e505f514d7b741bb400ac03d81cd5ce4b778a00c galt Tue Dec 31 23:56:47 2024 -0800 minor compiler fix for hgClonePos. diff --git src/hg/makeDb/hgClonePos/hgClonePos.c src/hg/makeDb/hgClonePos/hgClonePos.c index 0ad0553..97bb5f6 100644 --- src/hg/makeDb/hgClonePos/hgClonePos.c +++ src/hg/makeDb/hgClonePos/hgClonePos.c @@ -1,358 +1,358 @@ /* hgClonePos - create clonePos table in browser database. */ /* Copyright (C) 2013 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "portable.h" #include "linefile.h" #include "dystring.h" #include "hash.h" #include "hCommon.h" #include "jksql.h" #include "glDbRep.h" #include "clonePos.h" #include "gsSeqInfo.h" #include "options.h" void usage() /* Explain usage and exit. */ { errAbort( "hgClonePos - create clonePos table in browser database\n" "usage:\n" " hgClonePos [options] database ooDir ffa/sequence.inf gsDir\n" "options:\n" " -chromLst=chrom.lst - chromosomes subdirs are named in chrom.lst (1, 2, ...)\n" " -maxErr=N set maximum allowed errors before aborting (default 0)\n" " -maxWarn=N set maximum number of warnings to print (default 10)\n" " -verbose=N set verbose level to N\n" "example:\n" " cd /cluster/store5/gs.18/build35\n" " hgClonePos -chromLst=chrom.lst hg17 build35 ./sequence.inf \\\n" " /cluster/store5/gs.18 -maxErr=3 -maxWarn=2000"); } int maxErr = 0; int maxWarn = 10; void addCloneInfo(char *glFileName, struct hash *cloneHash, struct clonePos **pCloneList) /* Add in clone info from one .gl file. */ { -char dir[256], chrom[128], ext[64]; +char dir[PATH_LEN], chrom[FILENAME_LEN], ext[FILEEXT_LEN]; struct gl gl; struct lineFile *lf = lineFileOpen(glFileName, TRUE); struct clonePos *clone; char *line, *words[8]; int lineSize, wordCount; char cloneVerName[128]; char cloneName[128]; printf("Processing %s\n", glFileName); splitPath(glFileName, dir, chrom, ext); while (lineFileNext(lf, &line, &lineSize)) { wordCount = chopLine(line, words); if (wordCount == 0) continue; if (wordCount != 4) errAbort("Expecting %d words line %d of %s", 4, lf->lineIx, lf->fileName); glStaticLoad(words, &gl); fragToCloneVerName(gl.frag, cloneVerName); fragToCloneName(gl.frag, cloneName); if ((clone = hashFindVal(cloneHash, cloneName)) == NULL) { AllocVar(clone); clone->name = cloneString(cloneVerName); clone->chrom = cloneString(chrom); clone->chromStart = gl.start; clone->chromEnd = gl.end; clone->faFile = cloneString(""); slAddHead(pCloneList, clone); hashAdd(cloneHash, cloneName, clone); } else { if (!sameString(clone->chrom, chrom)) { warn("Clone %s is on chromosomes %s and %s. Ignoring %s", cloneName, clone->chrom, chrom, chrom); continue; } if (clone->chromStart > gl.start) clone->chromStart = gl.start; if (clone->chromEnd < gl.end) clone->chromEnd = gl.end; } } lineFileClose(&lf); } int cmpClonePos(const void *va, const void *vb) /* Compare to sort based on chromosome and chromStart. */ { const struct clonePos *a = *((struct clonePos **)va); const struct clonePos *b = *((struct clonePos **)vb); int dif; dif = strcmp(a->chrom, b->chrom); if (dif == 0) dif = a->chromStart - b->chromStart; return dif; } struct clonePos *readClonesFromOoDir(char *ooDir, struct hash *cloneHash) /* Read in clones from ooDir. */ { struct clonePos *cloneList = NULL; struct fileInfo *chrFiList = NULL, *chrFi; struct