533112afe2a2005e80cdb1f82904ea65032d4302 braney Sat Oct 2 11:37:34 2021 -0700 split hg/lib into two separate libaries, one only used by the cgis diff --git src/hg/lib/bgiSnp.c src/hg/lib/bgiSnp.c deleted file mode 100644 index 8800b63..0000000 --- src/hg/lib/bgiSnp.c +++ /dev/null @@ -1,236 +0,0 @@ -/* bgiSnp.c was originally generated by the autoSql program, which also - * generated bgiSnp.h and bgiSnp.sql. This module links the database and - * the RAM representation of objects. */ - -/* Copyright (C) 2014 The Regents of the University of California - * See README in this or parent directory for licensing information. */ - -#include "common.h" -#include "linefile.h" -#include "dystring.h" -#include "jksql.h" -#include "bgiSnp.h" - - -void bgiSnpStaticLoad(char **row, struct bgiSnp *ret) -/* Load a row from bgiSnp table into ret. The contents of ret will - * be replaced at the next call to this function. */ -{ -ret->chrom = row[0]; -ret->chromStart = sqlUnsigned(row[1]); -ret->chromEnd = sqlUnsigned(row[2]); -ret->name = row[3]; -strcpy(ret->snpType, row[4]); -ret->readStart = sqlUnsigned(row[5]); -ret->readEnd = sqlUnsigned(row[6]); -ret->qualChr = sqlUnsigned(row[7]); -ret->qualReads = sqlUnsigned(row[8]); -ret->snpSeq = row[9]; -ret->readName = row[10]; -strcpy(ret->readDir, row[11]); -strcpy(ret->inBroiler, row[12]); -strcpy(ret->inLayer, row[13]); -strcpy(ret->inSilkie, row[14]); -ret->primerL = row[15]; -ret->primerR = row[16]; -strcpy(ret->questionM, row[17]); -ret->extra = row[18]; -} - -struct bgiSnp *bgiSnpLoad(char **row) -/* Load a bgiSnp from row fetched with select * from bgiSnp - * from database. Dispose of this with bgiSnpFree(). */ -{ -struct bgiSnp *ret; -AllocVar(ret); -ret->chrom = cloneString(row[0]); -ret->chromStart = sqlUnsigned(row[1]); -ret->chromEnd = sqlUnsigned(row[2]); -ret->name = cloneString(row[3]); -strcpy(ret->snpType, row[4]); -ret->readStart = sqlUnsigned(row[5]); -ret->readEnd = sqlUnsigned(row[6]); -ret->qualChr = sqlUnsigned(row[7]); -ret->qualReads = sqlUnsigned(row[8]); -ret->snpSeq = cloneString(row[9]); -ret->readName = cloneString(row[10]); -strcpy(ret->readDir, row[11]); -strcpy(ret->inBroiler, row[12]); -strcpy(ret->inLayer, row[13]); -strcpy(ret->inSilkie, row[14]); -ret->primerL = cloneString(row[15]); -ret->primerR = cloneString(row[16]); -strcpy(ret->questionM, row[17]); -ret->extra = cloneString(row[18]); -return ret; -} - -struct bgiSnp *bgiSnpLoadAll(char *fileName) -/* Load all bgiSnp from a whitespace-separated file. - * Dispose of this with bgiSnpFreeList(). */ -{ -struct bgiSnp *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[19]; - -while (lineFileRow(lf, row)) - { - el = bgiSnpLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct bgiSnp *bgiSnpLoadAllByChar(char *fileName, char chopper) -/* Load all bgiSnp from a chopper separated file. - * Dispose of this with bgiSnpFreeList(). */ -{ -struct bgiSnp *list = NULL, *el; -struct lineFile *lf = lineFileOpen(fileName, TRUE); -char *row[19]; - -while (lineFileNextCharRow(lf, chopper, row, ArraySize(row))) - { - el = bgiSnpLoad(row); - slAddHead(&list, el); - } -lineFileClose(&lf); -slReverse(&list); -return list; -} - -struct bgiSnp *bgiSnpCommaIn(char **pS, struct bgiSnp *ret) -/* Create a bgiSnp out of a comma separated string. - * This will fill in ret if non-null, otherwise will - * return a new bgiSnp */ -{ -char *s = *pS; - -if (ret == NULL) - AllocVar(ret); -ret->chrom = sqlStringComma(&s); -ret->chromStart = sqlUnsignedComma(&s); -ret->chromEnd = sqlUnsignedComma(&s); -ret->name = sqlStringComma(&s); -sqlFixedStringComma(&s, ret->snpType, sizeof(ret->snpType)); -ret->readStart = sqlUnsignedComma(&s); -ret->readEnd = sqlUnsignedComma(&s); -ret->qualChr = sqlUnsignedComma(&s); -ret->qualReads = sqlUnsignedComma(&s); -ret->snpSeq = sqlStringComma(&s); -ret->readName = sqlStringComma(&s); -sqlFixedStringComma(&s, ret->readDir, sizeof(ret->readDir)); -sqlFixedStringComma(&s, ret->inBroiler, sizeof(ret->inBroiler)); -sqlFixedStringComma(&s, ret->inLayer, sizeof(ret->inLayer)); -sqlFixedStringComma(&s, ret->inSilkie, sizeof(ret->inSilkie)); -ret->primerL = sqlStringComma(&s); -ret->primerR = sqlStringComma(&s); -sqlFixedStringComma(&s, ret->questionM, sizeof(ret->questionM)); -ret->extra = sqlStringComma(&s); -*pS = s; -return ret; -} - -void bgiSnpFree(struct bgiSnp **pEl) -/* Free a single dynamically allocated bgiSnp such as created - * with bgiSnpLoad(). */ -{ -struct bgiSnp *el; - -if ((el = *pEl) == NULL) return; -freeMem(el->chrom); -freeMem(el->name); -freeMem(el->snpSeq); -freeMem(el->readName); -freeMem(el->primerL); -freeMem(el->primerR); -freeMem(el->extra); -freez(pEl); -} - -void bgiSnpFreeList(struct bgiSnp **pList) -/* Free a list of dynamically allocated bgiSnp's */ -{ -struct bgiSnp *el, *next; - -for (el = *pList; el != NULL; el = next) - { - next = el->next; - bgiSnpFree(&el); - } -*pList = NULL; -} - -void bgiSnpOutput(struct bgiSnp *el, FILE *f, char sep, char lastSep) -/* Print out bgiSnp. Separate fields with sep. Follow last field with lastSep. */ -{ -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->chrom); -if (sep == ',') fputc('"',f); -fputc(sep,f); -fprintf(f, "%u", el->chromStart); -fputc(sep,f); -fprintf(f, "%u", el->chromEnd); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->name); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->snpType); -if (sep == ',') fputc('"',f); -fputc(sep,f); -fprintf(f, "%u", el->readStart); -fputc(sep,f); -fprintf(f, "%u", el->readEnd); -fputc(sep,f); -fprintf(f, "%u", el->qualChr); -fputc(sep,f); -fprintf(f, "%u", el->qualReads); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->snpSeq); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->readName); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->readDir); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->inBroiler); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->inLayer); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->inSilkie); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->primerL); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->primerR); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->questionM); -if (sep == ',') fputc('"',f); -fputc(sep,f); -if (sep == ',') fputc('"',f); -fprintf(f, "%s", el->extra); -if (sep == ',') fputc('"',f); -fputc(lastSep,f); -} - -/* -------------------------------- End autoSql Generated Code -------------------------------- */ -