbac7ee36fef68fa6a150fce8 Wed Aug 24 14:39:51 2022 -0700
  Adding additional HGVS validTerms.txt line of output for new RefSeq transcript.
src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
- lines changed 33, context: html, text, full: html, text
  7bf716f89e4ee2e32bc34e5c0e196d3363b35f69 Fri Jul 1 14:57:42 2022 -0700
  Added new lineages BC.2, BG.3-4, BA.2.74-75, BA.4.1.3-4, BA.4.2-5, BA.5.1.1-3, BF.1.1, BF.2-5, BA.5.2.2-4, BE.1.1, BE.2-3, BA.5.3.3-4, BA.5.6. Also tweaked miscBA1BA2Post17k back a node to keep XM from including things it shouldn't, and added a couple proposed lineages.
- lines changed 6, context: html, text, full: html, text
  e3539f8a3105f813200f7f21928d9813a3f81b24 Tue Jul 5 11:53:29 2022 -0700
  Corrected path to BA.2.43. Added BA.2.76, BA.2.77, BA.4.6, BA.5.1.4. Removed proposed570 -- it was BC.2.
- lines changed 1, context: html, text, full: html, text
  fb7e6a7f3484531a39976a131c38662623adf824 Wed Jul 6 14:46:59 2022 -0700
  Corrected path for BA.2.53.
- lines changed 2, context: html, text, full: html, text
  be3ecf652180e0b491d02e4dc4fd1a8309a829b6 Wed Jul 6 18:13:18 2022 -0700
  Yikes, never added AY.5.7 (missing from Chris's spreadsheet but in pango-designation/lineages.csv since April 1; p-d#387). Also added B.1.1.28 since it wasn't annotated for some reason.
- lines changed 50, context: html, text, full: html, text
  8f10afb2f9cfde2ddfa5a1982fe4f7de0ce720de Mon Aug 1 14:15:19 2022 -0700
  Added BA.2.3.19, BA.2.9.5, BG.5, BA.2.13.1, BA.2.36.1 (may change to BA.2.X), BA.2.38.1-2, BA.2.78-81, BA.2.79.1, BA.4.7, BA.5.1.5-8, BF.6-12, BA.5.2.5, BA.5.6.1, BA.5.7-9, recombinants XAJ-XAP -- pango-designation v1.12 and v1.13. Also added proposed885; removed proposed757, 759, 789 since they were designated. Removed BA.2.3.9_rev241 because I started masking 241 in BA.2. Changed BA.2.13 path: removed G24368N, not needed. Changed BA.3.1 path after fixing tree: unmasked C28311T, removed C27874N and A28461N. Added BA.3.1_revs to catch split branch with reversions. Changed BA.4.3. path: removed C203T because it is now masked in BA.2 (would be pango-masked anyway). Changed BA.5.1: added T27438C to BA.5.1 path, added BA.5.1_no27438 split branch. Changed BA.5.2.1: unmask A28330G. Added BA.5.2_no28330 split branch.
- lines changed 29, context: html, text, full: html, text
  1909321bc89456da06cb8793a9dbe7541563420e Fri Aug 19 12:10:42 2022 -0700
  BA.2.36.1 renamed to BA.2.82. Added BA.2.9.6, BA.2.10.4, BA.2.38.3, BA.2.75.1-2, BA.2.76.1-2, BG.6, BH.1, BJ.1, BA.5.1.9-11, BA.5.5.1, BA.5.6.2, BA.5.10, BE.1.2, BF.13, BF.14, BK.1. Renamed proposed 798 to XAQ, addded XAR. -- pango-designation v1.14 Also added proposed882, proposed911, BA.5.2.1_no28330; tweaked BA.5.2_no28330 to be more explicit about 28330.
- lines changed 2, context: html, text, full: html, text
  7e4f3ed58a9c5632b6e65a8eb13447a84b9b5b5f Tue Aug 23 10:50:51 2022 -0700
  Added label BA.2_21765_no22792 for persistent problematic branch that resulted in misdesignation of BA.2.36.1 (corrected to BA.2.82). Tweaked path of BA.2.75.2 to handle a couple sites with reversions, ugh.
src/hg/utils/vcfToHgvs/tests/expected/stopLoss.tab
- lines changed 25, context: html, text, full: html, text
  0b8e4c09fe3a2cb3ab8a05807cebba50cbe1e94c Wed Aug 24 16:59:30 2022 -0700
  vcfToHgvs: Exclude XM_ and XR_ transcripts -- they're not 'real' HGVS and also very unstable from one version to the next.
src/hg/utils/vcfToHgvs/vcfToHgvs.c
- lines changed 4, context: html, text, full: html, text
  0b8e4c09fe3a2cb3ab8a05807cebba50cbe1e94c Wed Aug 24 16:59:30 2022 -0700
  vcfToHgvs: Exclude XM_ and XR_ transcripts -- they're not 'real' HGVS and also very unstable from one version to the next.
src/lib/vcf.c
- lines changed 2, context: html, text, full: html, text
  d517d7563a1e14f913bf2d21893daada5e35134d Wed Aug 24 14:15:31 2022 -0700
  Use chopTabs not chopLine for VCF header parsing. refs #29923

switch to commits view, user index