889acd1c73910e973c8325bbd44cfc64bb63a1e3 hiram Wed Aug 12 15:49:54 2026 -0700 following advice in code review remove obsolete files refs #38005 diff --git src/hg/lib/asmSummary.as src/hg/lib/asmSummary.as deleted file mode 100644 index 4e5b7b20778..00000000000 --- src/hg/lib/asmSummary.as +++ /dev/null @@ -1,41 +0,0 @@ -table asmSummary -"NCBI assembly_summary data, see: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_assembly_summary.txt" - ( - string assemblyAccession; "www.ncbi.nlm.nih.gov/assembly/?term=xxx" - string bioproject; "www.ncbi.nlm.nih.gov/bioproject/?term=xxx" - string biosample; "www.ncbi.nlm.nih.gov/biosample/?term=xxx" - string wgsMaster; "www.ncbi.nlm.nih.gov/nuccore/xxx" - string refseqCategory; "representative or reference" - uint taxId; "www.ncbi.nlm.nih.gov/taxonomy/?term=xxx" - uint speciesTaxid; "www.ncbi.nlm.nih.gov/taxonomy/?term=xxx" - string organismName; "binomial scientific name" - string infraspecificName; "strain/cultivar/ecotype/breed" - string isolate; "source of sample" - string versionStatus; "latest/suppressed/replaced" - string assemblyLevel; "Contig/Scaffold/Complete Genome/Chromosome" - string releaseType; "Major/Minor/Patch" - string genomeRep; "Full/Partial" - string seqRelDate; "date YYYY/MM/DD sequence released to INSDC" - string asmName; "submitter supplied name" - string asmSubmitter; "institution submitting assembly" - string gbrsPairedAsm; "GenBank<->RefSeq GCA/GCF relationship" - string pairedAsmComp; "identical/different for GCA<->GCF relationship" - string ftpPath; "ftp.ncbi.nlm.nih.gov/genomes/all/GCx/012/345/678/asmId" - string excludedFromRefseq; "noted reason for exclusion from RefSeq" - string relationToTypeMaterial; "note of assembly relation to sample" - string assemblyType; "haploid/diploid/haploid-with-alt-loci/alternate-pseudohaplotype" - string phyloGroup; "bacteria/viral/archaea/fungi/metagenomes/invertebrate/other/vertebrate_other/plant/vertebrate_mammalian/protozoa" - bigint genomeSize; "total length of all top-level sequences in the primary assembly" - bigint genomeSizeUngapped; "genome length not counting gaps (gap == 10 or more Ns)" - float gcPercent; "GC percent" - ushort repliconCount; "total number of chromosomes, organelle genomes and plasmids" - uint scaffoldCount; "number of scaffolds: placed, unlocalzes, unplace, alternate loci and patch" - uint contigCount; "number of conts in the primary assembly" - string annotationProvider; "the group that provied the annotation on the assembly" - string annotationName; "the name of the annotation" - string annotationDate; "annotation date YYYY/MM/DD" - string totalGeneCount; "total gene count in annotation" - uint proteinCodingGeneCount; "protein coding gene count in annotation" - string nonCodingGeneCount; "non coding gene count in annotation" - string pubmedId; "comma separated list of PubMed ID(s)" - )