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/oneShot/clonePos/clonePos.c src/hg/oneShot/clonePos/clonePos.c index f0b0d08..bb1aaea 100644 --- src/hg/oneShot/clonePos/clonePos.c +++ src/hg/oneShot/clonePos/clonePos.c @@ -1,241 +1,241 @@ /* clonePos.c - create table for clonePos. */ /* 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 "portable.h" #include "hash.h" #include "jksql.h" #include "hdb.h" #include "psl.h" #include "glDbRep.h" char *mapFile = "/projects/compbio/experiments/hg/clonemap.wu/jun15a.wu"; char *infFile = "/projects/cc/hg/gs.2/ffa/sequence.inf"; char *posName = "clonePos.tab"; char *aliName = "cloneAliPos.tab"; void usage() /* Explain usage and exit. */ { errAbort( "clonePos - make clonePos and cloneAliPos tables\n" "usage:\n" " clonePos here\n" "This will make clonePos.tab and cloneAliPos.tab in the current dir"); } struct cloneInfo /* Info on one clone. */ { struct cloneInfo *next; /* Next in list. */ char *name; /* Name of clone. */ int size; /* Clone size. */ int phase; /* HTG Phase. */ struct clonePos *pos; /* Position in chromosome. */ struct clonePos *aliPos; /* Position of alignment in chromosome. */ }; struct clonePos /* Position of a clone. */ { struct clonePos *next; /* Next in list. */ struct cloneInfo *info; /* Info about clone. */ int start, end; /* Offset within contig. */ }; int cmpClonePos(const void *va, const void *vb) /* Compare two slNames. */ { const struct clonePos *a = *((struct clonePos **)va); const struct clonePos *b = *((struct clonePos **)vb); return a->start - b->start; } void readSeqInfo(char *fileName, struct hash **pHash, struct cloneInfo **pList) /* Read info about clones. */ { struct lineFile *lf; struct hash *hash = newHash(16); struct hashEl *hel; struct cloneInfo *infoList = NULL, *info; int lineSize, wordCount; char *line, *words[16]; char *acc; char c; lf = lineFileOpen(fileName, TRUE); if (!lineFileNext(lf, &line, &lineSize)) errAbort("Empty %s", fileName); if (!startsWith("#Accession.ver", line)) errAbort("Unrecognized format on %s", fileName); while (lineFileNext(lf, &line, &lineSize)) { if (line[0] == '#') continue; wordCount = chopLine(line,words); if (wordCount != 8) errAbort("Expecting 8 words line %d of %s", lf->lineIx, lf->fileName); AllocVar(info); acc = words[0]; if (hashLookup(hash, acc) != NULL) errAbort("Duplicate %s line %d of %s", acc, lf->lineIx, lf->fileName); hel = hashAdd(hash, acc, info); info->name = hel->name; info->size = atoi(words[2]); if (info->size == 0) errAbort("Expecting clone size field 2 of line %d of %s", lf->lineIx, lf->fileName); c = words[3][0]; if (c == '0' || c == '1' || c == '2' || c == '3') info->phase = atoi(words[3]); else errAbort("Expecting phase field 3 of line %d of %s", lf->lineIx, lf->fileName); slAddHead(&infoList, info); } lineFileClose(&lf); slReverse(&infoList); *pList = infoList; *pHash = hash; } struct cloneInfo *findClone(struct hash *cloneHash, char *name) /* Find named clone in hash table. */ { struct hashEl *hel; if ((hel = hashLookup(cloneHash, name)) == NULL) errAbort("Clone %s is not in %s", name, infFile); return hel->val; } void fragNameToCloneName(char *cloneName) /* Chop off suffix to get clone name. */ { char *s = strchr(cloneName, '_'); if (s != NULL) *s = 0; } void writePosList(char *fileName, struct clonePos *posList, char *chromName) /* Write out tab-delimited position list. */ { struct clonePos *pos; struct cloneInfo *info; FILE *f = mustOpen(fileName, "w"); printf("Writing %d entries to %s\n", slCount(posList), fileName); for (pos = posList; pos != NULL; pos = pos->next) { info = pos->info; fprintf(f, "%s\t%d\t%d\t%s\t%d\t%d\n", info->name, info->size, info->phase, chromName, pos->start, pos->end); } fclose(f); } void clonePosTab(char *fileName, struct hash *cloneHash) /* Write out clonePos.tab. */ { char query[256]; struct sqlResult *sr; char **row; struct clonePos *posList = NULL, *pos; struct gl gl; struct cloneInfo *info; struct sqlConnection *conn = hAllocConn(); sqlSafef(query, sizeof query, "select * from chr18_gl"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { glStaticLoad(row, &gl); fragNameToCloneName(gl.frag); info = findClone(cloneHash, gl.frag); if ((pos = info->pos) == NULL) { AllocVar(pos); pos->info = info; info->pos = pos; pos->start = gl.start; pos->end = gl.end; slAddHead(&posList, pos); } else { if (pos->start > gl.start) pos->start = gl.start; if (pos->end < gl.end) pos->end = gl.end; } } sqlFreeResult(&sr); hFreeConn(&conn); slSort(&posList, cmpClonePos); writePosList(fileName, posList, "chr18"); } void cloneAliPosTab(char *fileName, struct hash *cloneHash) /* Write out clonePos.tab. */ { char query[256]; struct sqlResult *sr; char **row; struct clonePos *posList = NULL, *pos; struct cloneInfo *info; struct sqlConnection *conn = hAllocConn(); sqlSafef(query, sizeof query, "select * from chr18_frags"); sr = sqlGetResult(conn, query); while ((row = sqlNextRow(sr)) != NULL) { struct psl *psl = pslLoad(row); fragNameToCloneName(psl->qName); info = findClone(cloneHash, psl->qName); if ((pos = info->aliPos) == NULL) { AllocVar(pos); pos->info = info; info->aliPos = pos; pos->start = psl->tStart; pos->end = psl->tEnd; slAddHead(&posList, pos); } else { if (pos->start > psl->tStart) pos->start = psl->tStart; if (pos->end < psl->tEnd) pos->end = psl->tEnd; } pslFree(&psl); } sqlFreeResult(&sr); hFreeConn(&conn); slSort(&posList, cmpClonePos); writePosList(fileName, posList, "chr18"); } void clonePos() /* create tables for clonePos. */ { struct cloneInfo *infoList, *info; struct clonePos *aliList, *posList, *pos; struct hash *cloneHash; uglyf("mysqlHost is %s\n", mysqlHost()); readSeqInfo(infFile, &cloneHash, &infoList); clonePosTab(posName, cloneHash); cloneAliPosTab(aliName, cloneHash); } int main(int argc, char *argv[]) { if (argc != 2) usage(); clonePos(); }