Commits for angie

v410_preview2 to v410_base (2021-02-01 to 2021-02-08) v410

e616b1ad06be9b542979d2224de81fa26a355ada Tue Feb 2 11:36:05 2021 -0800

• Loosen up regex for BioSample attributes with stray quotes.
  • src/hg/utils/otto/sarscov2phylo/bioSampleTextToTab.pl - lines changed 1, context: html, text, full: html, text

6ab4a88e1c9d7de5e15ecc3a6699c53bb4c60935 Wed Feb 3 13:45:17 2021 -0800

• Use Date::Parse to handle more data formats that are finding their way into BioSample.
  • src/hg/utils/otto/sarscov2phylo/gbMetadataAddBioSample.pl - lines changed 27, context: html, text, full: html, text

161870e01da2bfa9723b388eec3fd590b921a1cf Wed Feb 3 13:46:42 2021 -0800

• Add NULL check in case metadata file is not found.
  • src/hg/hgPhyloPlace/phyloPlace.c - lines changed 2, context: html, text, full: html, text

38caeb2a3929a04b5e1cb518dd74e60eba6a9ccf Wed Feb 3 19:10:41 2021 -0800

• Don't hardcode VCF_MAX_COLUMNS -- count the number of actual columns in header.
  • src/lib/vcf.c - lines changed 9, context: html, text, full: html, text

2167996398e3f11c6eefa1c2b3676a7726a49e4f Fri Feb 5 09:28:08 2021 -0800

• Mention sources of public sequences so it doesn't sound like we only use GISAID sequences.
  • src/hg/hgPhyloPlace/hgPhyloPlace.c - lines changed 6, context: html, text, full: html, text

c05cfd40266e98367a883cd3737959533cef01cd Fri Feb 5 09:57:03 2021 -0800

• Initial work for mm10 patches: create db grcM38P6 with patch sequences and annotations. refs #25045
  • src/hg/makeDb/doc/grcM38P6.txt - lines changed 389, context: html, text, full: html, text
  • src/hg/makeDb/doc/mm10.scanAssemblyReport.pl - lines changed 99, context: html, text, full: html, text