0bc6be88baf4061ca10c6f207331ec04e36c17f1
hiram
  Fri Feb 2 11:34:37 2024 -0800
better name for this table refs #23589

diff --git src/hg/inc/asmSummary.h src/hg/inc/asmSummary.h
new file mode 100644
index 0000000..c1f7d32
--- /dev/null
+++ src/hg/inc/asmSummary.h
@@ -0,0 +1,117 @@
+/* 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 -------------------------------- */
+
+#endif /* ASMSUMMARY_H */
+