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/pslPseudo/checkExp/checkExp.c src/hg/pslPseudo/checkExp/checkExp.c index 29a97ae..92d81bc 100644 --- src/hg/pslPseudo/checkExp/checkExp.c +++ src/hg/pslPseudo/checkExp/checkExp.c @@ -1,725 +1,725 @@ /* checkExp - check if retroGene aligns better to parent or retroGene */ /* Copyright (C) 2011 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 "hash.h" #include "memalloc.h" #include "psl.h" #include "bed.h" #include "hdb.h" #include "axt.h" #include "dnautil.h" #include "dnaseq.h" #include "nib.h" #include "fa.h" #include "dlist.h" #include "dystring.h" #include "binRange.h" #include "options.h" #include "genePred.h" #include "genePredReader.h" #include "dystring.h" #include "pseudoGeneLink.h" #include "verbose.h" #include "chain.h" #include "twoBit.h" #include "chainToAxt.h" struct axtScoreScheme *ss = NULL; /* blastz scoring matrix */ struct dnaSeq *mrnaList = NULL; /* list of all input mrna sequences */ struct hash *pseudoHash = NULL, *mrnaHash = NULL, *chainHash = NULL, *faHash = NULL, *tHash = NULL; int maxGap = 100; struct dlList *fileCache = NULL; struct hash *nibHash = NULL; FILE *outFile = NULL; /* output tab sep file */ struct twoBitFile *twoBitFile = NULL; struct misMatch /* list of mismatches between gene and retrogene */ { struct misMatch *next; /* next in list. */ int retroLoc; /* genomic location of mismatch in retroGene */ int parentLoc; /* genomic location of mismatch in parent Gene */ char retroBase; /* contents of base in retroGene */ char parentBase; /* contents of base in parent gene */ }; struct cachedFile /* File in cache. */ { struct cachedFile *next; /* next in list. */ char *name; /* File name (allocated here) */ FILE *f; /* Open file. */ }; struct seqFilePos /* Where a sequence is in a file. */ { struct filePos *next; /* Next in list. */ char *name; /* Sequence name. Allocated in hash. */ char *file; /* Sequence file name, allocated in hash. */ long pos; /* Position in fa file/size of nib. */ bool isNib; /* True if a nib file. */ }; void usage() /* Print usage instructions and exit. */ { errAbort( "checkExp - check if retroGene aligns better to parent or retroGene \n" "usage:\n" " checkExp pseudoGeneLink.bed chrom.sizes all_mrna.psl target.lst mrna.2bit chrX_self.chain nibDir score.tab\n\n" "where \n" "pseudoGeneLink.bed is a list of retroGenes records \n" "chrom.sizes is a list of chromosome followed by size\n" "all_mrna.psl contains blat mRNA alignment file\n" "target.lst contains list nib files\n" "mrna.2bit contains fasta sequences of all mrnas \n" "chrX_self.chain blastz Self chain\n" "directory containing nibs for self alignment\n" "score.tab is output\n" ); } void writeGap(struct dyString *aRes, int aGap, char *aSeq, struct dyString *bRes, int bGap, char *bSeq) /* Write double - gap. Something like: * --c * ag- */ { dyStringAppendMultiC(aRes, '-', bGap); dyStringAppendN(bRes, bSeq, bGap); dyStringAppendN(aRes, aSeq, aGap); dyStringAppendMultiC(bRes, '-', aGap); } void writeInsert(struct dyString *aRes, struct dyString *bRes, char *aSeq, int gapSize) /* Write out gap, possibly shortened, to aRes, bRes. */ { dyStringAppendN(aRes, aSeq, gapSize); dyStringAppendMultiC(bRes, '-', gapSize); } struct hash *readChainToBinKeeper(char *sizeFileName, char *fileName) { struct binKeeper *bk; struct chain *chain; struct lineFile *lf = lineFileOpen(fileName, TRUE); struct lineFile *sf = lineFileOpen(sizeFileName, TRUE); struct hash *hash = newHash(0); char *chromRow[2]; while (lineFileRow(sf, chromRow)) { char *name = chromRow[0]; int size = lineFileNeedNum(sf, chromRow, 1); if (hashLookup(hash, name) != NULL) warn("Duplicate %s, ignoring all but first\n", name); else { bk = binKeeperNew(0, size); assert(size > 1); hashAdd(hash, name, bk); } } while ((chain = chainRead(lf)) != NULL) { bk = hashMustFindVal(hash, chain->tName); binKeeperAdd(bk, chain->tStart, chain->tEnd, chain); } lineFileClose(&lf); return hash; } struct dnaSeq *nibInfoLoadSeq(struct nibInfo *nib, int start, int size) /* Load in a sequence in mixed case from nib file. */ { return nibLdPartMasked(NIB_MASK_MIXED, nib->fileName, nib->f, nib->size, start, size); } struct dnaSeq *nibInfoLoadStrand(struct nibInfo *nib, int start, int end, char strand) /* Load in a mixed case sequence from nib file, from reverse strand if * strand is '-'. */ { struct dnaSeq *seq; int size = end - start; assert(size >= 0); if (strand == '-') { reverseIntRange(&start, &end, nib->size); seq = nibInfoLoadSeq(nib, start, size); reverseComplement(seq->dna, seq->size); } else { seq = nibInfoLoadSeq(nib, start, size); } return seq; } /* struct hash *readPslToHash(char *pslFileName) { int size; struct psl *psl; struct lineFile *pf = lineFileOpen(pslFileName , TRUE); struct hash *hash = newHash(0); char *chromRow[2]; char *row[21] ; } while (lineFileNextRow(pf, row, ArraySize(row))) { psl = pslLoad(row); if (hashFindVal(hash, psl->qName) == NULL) hashAdd(hash, name, psl); } lineFileClose(&pf); return hash; } */ struct dnaSeq *readSeqFromFaPos(struct seqFilePos *sfp, FILE *f) /* Read part of FA file. */ { struct dnaSeq *seq; fseek(f, sfp->pos, SEEK_SET); if (!faReadNext(f, "", TRUE, NULL, &seq)) errAbort("Couldn't faReadNext on %s in %s\n", sfp->name, sfp->file); return seq; } FILE *openFromCache(struct dlList *cache, char *fileName) /* Return open file handle via cache. The simple logic here * depends on not more than N files being returned at once. */ { static int maxCacheSize=32; int cacheSize = 0; struct dlNode *node; struct cachedFile *cf; /* First loop through trying to find it in cache, counting * cache size as we go. */ for (node = cache->head; !dlEnd(node); node = node->next) { ++cacheSize; cf = node->val; if (sameString(fileName, cf->name)) { dlRemove(node); dlAddHead(cache, node); return cf->f; } } /* If cache has reached max size free least recently used. */ if (cacheSize >= maxCacheSize) { node = dlPopTail(cache); cf = node->val; carefulClose(&cf->f); freeMem(cf->name); freeMem(cf); freeMem(node); } /* Cache new file. */ AllocVar(cf); cf->name = cloneString(fileName); cf->f = mustOpen(fileName, "rb"); dlAddValHead(cache, cf); return cf->f; } void readCachedSeqPart(char *seqName, int start, int size, struct hash *hash, struct dlList *fileCache, struct dnaSeq **retSeq, int *retOffset, boolean *retIsNib) /* Read sequence hopefully using file cashe. If sequence is in a nib * file just read part of it. */ { struct seqFilePos *sfp = hashMustFindVal(hash, seqName); FILE *f = openFromCache(fileCache, sfp->file); unsigned options = NIB_MASK_MIXED; if (sfp->isNib) { *retSeq = nibLdPartMasked(options, sfp->file, f, sfp->pos, start, size); *retOffset = start; *retIsNib = TRUE; } else { *retSeq = readSeqFromFaPos(sfp, f); *retOffset = 0; *retIsNib = FALSE; } } struct axt *axtCreate(char *q, char *t, int size, struct psl *psl) /* create axt */ { int qs = psl->qStart, qe = psl->qEnd; int ts = psl->tStart, te = psl->tEnd; int symCount = 0; struct axt *axt = NULL; AllocVar(axt); if (psl->strand[0] == '-') reverseIntRange(&qs, &qe, psl->qSize); if (psl->strand[1] == '-') reverseIntRange(&ts, &te, psl->tSize); axt->qName = cloneString(psl->qName); axt->tName = cloneString(psl->tName); axt->qStart = qs+1; axt->qEnd = qe; axt->qStrand = psl->strand[0]; axt->tStrand = '+'; if (psl->strand[1] != 0) { axt->tStart = ts+1; axt->tEnd = te; } else { axt->tStart = psl->tStart+1; axt->tEnd = psl->tEnd; } axt->symCount = symCount = strlen(t); axt->tSym = cloneString(t); if (strlen(q) != symCount) warn("Symbol count %d != %d inconsistent at t %s:%d and qName %s\n%s\n%s\n", symCount, (int)strlen(q), psl->tName, psl->tStart, psl->qName, t, q); axt->qSym = cloneString(q); axt->score = axtScoreFilterRepeats(axt, ss); verbose(1,"axt score = %d\n",axt->score); //for (i=0; i<size ; i++) // fputc(t[i],f); //for (i=0; i<size ; i++) // fputc(q[i],f); return axt; } struct axt *pslToAxt(struct psl *psl, struct hash *qHash, char *tNibDir, struct dlList *fileCache) { static char *tName = NULL, *qName = NULL; static struct dnaSeq *tSeq = NULL; struct dyString *q = newDyString(16*1024); struct dyString *t = newDyString(16*1024); int blockIx; int qs, ts ; int lastQ = 0, lastT = 0, size; int qOffset = 0; int tOffset = 0; struct axt *axt = NULL; boolean qIsNib = FALSE; boolean tIsNib = FALSE; int cnt = 0; //struct dnaSeq *tSeq = NULL; struct nibInfo *tNib = NULL; struct dnaSeq *qSeq = twoBitReadSeqFrag(twoBitFile, psl->qName, 0, 0); // hGenBankGetMrna(psl->qName, NULL); /* freeDnaSeq(&qSeq); freez(&qName); assert(mrnaList != NULL); for (mrna = mrnaList; mrna != NULL ; mrna = mrna->next) { assert(mrna != NULL); cnt++; if (sameString(mrna->name, psl->qName)) { qSeq = cloneDnaSeq(mrna); assert(qSeq != NULL); break; } } */ if (qSeq == NULL) { warn("mrna sequence data not found %s, searched %d sequences\n",psl->qName,cnt); dyStringFree(&q); dyStringFree(&t); dnaSeqFree(&tSeq); dnaSeqFree(&qSeq); return NULL; } if (qSeq->size != psl->qSize) { warn("sequence %s aligned is different size %d from mrna.fa file %d \n",psl->qName,psl->qSize,qSeq->size); dyStringFree(&q); dyStringFree(&t); dnaSeqFree(&tSeq); dnaSeqFree(&qSeq); return NULL; } qName = cloneString(psl->qName); if (qIsNib && psl->strand[0] == '-') qOffset = psl->qSize - psl->qEnd; else qOffset = 0; verbose(5,"qString len = %d qOffset = %d\n",qSeq->size,qOffset); if (tName == NULL || !sameString(tName, psl->tName) || tIsNib) { freeDnaSeq(&tSeq); freez(&tName); tName = cloneString(psl->tName); tNib = nibInfoFromCache(nibHash, tNibDir, tName); assert(tNib !=NULL); tSeq = nibInfoLoadStrand(tNib, psl->tStart, psl->tEnd, '+'); assert(tSeq !