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/hgLoadChromGraph/hgLoadChromGraph.c src/hg/makeDb/hgLoadChromGraph/hgLoadChromGraph.c index f2c0135..577c0e0 100644 --- src/hg/makeDb/hgLoadChromGraph/hgLoadChromGraph.c +++ src/hg/makeDb/hgLoadChromGraph/hgLoadChromGraph.c @@ -1,228 +1,228 @@ /* hgLoadChromGraph - Load up chromosome graph. */ /* 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 "obscure.h" #include "linefile.h" #include "hash.h" #include "options.h" #include "portable.h" #include "jksql.h" #include "hdb.h" #include "hgRelate.h" #include "chromGraph.h" void usage() /* Explain usage and exit. */ { errAbort( "hgLoadChromGraph - Load up chromosome graph.\n" "usage:\n" " hgLoadChromGraph database track input.tab\n" "options:\n" " -noLoad - don't load database\n" " -idTable - Use a table on the same database to fetch coordinates\n" " e.g. \"snp127\".\n" " -minusLog10 - log10 the data then minus it before loading.\n" " -pathPrefix - Specify a location to use in metaChromGraph \n" " instead of /gbdb/<database>/chromGraph for the\n" " .cgb file.\n\n" "*NOTE: remember to put .cgb file in a good place for the web server\n" " and make a link to the file in /gbdb/<database>/chromGraph.\n" ); } static struct optionSpec options[] = { {"noLoad", OPTION_BOOLEAN}, {"idTable", OPTION_STRING}, {"minusLog10", OPTION_BOOLEAN}, {"pathPrefix", OPTION_STRING}, {NULL, 0}, }; char *createString = "CREATE TABLE %s (\n" " chrom varchar(255) not null, # Chromosome\n" " chromStart int not null, # Start coordinate\n" " val double not null, # Value at coordinate\n" " #Indices\n" " PRIMARY KEY(chrom(%d),chromStart)\n" ");\n"; char *metaCreateString = NOSQLINJ "CREATE TABLE metaChromGraph (\n" " name varchar(255) not null, # Corresponds to chrom graph table name\n" " minVal double not null, # Minimum value observed\n" " maxVal double not null, # Maximum value observed\n" " binaryFile varchar(255) not null, # Location of binary data point file if any\n" " #Indices\n" " PRIMARY KEY(name(32))\n" ");\n"; void checkTableForFields(struct sqlConnection *conn, char *tableName) /* Do basic checks on the table to make sure it's kosher. i.e. */ /* chrom, chromStart, name all exist along with the table itself. */ { struct slName *fieldList; if (!sqlTableExists(conn, tableName)) errAbort("table %s not found.", tableName); fieldList = sqlListFields(conn, tableName); if (!slNameInList(fieldList, "chrom")) errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName); if (!slNameInList(fieldList, "chromStart")) errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName); if (!slNameInList(fieldList, "name")) errAbort("table %s doesn't have a chrom field. It must have chrom, chromStart, and name at the minimum.", tableName); slNameFreeList(&fieldList); } struct hash *posHashFromTable(struct sqlConnection *conn, char *table) /* Store name, chrom, chromStart in a hash of slPairs. (cheap) */ { struct hash *posHash = newHash(24); struct sqlResult *sr = NULL; char query[256]; char **row; sqlSafef(query, sizeof(query), "select name,chrom,chromStart from %s", table); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { int chromStart = (int)sqlUnsigned(row[2]); struct slPair *pair; AllocVar(pair); pair->name = cloneString(row[1]); pair->val = intToPt(chromStart); hashAdd(posHash, row[0], pair); } sqlFreeResult(&sr); return posHash; } struct chromGraph *chromGraphListWithTable(char *fileName, char *db, char *table) /* Read the chromGraph file and convert to the chr,chromStart format. */ { struct sqlConnection *conn = sqlConnect(db); struct hash *posHash = NULL; struct lineFile *lf; struct chromGraph *list = NULL; char *words[2]; checkTableForFields(conn, table); posHash = posHashFromTable(conn, table); sqlDisconnect(&conn); lf = lineFileOpen(fileName, TRUE); while (lineFileRow(lf, words)) { struct chromGraph *cg; /* Look up ID in hash. */ struct slPair *infoFromHash = hashFindVal(posHash, words[0]); if (!infoFromHash) warn("%s line %d: %s not found in %s table", fileName, lf->lineIx, words[0], table); else { AllocVar(cg); cg->chrom = cloneString(infoFromHash->name); cg->chromStart = ptToInt(infoFromHash->val); cg->val = sqlDouble(words[1]); slAddHead(&list, cg); } } slReverse(&list); /* Free stuff up. */ lineFileClose(&lf); hashFreeWithVals(&posHash, slPairFree); return list; } void hgLoadChromGraph(boolean doLoad, char *db, char *track, char *fileName) /* hgLoadChromGraph - Load up chromosome graph. */ { double minVal,maxVal; struct chromGraph *el, *list; FILE *f; char *tempDir = "."; char path[PATH_LEN], gbdbPath[PATH_LEN]; char *idTable = optionVal("idTable", NULL); char *pathPrefix = NULL; if (idTable == NULL) list = chromGraphLoadAll(fileName); else list = chromGraphListWithTable(fileName, db, idTable); if (list == NULL) errAbort("%s is empty", fileName); /* Figure out min/max values */ minVal = maxVal = list->val; for (el = list->next; el != NULL; el = el->next) { if (optionExists("minusLog10")) { if (el->val == 1) el->val = 0; else if (el->val > 0) el->val = -1 * log(el->val)/log(10); } if (el->val < minVal) minVal = el->val; if (el->val > maxVal) maxVal = el->val; } /* Sort and write out temp file. */ slSort(&list, chromGraphCmp); f = hgCreateTabFile(tempDir, track); for (el = list; el != NULL; el = el->next) chromGraphTabOut(el, f); if (doLoad) { struct dyString *dy = dyStringNew(0); struct sqlConnection *conn; /* Set up connection to database and create main table. */ conn = hAllocConn(db); sqlDyStringPrintf(dy, createString, track, hGetMinIndexLength(db)); sqlRemakeTable(conn, track, dy->string); /* Load main table and clean up file handle. */ hgLoadTabFile(conn, tempDir, track, &f); hgRemoveTabFile(tempDir, track); /* If need be create meta table. If need be delete old row. */ if (!sqlTableExists(conn, "metaChromGraph")) sqlUpdate(conn, metaCreateString); else { dyStringClear(dy); sqlDyStringPrintf(dy, "delete from metaChromGraph where name = '%s'", track); sqlUpdate(conn, dy->string); } /* Make chrom graph file */ safef(path, sizeof(path), "%s.cgb", track); chromGraphToBin(list, path); safef(path, sizeof(path), "/gbdb/%s/chromGraph", db); pathPrefix = optionVal("pathPrefix", path); safef(gbdbPath, sizeof(gbdbPath), "%s/%s.cgb", pathPrefix, track); /* Create new line in meta table */ dyStringClear(dy); sqlDyStringPrintf(dy, "insert into metaChromGraph values('%s',%f,%f,'%s');", track, minVal, maxVal, gbdbPath); sqlUpdate(conn, dy->string); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, options); if (argc != 4) usage(); hgLoadChromGraph(!optionExists("noLoad"), argv[1], argv[2], argv[3]); return 0; }