fileInfo *glFiList = NULL, *glFi; char pathName[512]; struct hash *chromDirHash = newHash(4); char *chromLst = optionVal("chromLst", NULL); if (chromLst != NULL) { struct lineFile *clf = lineFileOpen(chromLst, TRUE); char *row[1]; while (lineFileRow(clf, row)) { hashAdd(chromDirHash, row[0], NULL); verbose(3,"%s\n",row[0]); } lineFileClose(&clf); } verbose(2,"ooDir: %s\n",ooDir); chrFiList = listDirX(ooDir, "*", FALSE); for (chrFi = chrFiList; chrFi != NULL; chrFi = chrFi->next) { verbose(2,"%s\n",chrFi->name); if ( ((chrFi->isDir && strlen(chrFi->name) <= 2)) || hashLookup(chromDirHash, chrFi->name) ) { sprintf(pathName, "%s/%s", ooDir, chrFi->name); verbose(2,"%s\n",pathName); glFiList = listDirX(pathName, "*.gl", TRUE); for (glFi = glFiList; glFi != NULL; glFi = glFi->next) addCloneInfo(glFi->name, cloneHash, &cloneList); slFreeList(&glFiList); } } slFreeList(&chrFiList); slReverse(&cloneList); slSort(&cloneList, cmpClonePos); if (slCount(cloneList) < 0) errAbort("No .gl files in %s\n", ooDir); printf("Got %d clones\n", slCount(cloneList)); hashFree(&chromDirHash); return cloneList; } void addStageInfo(char *gsDir, struct hash *cloneHash) /* Add info about which file and what stage clone is in. */ /* TSF - This is no longer used due to unavailability of *.finf files - 4/7/2003 */ { static char *finfFiles[] = {"ffa/finished.finf", "ffa/draft.finf", "ffa/predraft.finf", "ffa/extras.finf"}; static char stages[] = "FDPD"; struct lineFile *lf; char *line; char *words[7]; int numStages = strlen(stages); int i; char pathName[512]; char *finfFile, stage; int warnsLeft = maxWarn; /* Only show first maxWarn warnings about missing clones. */ char cloneName[256]; struct clonePos *clone; int wordCount, cloneCount; for (i=0; i<numStages; ++i) { finfFile = finfFiles[i]; stage = stages[i]; sprintf(pathName, "%s/%s", gsDir, finfFile); printf("Processing %s\n", pathName); lf = lineFileOpen(pathName, TRUE); cloneCount = 0; while (lineFileNext(lf, &line, NULL)) { wordCount = chopLine(line, words); assert(wordCount == 7); strncpy(cloneName, words[1], sizeof(cloneName)); chopSuffix(cloneName); if ((clone = hashFindVal(cloneHash, cloneName)) == NULL) { if (warnsLeft > 0) { --warnsLeft; warn("%s is in %s but not in ooDir/*/*.gl", cloneName, pathName); } else if (warnsLeft == 0) { --warnsLeft; warn("(Truncating additional warnings)"); } continue; } clone->stage[0] = stage; cloneCount++; } lineFileClose(&lf); printf("Got %d clones in %s\n", cloneCount, pathName); } } void addSeqInfo(char *seqInfoName, struct hash *cloneHash) /* Add in information from sequence.info file. */ /* TSF - stage info now being derived from here - 4/7/2003 */ { struct lineFile *lf = lineFileOpen(seqInfoName, TRUE); char *line, *words[16]; int lineSize, wordCount; struct clonePos *clone; struct gsSeqInfo gs; int warnsLeft = maxWarn; /* Only show first maxWarn warnings about missing clones. */ static char stages[] = "PPDF"; printf("Processing %s\n", seqInfoName); while (lineFileNext(lf, &line, &lineSize)) { if (line[0] == '#') continue; wordCount = chopLine(line, words); if (wordCount == 0) continue; if (wordCount < 8) errAbort("Expecting 8 words line %d of %s", lf->lineIx, lf->fileName); gsSeqInfoStaticLoad(words, &gs); /* TSF - Phase 0 clones now included