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/makeDb/hgLoadSample/hgLoadSample.c src/hg/makeDb/hgLoadSample/hgLoadSample.c index 52912e2..cecc8b6 100644 --- src/hg/makeDb/hgLoadSample/hgLoadSample.c +++ src/hg/makeDb/hgLoadSample/hgLoadSample.c @@ -1,224 +1,224 @@ /* hgLoadBed - Load a generic bed file into database. */ /* 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 "linefile.h" #include "obscure.h" #include "hash.h" #include "cheapcgi.h" #include "jksql.h" #include "dystring.h" #include "sample.h" #include "hdb.h" /* Command line switches. */ boolean noBin = FALSE; /* Suppress bin field. */ boolean strictTab = FALSE; /* Separate on tabs. */ boolean oldTable = FALSE; /* Don't redo table. */ char *sqlTable = NULL; /* Read table from this .sql if non-NULL. */ void usage() /* Explain usage and exit. */ { errAbort( "hgLoadSample - Load a sample 9 (wiggle) file into database\n" "usage:\n" " hgLoadSample database track files(s).smp\n" "options:\n" " -noBin suppress bin field\n" " -oldTable add to existing table\n" " -sqlTable=table.sql Create table from .sql file\n" " -tab Separate by tabs rather than space\n" ); } int findBedSize(char *fileName) /* Read first line of file and figure out how many words in it. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); char *words[64], *line; int wordCount; lineFileNeedNext(lf, &line, NULL); if (strictTab) wordCount = chopTabs(line, words); else wordCount = chopLine(line, words); if (wordCount == 0) errAbort("%s appears to be empty", fileName); lineFileClose(&lf); return wordCount; } struct bedStub /* A line in a bed file with chromosome, start, end position parsed out. */ { struct bedStub *next; /* Next in list. */ char *chrom; /* Chromosome . */ int chromStart; /* Start position. */ int chromEnd; /* End position. */ char *line; /* Line. */ }; int bedStubCmp(const void *va, const void *vb) /* Compare to sort based on query. */ { const struct bedStub *a = *((struct bedStub **)va); const struct bedStub *b = *((struct bedStub **)vb); int dif; dif = strcmp(a->chrom, b->chrom); if (dif == 0) dif = a->chromStart - b->chromStart; return dif; } void loadOneBed(char *fileName, int bedSize, struct bedStub **pList) /* Load one bed file. Make sure all lines have bedSize fields. * Put results in *pList. */ { struct lineFile *lf = lineFileOpen(fileName, TRUE); char *words[64], *line, *dupe; int wordCount; struct bedStub *bed; verbose(1, "Reading %s\n", fileName); while (lineFileNext(lf, &line, NULL)) { dupe = cloneString(line); if (strictTab) wordCount = chopTabs(line, words); else wordCount = chopLine(line, words); lineFileExpectWords(lf, bedSize, wordCount); AllocVar(bed); bed->chrom = cloneString(words[0]); bed->chromStart = lineFileNeedNum(lf, words, 1); bed->chromEnd = lineFileNeedNum(lf, words, 2); bed->line = dupe; slAddHead(pList, bed); } lineFileClose(&lf); } void writeBedTab(char *fileName, struct bedStub *bedList, int bedSize) /* Write out bed list to tab-separated file. */ { struct bedStub *bed; FILE *f = mustOpen(fileName, "w"); char *words[64]; int i, wordCount; for (bed = bedList; bed != NULL; bed = bed->next) { if (!noBin) fprintf(f, "%u\t", hFindBin(bed->chromStart, bed->chromEnd)); if (strictTab) wordCount = chopTabs(bed->line, words); else wordCount = chopLine(bed->line, words); for (i=0; i<wordCount; ++i) { fputs(words[i], f); if (i == wordCount-1) fputc('\n', f); else fputc('\t', f); } } fclose(f); } void loadDatabase(char *database, char *track, int bedSize, struct bedStub *bedList) /* Load database from bedList. */ { struct sqlConnection *conn = sqlConnect(database); struct dyString *dy = newDyString(1024); char *tab = "sample.tab"; /* First make table definition. */ if (sqlTable != NULL) { /* Read from file. */ char *sql, *s; readInGulp(sqlTable, &sql, NULL); /* Chop of end-of-statement semicolon if need be. */ s = strchr(sql, ';'); if (s != NULL) *s = 0; sqlRemakeTable(conn, track, sql); freez(&sql); } else if (!oldTable) { /* Create definition statement. */ verbose(1, "Creating table definition for \n"); sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track); if (!noBin) dyStringAppend(dy, " bin smallint unsigned not null,\n"); dyStringAppend(dy, " chrom varchar(255) not null,\n"); dyStringAppend(dy, " chromStart int unsigned not null,\n"); dyStringAppend(dy, " chromEnd int unsigned not null,\n"); if (bedSize >= 4) dyStringAppend(dy, " name varchar(255) not null,\n"); if (bedSize >= 5) dyStringAppend(dy, " score int unsigned not null,\n"); if (bedSize >= 6) dyStringAppend(dy, " strand char(1) not null,\n"); if (bedSize >= 7) dyStringAppend(dy, " sampleCount int unsigned not null,\n"); if (bedSize >= 8) dyStringAppend(dy, " samplePosition longblob not null,\n"); if (bedSize >= 9) dyStringAppend(dy, " sampleHeight longblob not null,\n"); dyStringAppend(dy, "#Indices\n"); if (!noBin) dyStringAppend(dy, " INDEX(chrom(8),bin),\n"); if (bedSize >= 4) dyStringAppend(dy, " INDEX(name(16)),\n"); dyStringAppend(dy, " INDEX(chrom(8),chromStart)\n"); dyStringAppend(dy, ")\n"); sqlRemakeTable(conn, track, dy->string); } verbose(1, "Saving %s\n", tab); writeBedTab(tab, bedList, bedSize); verbose(1, "Loading %s\n", database); dyStringClear(dy); sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track); sqlUpdate(conn, dy->string); sqlDisconnect(&conn); } void hgLoadBed(char *database, char *track, int bedCount, char *bedFiles[]) /* hgLoadBed - Load a generic bed file into database. */ { int bedSize = findBedSize(bedFiles[0]); struct bedStub *bedList = NULL; int i; for (i=0; i<bedCount; ++i) loadOneBed(bedFiles[i], bedSize, &bedList); verbose(1, "Loaded %d elements\n", slCount(bedList)); slSort(&bedList, bedStubCmp); verbose(1, "Sorted\n"); loadDatabase(database, track, bedSize, bedList); } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); if (argc < 4) usage(); noBin = cgiBoolean("noBin"); strictTab = cgiBoolean("tab"); uglyf("stringTab = %d\n", strictTab); oldTable = cgiBoolean("oldTable"); sqlTable = cgiOptionalString("sqlTable"); hgLoadBed(argv[1], argv[2], argc-3, argv+3); return 0; }