File Changes for angie

v465_base to v466_preview (2024-05-13 to 2024-05-20) v466

• src/hg/hgPhyloPlace/phyloPlace.c
  • lines changed 157, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/hgPhyloPlace/phyloPlace.h
  • lines changed 19, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/hgPhyloPlace/runUsher.c
  • lines changed 10, context: html, text, full: html, text
    540a3af876ace305fdd16c70ef29b83a1c139f39 Fri May 17 15:37:47 2024 -0700
    minor: make reportTiming messages more explicit about when server is failing over to command line
• src/hg/hgPhyloPlace/treeToAuspiceJson.c
  • lines changed 55, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/hgPhyloPlace/vcfFromFasta.c
  • lines changed 14, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/hg/makeDb/doc/bigDbSnp.txt
  • lines changed 101, context: html, text, full: html, text
    91814318ba5e9eec945f690b2598e390f407c7a0 Fri May 17 17:24:12 2024 -0700
    Update dbSnp153 to fix comma-formatting problem as Galt did for dbSnp155. refs #33070
• src/hg/utils/otto/sarscov2phylo/getNcbi.sh
  • lines changed 3, context: html, text, full: html, text
    07d759a94ed39950bd7634e0f3e0cc717d7a7b3c Tue May 14 16:26:03 2024 -0700
    Remove unused annotation option from datasets download command; split into larger chunks when rerunning pangolin on all sequences.
• src/hg/utils/otto/sarscov2phylo/nextstrain.clade-mutations.tsv
  • lines changed 3, context: html, text, full: html, text
    871f3a2b4ce77de9ef002db5098411d25022cb75 Tue May 14 16:24:27 2024 -0700
    Fixed 21F (Iota) path, added 24A (JN.1) and 24B (JN.1.11.1).
• src/hg/utils/otto/sarscov2phylo/pango.clade-mutations.tsv
  • lines changed 34, context: html, text, full: html, text
    b6e717ddc3b002501765ad91dd087253669311ee Wed May 15 15:49:21 2024 -0700
    Added latest newly designated lineages.
• src/inc/common.h
  • lines changed 4, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/inc/mmHash.h
  • lines changed 71, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/common.c
  • lines changed 2, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/makefile
  • lines changed 1, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/mmHash.c
  • lines changed 153, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/expected/mmHashTest.mmh
  • lines changed 0, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/expected/mmHashTest.out
  • lines changed 22, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/input/mmHashTest.txt
  • lines changed 22, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/makefile
  • lines changed 12, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/lib/tests/mmHashTest.c
  • lines changed 105, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/utils/makefile
  • lines changed 1, context: html, text, full: html, text
    ad7ff98d8aeec25df511d5f764ce1b6697321c7c Fri May 17 16:33:34 2024 -0700
    Added new util tabToMmHash to UCSC_APPS so it's in top-level build but not userApps.
• src/utils/tabToMmHash/makefile
  • lines changed 3, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.
• src/utils/tabToMmHash/tabToMmHash.c
  • lines changed 67, context: html, text, full: html, text
    2d05d30ed4df1612d72ba84c812d004de935b122 Fri May 17 16:08:54 2024 -0700
    Add lib module mmHash (memory-mapped hash), util tabToMmHash, and hgPhyloPlace support for using mmHash files instead of tab-separated files for metadata and name lookup. Using mmHash for name lookup saves about 50-55 seconds for SARS-CoV-2 hgPhyloPlace name/ID queries.