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/hgLoadChain/hgLoadChain.c src/hg/makeDb/hgLoadChain/hgLoadChain.c index d7ff372..b3192fe 100644 --- src/hg/makeDb/hgLoadChain/hgLoadChain.c +++ src/hg/makeDb/hgLoadChain/hgLoadChain.c @@ -1,302 +1,302 @@ /* hgLoadChain - Load a chain 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 "jksql.h" #include "dystring.h" #include "bed.h" #include "hdb.h" #include "chainBlock.h" #include "options.h" /* command line option specifications */ static struct optionSpec optionSpecs[] = { {"noBin", OPTION_BOOLEAN}, {"noSort", OPTION_BOOLEAN}, {"tIndex", OPTION_BOOLEAN}, {"oldTable", OPTION_BOOLEAN}, {"normScore", OPTION_BOOLEAN}, {"sqlTable", OPTION_STRING}, {"qPrefix", OPTION_STRING}, {"test", OPTION_BOOLEAN}, {NULL, 0} }; /* Command line switches. */ static boolean noBin = FALSE; /* Suppress bin field. */ static boolean noSort = FALSE; /* Suppress sorting of input. */ static boolean tIndex = FALSE; /* Include tName in index. */ static boolean oldTable = FALSE; /* Don't redo table. */ static boolean normScore = FALSE; /* Add normScore column */ static char *sqlTable = NULL; /* Read table from this .sql if non-NULL. */ static char *qPrefix = NULL; /* prefix to prepend (with -) to query name */ static boolean test = FALSE; /* suppress loading to table */ static void usage() /* Explain usage and exit. */ { errAbort( "hgLoadChain - Load a generic Chain file into database\n" "usage:\n" " hgLoadChain database chrN_track chrN.chain\n" "options:\n" " -tIndex Include tName in indexes (for non-split chain tables)\n" " -noBin suppress bin field, default: bin field is added\n" " -noSort Don't sort by target (memory-intensive) -- input *must* be\n" " sorted by target already if this option is used.\n" " -oldTable add to existing table, default: create new table\n" " -sqlTable=table.sql Create table from .sql file\n" " -normScore add normalized score column to table, default: not added\n" " -qPrefix=xxx prepend \"xxx\" to query name\n" " -test suppress loading to database\n" ); } static void writeLink(struct cBlock *b, char *tName, int chainId, FILE *f) /* Write out a single link in tab separated format. */ { if (!noBin) fprintf(f, "%u\t", hFindBin(b->tStart, b->tEnd)); fprintf(f,"%s\t%d\t%d\t%d\t%d\n", tName, b->tStart, b->tEnd, b->qStart, chainId); } static void writeChain(struct chain *a, FILE *f, int basesMatched) /* Write out chain (just the header parts) in tab separated format. */ { char qName[64]; if (!noBin) fprintf(f,"%u\t", hFindBin(a->tStart, a->tEnd)); qName[0] = 0; if (qPrefix != NULL) strcat(qName, qPrefix); strcat(qName, a->qName); if (normScore) fprintf(f, "%f\t%s\t%d\t%d\t%d\t%s\t%d\t%c\t%d\t%d\t%d\t%.1f\n", a->score, a->tName, a->tSize, a->tStart, a->tEnd, qName, a->qSize, a->qStrand, a->qStart, a->qEnd, a->id, a->score/basesMatched); else fprintf(f, "%f\t%s\t%d\t%d\t%d\t%s\t%d\t%c\t%d\t%d\t%d\n", a->score, a->tName, a->tSize, a->tStart, a->tEnd, qName, a->qSize, a->qStrand, a->qStart, a->qEnd, a->id); } static void loadDatabaseLink(char *database, char *tab, char *track) /* Load database from tab file. */ { struct sqlConnection *conn = sqlConnect(database); struct dyString *dy = newDyString(1024); /* 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) { int minLength = hGetMinIndexLength(database); /* Create definition statement. */ sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track); if (!noBin) dyStringAppend(dy, " bin smallint unsigned not null,\n"); dyStringAppend(dy, " tName varchar(255) not null,\n"); dyStringAppend(dy, " tStart int unsigned not null,\n"); dyStringAppend(dy, " tEnd int unsigned not null,\n"); dyStringAppend(dy, " qStart int unsigned not null,\n"); dyStringAppend(dy, " chainId int unsigned not null,\n"); dyStringAppend(dy, "#Indices\n"); if (tIndex) { if (!noBin) dyStringPrintf(dy, " INDEX(tName(%d),bin),\n", minLength); } else { if (!noBin) dyStringAppend(dy, " INDEX(bin),\n"); } dyStringAppend(dy, " INDEX(chainId)\n"); dyStringAppend(dy, ")\n"); sqlRemakeTable(conn, track, dy->string); } dyStringClear(dy); sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track); sqlUpdate(conn, dy->string); sqlDisconnect(&conn); } static void