=NULL); tOffset = psl->tStart; //readCachedSeqPart(tName, psl->tStart, psl->tEnd-psl->tStart, // tHash, fileCache, &tSeq, &tOffset, &tIsNib); } verbose(4,"strand t %s \n",psl->strand); if (tSeq != NULL) verbose(5,"tString len = %d tOffset = %d\n",tSeq->size,tOffset); else errAbort("tSeq is NULL\n"); if (psl->strand[0] == '-') reverseComplement(qSeq->dna, qSeq->size); //if (strlen(psl->strand) > 1 ) // if (psl->strand[1] == '-') // reverseComplement(tSeq->dna, tSeq->size); for (blockIx=0; blockIx < psl->blockCount; ++blockIx) { qs = psl->qStarts[blockIx] - qOffset; ts = psl->tStarts[blockIx] - tOffset; if (blockIx != 0) { int qGap, tGap, minGap; qGap = qs - lastQ; tGap = ts - lastT; minGap = min(qGap, tGap); if (minGap > 0) { writeGap(q, qGap, qSeq->dna + lastQ, t, tGap, tSeq->dna + lastT); } else if (qGap > 0) { writeInsert(q, t, qSeq->dna + lastQ, qGap); } else if (tGap > 0) { writeInsert(t, q, tSeq->dna + lastT, tGap); } } size = psl->blockSizes[blockIx]; assert(qSeq != NULL); dyStringAppendN(q, qSeq->dna + qs, size); lastQ = qs + size; dyStringAppendN(t, tSeq->dna + ts, size); lastT = ts + size; } if (strlen(q->string) != strlen(t->string)) warn("Symbol count(t) %d != %d inconsistent at t %s:%d and qName %s\n%s\n%s\n", (int)strlen(t->string), (int)strlen(q->string), psl->tName, psl->tStart, psl->qName, t->string, q->string); if (psl->strand[0] == '-') { reverseComplement(q->string, q->stringSize); reverseComplement(t->string, t->stringSize); } axt = axtCreate(q->string, t->string, min(q->stringSize,t->stringSize), psl); dyStringFree(&q); dyStringFree(&t); //dnaSeqFree(&tSeq); dnaSeqFree(&qSeq); if (qIsNib) freez(&qName); //if (tIsNib) // freez(&tName); return axt; } struct misMatch *matchFound(struct misMatch **misMatchList, int retroLoc) { struct misMatch *el; for (el = *misMatchList; el != NULL ; el = el->next) { verbose(5,"%d == %d %c %c\n",el->retroLoc, retroLoc, el->retroBase, el->parentBase); if (el->retroLoc == retroLoc && el->retroBase != '-' && el->parentBase != '-') return el; } return NULL; } void addMisMatch(struct misMatch **misMatchList, struct axt *axt, int qSize) { int i; struct misMatch *misMatch = NULL; for (i = 0 ; i <= axt->symCount ; i++) { if (axt->tSym[i] != axt->qSym[i]) { /* check to see if we already have this one * if not, add it */ if (matchFound(misMatchList, axt->tStart+i) == NULL) { AllocVar(misMatch); misMatch->retroLoc = axt->tStart+i; if (axt->qStrand == '+') misMatch->parentLoc = axt->qStart+i; else misMatch->parentLoc = qSize-(axt->qStart+i); misMatch->retroBase = axt->tSym[i]; misMatch->parentBase = axt->qSym[i]; slAddHead(misMatchList, misMatch); verbose(5, "listLen = %d\n",slCount(misMatchList)); verbose(4,"add [%d] %d %d R %c P %c\n", i, misMatch->retroLoc , misMatch->parentLoc, misMatch->retroBase, misMatch->parentBase); } } else { verbose(8,"don't add [%d] %d \n",i, axt->tStart+i); } } } void checkExp(char *bedFileName, char *tNibDir, char *nibList) { struct lineFile *bf = lineFileOpen(bedFileName , TRUE), *af = NULL; char *row[PSEUDOGENELINK_NUM_COLS] ; struct pseudoGeneLink *ps; char *tmpName[512], cmd[512]; struct axt *axtList = NULL, *axt, *mAxt = NULL; struct dnaSeq *qSeq = NULL, *tSeq = NULL, *seqList = NULL; struct nibInfo *qNib = NULL, *tNib = NULL; FILE *op; int ret; if (nibHash == NULL) nibHash = hashNew(0); while (lineFileNextRow(bf, row, ArraySize(row))) { struct misMatch *misMatchList = NULL; struct binKeeper *bk = NULL; struct binElement *el, *elist = NULL; struct psl *mPsl = NULL, *rPsl = NULL, *pPsl = NULL, *psl ; struct misMatch *mf = NULL; ps = pseudoGeneLinkLoad(row); tmpName[0] = cloneString(ps->name); chopByChar(tmpName[0], '.', tmpName, sizeof(tmpName)); verbose(2,"name %s %s:%d-%d\n", ps->name, ps->chrom, ps->chromStart,ps->chromEnd); /* get expressed retro from hash */ bk = hashFindVal(mrnaHash, ps->chrom); elist = binKeeperFindSorted(bk, ps->chromStart, ps->chromEnd ) ; for (el = elist; el != NULL ; el = el->next) { rPsl = el->val; verbose(2,"retroGene %s %s:%d-%d\n",rPsl->qName, ps->chrom, ps->chromStart,ps->chromEnd); } /* find mrnas that overlap parent gene */ bk = hashFindVal(mrnaHash, ps->gChrom); elist = binKeeperFindSorted(bk, ps->gStart , ps->gEnd ) ; for (el = elist; el != NULL ; el = el->next) { pPsl = el->val; verbose(2,"parent %s %s:%d %d,%d\n", pPsl->qName, pPsl->tName,pPsl->tStart, pPsl->match, pPsl->misMatch); } /* find self chain */ bk = hashFindVal(chainHash, ps->chrom); elist = binKeeperFind(bk, ps->chromStart , ps->chromEnd ) ; slSort(&elist, chainCmpScoreDesc); for (el = elist; el != NULL ; el = el->next) { struct chain *chain = el->val, *subChain, *retChainToFree, *retChainToFree2; int qs = chain->qStart; int qe = chain->qEnd; int id = chain->id; if (chain->qStrand == '-') { qs = chain->qSize - chain->qEnd; qe = chain->qSize - chain->qStart; } if (!sameString(chain->qName , ps->gChrom) || !positiveRangeIntersection(qs, qe, ps->gStart, ps->gEnd)) { verbose(2," wrong chain %s:%d-%d %s:%d-%d parent %s:%d-%d\n", chain->qName, qs, qe, chain->tName,chain->tStart,chain->tEnd, ps->gChrom,ps->gStart,ps->gEnd); continue; } verbose(2,"chain id %d %4.0f",chain->id, chain->score); chainSubsetOnT(chain, ps->chromStart+7, ps->chromEnd-7, &subChain, &retChainToFree); if (subChain != NULL) chain = subChain; chainSubsetOnQ(chain, ps->gStart, ps->gEnd, &subChain, &retChainToFree2); if (subChain != NULL) chain = subChain; if (chain->qStrand == '-') { qs = chain->qSize - chain->qEnd; qe = chain->qSize - chain->qStart; } verbose(2," %s:%d-%d %s:%d-%d ", chain->qName, qs, qe, chain->tName,chain->tStart,chain->tEnd); if (subChain != NULL) verbose(2,"subChain %s:%d-%d %s:%d-%d\n", subChain->qName, subChain->qStart, subChain->qEnd, subChain->tName,subChain->tStart,subChain->tEnd); qNib = nibInfoFromCache(nibHash, tNibDir, chain->qName); tNib = nibInfoFromCache(nibHash, tNibDir, chain->tName); tSeq = nibInfoLoadStrand(tNib, chain->tStart, chain->tEnd, '+'); qSeq = nibInfoLoadStrand(qNib, chain->qStart, chain->qEnd, chain->qStrand); axtList = chainToAxt(chain, qSeq, chain->qStart, tSeq, chain->tStart, maxGap, BIGNUM); verbose(2,"axt count %d misMatch cnt %d\n",slCount(axtList), slCount(misMatchList)); for (axt = axtList; axt != NULL ; axt = axt->next) { addMisMatch(&misMatchList, axt, chain->qSize); } verbose(2,"%d in mismatch list %s id %d \n",slCount(misMatchList), chain->qName, id); chainFree(&retChainToFree); chainFree(&retChainToFree2); break; } /* create axt of each expressed retroGene to parent gene */ /* get alignment for each mrna overlapping retroGene */ bk = hashFindVal(mrnaHash, ps->chrom); elist = binKeeperFindSorted(bk, ps->chromStart , ps->chromEnd ) ; { char queryName[512]; char axtName[512]; char pslName[512]; safef(queryName, sizeof(queryName), "/tmp/query.%s.fa", ps->chrom); safef(axtName, sizeof(axtName), "/tmp/tmp.%s.axt", ps->chrom); safef(pslName, sizeof(pslName), "/tmp/tmp.