4898794edd81be5285ea6e544acbedeaeb31bf78 max Tue Nov 23 08:10:57 2021 -0800 Fixing pointers to README file for license in all source code files. refs #27614 diff --git src/hg/snp/snpLoad/affyCheck.c src/hg/snp/snpLoad/affyCheck.c index 161faf8..879a280 100644 --- src/hg/snp/snpLoad/affyCheck.c +++ src/hg/snp/snpLoad/affyCheck.c @@ -1,230 +1,230 @@ /* affyCheck - Check Affy SNPs. */ /* Copyright (C) 2013 The Regents of the University of California - * See README in this or parent directory for licensing information. */ + * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "hdb.h" char *database = NULL; char *affyTable = NULL; char *lookupTable = NULL; void usage() /* Explain usage and exit. */ { errAbort( "affyCheck - check Affy snps\n" "usage:\n" " affyCheck database affyTable lookupTable\n"); } struct snpSimple /* Get only what is needed from snp. */ /* Assuming observed string is always in alphabetical order. */ /* Assuming observed string is upper case. */ { struct snpSimple *next; char *name; /* rsId */ char *chrom; int chromStart; int chromEnd; char strand; char *observed; }; struct snpSimple *snpSimpleLoad(char **row) /* Load a snpSimple from row fetched from snp table * in database. Dispose of this with snpSimpleFree(). Complement observed if negative strand, preserving alphabetical order. */ { struct snpSimple *ret; int obsLen, i; char *obsComp; AllocVar(ret); ret->name = cloneString(row[0]); ret->chrom = cloneString(row[1]); ret->chromStart = atoi(row[2]); ret->chromEnd = atoi(row[3]); // use cloneString rather than strcpy strcpy(&ret->strand, row[4]); ret->observed = cloneString(row[5]); if (ret->strand == '+') return ret; obsLen = strlen(ret->observed); obsComp = needMem(obsLen + 1); obsComp = cloneString(ret->observed); for (i = 0; i < obsLen; i = i+2) { char c = ret->observed[i]; obsComp[obsLen-i-1] = ntCompTable[c]; } verbose(2, "negative strand detected for snp %s\n", ret->name); verbose(2, "original observed string = %s\n", ret->observed); verbose(2, "complemented observed string = %s\n", obsComp); freeMem(ret->observed); ret->observed=obsComp; return ret; } void snpSimpleFree(struct snpSimple **pEl) /* Free a single dynamically allocated snpSimple such as created with snpSimpleLoad(). */ { struct snpSimple *el; if ((el = *pEl) == NULL) return; freeMem(el->name); freeMem(el->observed); freez(pEl); } void snpSimpleFreeList(struct snpSimple **pList) /* Free a list of dynamically allocated snpSimple's */ { struct snpSimple *el, *next; for (el = *pList; el != NULL; el = next) { next = el->next; snpSimpleFree(&el); } *pList = NULL; } struct snpSimple *readSnps() /* Slurp in the snpSimple rows */ { struct snpSimple *list=NULL, *el; char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; int count = 0; verbose(1, "reading in from %s...\n", affyTable); sqlSafef(query, sizeof(query), "select name, chrom, chromStart, chromEnd, strand, observed from %s ", affyTable); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { count++; el = snpSimpleLoad(row); slAddHead(&list,el); } sqlFreeResult(&sr); hFreeConn(&conn); slReverse(&list); /* could possibly skip if it made much difference in speed. */ return list; } void affyCheck() /* affyCheck - read in all Affy SNPs, compare to lookupTable. */ { struct snpSimple *snps = NULL; struct snpSimple *snp = NULL; struct snpSimple *newSnp = NULL; char query[512]; struct sqlConnection *conn = hAllocConn(); struct sqlResult *sr; char **row; int count = 0; int obsLen = 0; snps = readSnps(); verbose(1, "checking....\n"); for (snp = snps; snp != NULL; snp = snp->next) { count++; verbose(2, "----------------------\n"); verbose(2, "%d: %s:%d-%d\n", count, snp->chrom, snp->chromStart, snp->chromEnd); sqlSafef(query, sizeof(query), "select name, chrom, chromStart, chromEnd, strand, observed from %s" " where chrom = '%s' and chromStart = %d and chromEnd = %d", lookupTable, snp->chrom, snp->chromStart, snp->chromEnd); sr = sqlGetResult(conn, query); row = sqlNextRow(sr); if (row == NULL) { verbose(2, "no matches for %s %s\n", affyTable, snp->name); continue; } newSnp = snpSimpleLoad(row); verbose(2, "comparing %s %s to %s %s\n", affyTable, snp->name, lookupTable, newSnp->name); if (sameString(newSnp->observed, "n/a")) { while ((row = sqlNextRow(sr)) != NULL) { } continue; } if (sameString(newSnp->observed, "t/n")) { while ((row = sqlNextRow(sr)) != NULL) { } continue; } if (sameString(snp->observed, newSnp->observed)) { while ((row = sqlNextRow(sr)) != NULL) { } continue; } obsLen = strlen(newSnp->observed); if (obsLen > 3) { verbose(2, "%s is not bi-allelic (%s)\n", newSnp->name, newSnp->observed); while ((row = sqlNextRow(sr)) != NULL) { } continue; } verbose(1, "----------------------\n"); verbose(1, "%d: %s:%d-%d\n", count, snp->chrom, snp->chromStart, snp->chromEnd); verbose(1, "comparing %s %s to %s %s\n", affyTable, snp->name, lookupTable, newSnp->name); verbose(1, "observed difference\n"); verbose(1, "%s observed = %s, %s observed = %s\n", affyTable, snp->observed, lookupTable, newSnp->observed); if (snp->strand == '-' && newSnp->strand == '+') { verbose(1, "strand difference\n"); verbose(1, "%s strand = %c, %s strand = %c\n", affyTable, snp->strand, lookupTable, newSnp->strand); } if (snp->strand == '+' && newSnp->strand == '-') { verbose(1, "strand difference\n"); verbose(1, "%s strand = %c, %s strand = %c\n", affyTable, snp->strand, lookupTable, newSnp->strand); } /* check here for multiple matches */ while ((row = sqlNextRow(sr)) != NULL) { } /* free newSnp */ } snpSimpleFreeList(&snps); } int main(int argc, char *argv[]) /* Check args and call affyCheck. */ { if (argc != 4) usage(); database = argv[1]; affyTable = argv[2]; lookupTable = argv[3]; hSetDb(database); /* initialize ntCompTable[] */ dnaUtilOpen(); affyCheck(); return 0; }