loadDatabaseChain(char *database, char *tab, char *track, int count) /* Load database from tab file. */ { struct sqlConnection *conn = sqlConnect(database); struct dyString *dy = newDyString(1024); /* 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) { int minLength = hGetMinIndexLength(database); /* Create definition statement. */ sqlDyStringPrintf(dy, "CREATE TABLE %s (\n", track); if (!noBin) dyStringAppend(dy, " bin smallint unsigned not null,\n"); dyStringAppend(dy, " score double not null,\n"); dyStringAppend(dy, " tName varchar(255) not null,\n"); dyStringAppend(dy, " tSize int unsigned not null, \n"); dyStringAppend(dy, " tStart int unsigned not null,\n"); dyStringAppend(dy, " tEnd int unsigned not null,\n"); dyStringAppend(dy, " qName varchar(255) not null,\n"); dyStringAppend(dy, " qSize int unsigned not null,\n"); dyStringAppend(dy, " qStrand char(1) not null,\n"); dyStringAppend(dy, " qStart int unsigned not null,\n"); dyStringAppend(dy, " qEnd int unsigned not null,\n"); dyStringAppend(dy, " id int unsigned not null,\n"); if (normScore) dyStringAppend(dy, " normScore double not null,\n"); dyStringAppend(dy, "#Indices\n"); if (tIndex) { if (noBin) { dyStringPrintf(dy, " INDEX(tName(%d),tStart),\n", minLength); dyStringPrintf(dy, " INDEX(tName(%d),tEnd),\n", minLength); } else dyStringPrintf(dy, " INDEX(tName(%d),bin),\n", minLength); } else { if (noBin) { dyStringAppend(dy, " INDEX(tStart),\n"); dyStringAppend(dy, " INDEX(tEnd),\n"); } else dyStringAppend(dy, " INDEX(bin),\n"); } dyStringAppend(dy, " INDEX(id)\n"); dyStringAppend(dy, ")\n"); sqlRemakeTable(conn, track, dy->string); } dyStringClear(dy); sqlDyStringPrintf(dy, "load data local infile '%s' into table %s", tab, track); sqlUpdate(conn, dy->string); /* add a comment to the history table and finish up connection */ hgHistoryComment(conn, "Loaded %d chains into %s chain table", count, track); sqlDisconnect(&conn); } static void oneChain(struct chain *chain, FILE *linkFile, FILE *chainFile) /* Put one chain into tab delimited chain and link files. */ { int basesMatched = 0; struct cBlock *b; for (b = chain->blockList; b != NULL; b = b->next) { basesMatched += b->qEnd - b->qStart; writeLink(b, chain->tName, chain->id, linkFile); } writeChain(chain, chainFile, basesMatched); } static void hgLoadChain(char *database, char *track, char *fileName) /* hgLoadChain - Load a Chain file into database. */ { int count = 0; struct lineFile *lf ; struct chain *chain, *chainList = NULL; char chainFileName[] ="chain.tab"; char linkFileName[] ="link.tab"; FILE *chainFile = mustOpen(chainFileName,"w"); FILE *linkFile = mustOpen(linkFileName,"w"); char linkTrack[128]; sprintf(linkTrack, "%sLink",track); lf = lineFileOpen(fileName, TRUE); while ((chain = chainRead(lf)) != NULL) { if (noSort) { oneChain(chain, linkFile, chainFile); /* Freeing slows us down a bit but the purpose of the noSort option */ /* is to prevent us from running out of memory: */ chainFree(&chain); } else { slAddHead(&chainList, chain); } ++count; } if (!noSort) { slSort(&chainList, chainCmpTarget); for (chain = chainList; chain != NULL; chain = chain->next) oneChain(chain, linkFile, chainFile); /* chainFreeList(&chainList); */ /* This slows things way down, especially on * chromosome 19. I'm not sure if it's just * the usual slow Linux free on 100 million * items or so, or something else. It's a * good thing hgTracks uses lmAlloc on the * chain links it looks like! */ } fclose(chainFile); fclose(linkFile); if (!test) { verbose(1, "Loading %d chains into %s.%s\n", count, database, track); loadDatabaseChain(database, chainFileName, track, count); loadDatabaseLink(database, linkFileName, linkTrack); remove(chainFileName); remove(linkFileName); } } int main(int argc, char *argv[]) /* Process command line. */ { optionInit(&argc, argv, optionSpecs); if (argc != 4) usage(); noBin = optionExists("noBin"); noSort = optionExists("noSort"); oldTable = optionExists("oldTable"); normScore = optionExists("normScore"); sqlTable = optionVal("sqlTable", NULL); qPrefix = optionVal("qPrefix", NULL); test = optionExists("test"); tIndex = optionExists("tIndex"); hgLoadChain(argv[1], argv[2], argv[3]); return 0; }