%s.psl", ps->chrom); op = fopen(pslName,"w"); for (el = elist ; el != NULL ; el = el->next) { psl = el->val; pslOutput(psl, op, '\t','\n'); qSeq = twoBitReadSeqFrag(twoBitFile, psl->qName, 0, 0); if (qSeq != NULL) slAddHead(&seqList, qSeq); else errAbort("seq %s not found \n", psl->qName); } fclose(op); faWriteAll(queryName, seqList); safef(cmd,sizeof(cmd),"pslPretty -long -axt %s %s %s %s",pslName , nibList, queryName, axtName); ret = system(cmd); if (ret != 0) errAbort("ret is %d %s\n",ret,cmd); verbose(2, "ret is %d %s\n",ret,cmd); af = lineFileOpen(axtName, TRUE); while ((axt = axtRead(af)) != NULL) slAddHead(&mAxt, axt); lineFileClose(&af); } slReverse(&mAxt); /* for each parent/retro pair, count bases matching retro and parent better */ for (el = elist; el != NULL ; el = el->next) { int i, scoreRetro=0, scoreParent=0, scoreNeither=0; struct dyString *parentMatch = newDyString(16*1024); struct dyString *retroMatch = newDyString(16*1024); mPsl = el->val; if (mAxt != NULL) { verbose(2,"mrna %s %s:%d %d,%d axt %s\n", mPsl->qName, mPsl->tName,mPsl->tStart, mPsl->match, mPsl->misMatch, mAxt->qName); assert(sameString(mPsl->qName, mAxt->qName)); for (i = 0 ; i< (mPsl->tEnd-mPsl->tStart) ; i++) { int j = mAxt->tStart - mPsl->tStart; verbose(5, "listLen = %d\n",slCount(&misMatchList)); if ((mf = matchFound(&misMatchList, (mPsl->tStart)+i)) != NULL) { if (toupper(mf->retroBase) == toupper(mAxt->qSym[j+i])) { verbose (3,"match retro[%d] %d %c == %c parent %c %d\n", i,mf->retroLoc, mf->retroBase, mAxt->qSym[j+i], mf->parentBase, mf->parentLoc); dyStringPrintf(retroMatch, "%d,", mf->retroLoc); scoreRetro++; } else if (toupper(mf->parentBase) == toupper(mAxt->qSym[j+i])) { verbose (3,"match parent[%d] %d %c == %c retro %c %d\n", i,mf->parentLoc, mf->parentBase, mAxt->qSym[j+i], mf->retroBase, mf->retroLoc); dyStringPrintf(parentMatch, "%d,", mf->parentLoc); scoreParent++; } else { verbose (3,"match neither[%d] %d %c != %c retro %c %d\n", i,mf->parentLoc, mf->parentBase, mAxt->tSym[j+i], mf->retroBase, mf->retroLoc); scoreNeither++; } } } verbose(2,"final score %s parent %d retro %d neither %d\n", mPsl->qName, scoreParent, scoreRetro, scoreNeither); fprintf(outFile,"%s\t%d\t%d\t%s\t%d\t%s\t%d\t%d\t%s\t%d\t%d\t%d\t%s\t%s\n", ps->chrom, ps->chromStart, ps->chromEnd, ps->name, ps->score, mPsl->tName, mPsl->tStart, mPsl->tEnd, mPsl->qName, scoreParent, scoreRetro, scoreNeither, parentMatch->string, retroMatch->string); mAxt = mAxt->next; } dyStringFree(&parentMatch); dyStringFree(&retroMatch); } } } int main(int argc, char *argv[]) /* Process command line. */ { optionHash(&argc, argv); if (argc != 9) usage(); fileCache = newDlList(); maxGap = optionInt("maxGap", maxGap); verboseSetLogFile("stdout"); ss = axtScoreSchemeDefault(); verbose(1,"Reading alignments from %s\n",argv[3]); mrnaHash = readPslToBinKeeper(argv[2], argv[3]); twoBitFile = twoBitOpen(argv[5]); //verbose(1,"Reading alignments from %s\n",argv[]); //pseudoHash = readPslToBinKeeper(argv[3], argv[]); //verbose(1,"Reading mRNA sequences from %s\n",argv[5]); //mrnaList = faReadAllMixed(argv[5]); //if (mrnaList == NULL) //errAbort("could not open %s\n",argv[5]); //faHash = newHash(0); //for (el = mrnaList; el != NULL ; el = el->next) //hashAdd(faHash, el->name, el); verbose(1,"Reading chains from %s\n",argv[6]); chainHash = readChainToBinKeeper(argv[2], argv[6]); outFile = fopen(argv[8],"w"); verbose(1,"Scoring %s\n",argv[1]); checkExp(argv[1], argv[7], argv[4]); fclose(outFile); freeDnaSeqList(&mrnaList); return(0); }