c88b8a093cac2bc72ca4b4e3ff1fc2d1aea17f55 hiram Sat Feb 3 13:59:52 2024 -0800 the NULL specification confused autoSql for numbers that should be zero refs #23589 diff --git src/hg/inc/asmSummary.h src/hg/inc/asmSummary.h index 05e9019..6362c7f 100644 --- src/hg/inc/asmSummary.h +++ src/hg/inc/asmSummary.h @@ -7,60 +7,60 @@ #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 */ + 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 */ + 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 */ + 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(). */