in contig_overlaps.agp 4/23/2003 */ /*if (gs.phase != 0) {*/ chopSuffix(gs.acc); if ((clone = hashFindVal(cloneHash, gs.acc)) == NULL) { if (warnsLeft > 0) { --warnsLeft; warn("%s is in %s but not in ooDir/*/*.gl", gs.acc, seqInfoName); } else if (warnsLeft == 0) { --warnsLeft; warn("(Truncating additional warnings)"); } continue; } clone->seqSize = gs.size; clone->phase = gs.phase; clone->stage[0] = stages[atoi(words[3])]; /* } */ } lineFileClose(&lf); } void checkClonePos(struct clonePos *cloneList) /* Make sure that all necessary bits of cloneList are filled in. */ { struct clonePos *clone; int errCount = 0; for (clone = cloneList; clone != NULL; clone = clone->next) { if (clone->seqSize == 0) { if (errCount < 20) warn("Missing size info on %s (not in sequence.inf)", clone->name); ++errCount; } if (clone->stage[0] == 0) { if (errCount < 20) warn("Missing stage info on %s (not in *.finf)", clone->name); clone->stage[0] = 'D'; ++errCount; } } if (errCount > maxErr) { errAbort("Aborting with %d errors\n", errCount); } } void saveClonePos(struct clonePos *cloneList, char *database) /* Save sorted clone position list to database. */ { struct sqlConnection *conn = sqlConnect(database); struct clonePos *clone; struct tempName tn; FILE *f; struct dyString *ds = dyStringNew(2048); /* Create tab file from clone list. */ printf("Creating tab file\n"); makeTempName(&tn, "hgCP", ".tab"); f = mustOpen(tn.forCgi, "w"); for (clone = cloneList; clone != NULL; clone = clone->next) clonePosTabOut(clone, f); fclose(f); /* Create table if it doesn't exist, delete whatever is * already in it, and fill it up from tab file. */ printf("Loading clonePos table\n"); char query[1024]; sqlSafef(query, sizeof query, "CREATE TABLE clonePos (\n" " name varchar(255) not null, # Name of clone including version\n" " seqSize int unsigned not null, # base count not including gaps\n" " phase tinyint unsigned not null, # htg phase\n" " chrom varchar(255) not null, # Chromosome name\n" " chromStart int unsigned not null, # Start in chromosome\n" " chromEnd int unsigned not null, # End in chromosome\n" " stage char(1) not null, # F/D/P for finished/draft/predraft\n" " faFile varchar(255) not null, # File with sequence.\n" " #Indices\n" " INDEX(name(12)),\n" " INDEX(chrom(12),chromStart)\n" ")\n"); sqlMaybeMakeTable(conn, "clonePos", query); sqlSafef(query, sizeof query, "DELETE from clonePos"); sqlUpdate(conn, query); sqlDyStringPrintf(ds, "LOAD data local infile '%s' into table clonePos", tn.forCgi); sqlUpdate(conn, ds->string); /* Clean up. */ remove(tn.forCgi); sqlDisconnect(&conn); } void hgClonePos(char *database, char *ooDir, char *seqInfoName, char *gsDir) /* hgClonePos - create clonePos table in browser database. */ { struct hash *cloneHash = newHash(16); struct clonePos *cloneList = NULL; cloneList = readClonesFromOoDir(ooDir, cloneHash); /* addStageInfo(gsDir, cloneHash); */ addSeqInfo(seqInfoName, cloneHash); checkClonePos(cloneList); saveClonePos(cloneList, database); freeHash(&cloneHash); clonePosFreeList(&cloneList); } int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); if (argc != 5) usage(); maxErr = optionInt("maxErr", maxErr); maxWarn = optionInt("maxWarn", maxWarn); hgClonePos(argv[1], argv[2], argv[3], argv[4]); return 0; }