889acd1c73910e973c8325bbd44cfc64bb63a1e3 hiram Wed Aug 12 15:49:54 2026 -0700 following advice in code review remove obsolete files refs #38005 diff --git src/hg/inc/asmSummary.h src/hg/inc/asmSummary.h deleted file mode 100644 index 6362c7fd802..00000000000 --- src/hg/inc/asmSummary.h +++ /dev/null @@ -1,124 +0,0 @@ -/* asmSummary.h was originally generated by the autoSql program, which also - * generated asmSummary.c and asmSummary.sql. This header links the database and - * the RAM representation of objects. */ - -#ifndef ASMSUMMARY_H -#define ASMSUMMARY_H - -#include "jksql.h" -#define ASMSUMMARY_NUM_COLS 37 - -extern char *asmSummaryCommaSepFieldNames; - -struct asmSummary -/* NCBI assembly_summary data, see: https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/README_assembly_summary.txt */ - { - struct asmSummary *next; /* Next in singly linked list. */ - char *assemblyAccession; /* www.ncbi.nlm.nih.gov/assembly/?term=xxx */ - char *bioproject; /* www.ncbi.nlm.nih.gov/bioproject/?term=xxx */ - char *biosample; /* www.ncbi.nlm.nih.gov/biosample/?term=xxx */ - char *wgsMaster; /* www.ncbi.nlm.nih.gov/nuccore/xxx */ - char *refseqCategory; /* representative or reference */ - unsigned taxId; /* www.ncbi.nlm.nih.gov/taxonomy/?term=xxx */ - unsigned speciesTaxid; /* www.ncbi.nlm.nih.gov/taxonomy/?term=xxx */ - char *organismName; /* binomial scientific name */ - char *infraspecificName; /* strain/cultivar/ecotype/breed */ - char *isolate; /* source of sample */ - char *versionStatus; /* latest/suppressed/replaced */ - char *assemblyLevel; /* Contig/Scaffold/Complete Genome/Chromosome */ - char *releaseType; /* Major/Minor/Patch */ - char *genomeRep; /* Full/Partial */ - char *seqRelDate; /* date YYYY/MM/DD sequence released to INSDC */ - char *asmName; /* submitter supplied name */ - char *asmSubmitter; /* institution submitting assembly */ - char *gbrsPairedAsm; /* GenBank<->RefSeq GCA/GCF relationship */ - char *pairedAsmComp; /* identical/different for GCA<->GCF relationship */ - char *ftpPath; /* ftp.ncbi.nlm.nih.gov/genomes/all/GCx/012/345/678/asmId */ - char *excludedFromRefseq; /* noted reason for exclusion from RefSeq */ - char *relationToTypeMaterial; /* note of assembly relation to sample */ - char *assemblyType; /* haploid/diploid/haploid-with-alt-loci/alternate-pseudohaplotype */ - char *phyloGroup; /* bacteria/viral/archaea/fungi/metagenomes/invertebrate/other/vertebrate_other/plant/vertebrate_mammalian/protozoa */ - long long genomeSize; /* total length of all top-level sequences in the primary assembly */ - long long genomeSizeUngapped; /* genome length not counting gaps (gap == 10 or more Ns) */ - float gcPercent; /* GC percent */ - unsigned short repliconCount; /* total number of chromosomes, organelle genomes and plasmids */ - unsigned scaffoldCount; /* number of scaffolds: placed, unlocalzes, unplace, alternate loci and patch */ - unsigned contigCount; /* number of conts in the primary assembly */ - char *annotationProvider; /* the group that provied the annotation on the assembly */ - char *annotationName; /* the name of the annotation */ - char *annotationDate; /* annotation date YYYY/MM/DD */ - char *totalGeneCount; /* total gene count in annotation */ - unsigned proteinCodingGeneCount; /* protein coding gene count in annotation */ - char *nonCodingGeneCount; /* non coding gene count in annotation */ - char *pubmedId; /* comma separated list of PubMed ID(s) */ - }; - -void asmSummaryStaticLoadWithNull(char **row, struct asmSummary *ret); -/* Load a row from asmSummary table into ret. The contents of ret will - * be replaced at the next call to this function. */ - -struct asmSummary *asmSummaryLoadByQuery(struct sqlConnection *conn, char *query); -/* Load all asmSummary from table that satisfy the query given. - * Where query is of the form 'select * from example where something=something' - * or 'select example.* from example, anotherTable where example.something = - * anotherTable.something'. - * Dispose of this with asmSummaryFreeList(). */ - -void asmSummarySaveToDb(struct sqlConnection *conn, struct asmSummary *el, char *tableName, int updateSize); -/* Save asmSummary as a row to the table specified by tableName. - * As blob fields may be arbitrary size updateSize specifies the approx size - * of a string that would contain the entire query. Arrays of native types are - * converted to comma separated strings and loaded as such, User defined types are - * inserted as NULL. This function automatically escapes quoted strings for mysql. */ - -struct asmSummary *asmSummaryLoadWithNull(char **row); -/* Load a asmSummary from row fetched with select * from asmSummary - * from database. Dispose of this with asmSummaryFree(). */ - -struct asmSummary *asmSummaryLoadAll(char *fileName); -/* Load all asmSummary from whitespace-separated file. - * Dispose of this with asmSummaryFreeList(). */ - -struct asmSummary *asmSummaryLoadAllByChar(char *fileName, char chopper); -/* Load all asmSummary from chopper separated file. - * Dispose of this with asmSummaryFreeList(). */ - -#define asmSummaryLoadAllByTab(a) asmSummaryLoadAllByChar(a, '\t'); -/* Load all asmSummary from tab separated file. - * Dispose of this with asmSummaryFreeList(). */ - -struct asmSummary *asmSummaryCommaIn(char **pS, struct asmSummary *ret); -/* Create a asmSummary out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new asmSummary */ - -void asmSummaryFree(struct asmSummary **pEl); -/* Free a single dynamically allocated asmSummary such as created - * with asmSummaryLoad(). */ - -void asmSummaryFreeList(struct asmSummary **pList); -/* Free a list of dynamically allocated asmSummary's */ - -void asmSummaryOutput(struct asmSummary *el, FILE *f, char sep, char lastSep); -/* Print out asmSummary. Separate fields with sep. Follow last field with lastSep. */ - -#define asmSummaryTabOut(el,f) asmSummaryOutput(el,f,'\t','\n'); -/* Print out asmSummary as a line in a tab-separated file. */ - -#define asmSummaryCommaOut(el,f) asmSummaryOutput(el,f,',',','); -/* Print out asmSummary as a comma separated list including final comma. */ - -void asmSummaryJsonOutput(struct asmSummary *el, FILE *f); -/* Print out asmSummary in JSON format. */ - -/* -------------------------------- End autoSql Generated Code -------------------------------- */ - -struct asmSummary *asmSummaryFullText(struct sqlConnection *conn, char *words, long long rowLimit, long long *totalMatch); -/* perform a FULLTEXT search on the asmSummary table with the list - * of words string (may be only a single word) - * return is a list of items found up to rowLimit, or NULL if none found - * also returning totalMatch to understand if it is more than the rowLimit - */ - -#endif /* ASMSUMMARY_H */ -