f952b14fca3833e9d8fef0ae8a086ad15485b552 galt Wed Jan 1 02:11:38 2025 -0800 fix various errors for utils compiled on Rocky 9 hgwdev-new. diff --git src/hg/mouseStuff/knownVsBlat/kvsSummary.c src/hg/mouseStuff/knownVsBlat/kvsSummary.c index 4b3d3f4..c6a446b 100644 --- src/hg/mouseStuff/knownVsBlat/kvsSummary.c +++ src/hg/mouseStuff/knownVsBlat/kvsSummary.c @@ -1,245 +1,252 @@ /* kvsSummary - Summarize output of a bunch of knownVsBlats. */ /* Copyright (C) 2011 The Regents of the University of California * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */ #include "common.h" #include "linefile.h" #include "hash.h" #include "cheapcgi.h" #include "blatStats.h" #define maxRuns 256 #define maxChroms 256 void usage() /* Explain usage and exit. */ { errAbort( "kvsSummary - Summarize output of a bunch of knownVsBlats\n" "usage:\n" " kvsSummary outputFile inputFile(s)\n" "options:\n" " -xxx=XXX\n" ); } struct chrom /* Keep track of one chromosome's data. */ { struct chrom *next; char *name; struct hash *statHash; /* Filled with stats. */ }; struct run /* Keep tabs on a single run. */ { struct run *next; char *name; /* Derived from file name. */ struct hash *chromHash; /* Filled with chrom's. */ }; void parseRatio(char *ratio, int *retP, int *retQ, char *fileName, int lineIx) /* Parse something that looks like p/q or (p/q) */ { char *words[3]; int wordCount; wordCount = chopString(ratio, "()/", words, ArraySize(words)); if (wordCount != 2) errAbort("Malformed ratio line %d of %s", lineIx, fileName); *retP = atoi(words[0]); *retQ = atoi(words[1]); } struct hash *readChromStats(struct lineFile *lf, struct hash *catHash, struct slName **pCatList) /* Read from next '-------' to blank line into a hash of stats and return. */ { char *line, *words[32]; char *s, *e; int i, wordCount; char *catName; struct oneStat *stat; struct hash *hash = newHash(5); for (;;) { if (!lineFileNext(lf, &line, NULL)) errAbort("Couldn't find '--------' line by end of %s.", lf->fileName); if (startsWith("--------", line)) break; } for (;;) { if (!lineFileNext(lf, &line, NULL)) { warn("Missing final blank line in %s", lf->fileName); break; } if ((line = skipLeadingSpaces(line)) == NULL || line[0] == 0) break; /* Parse line initially by inserting a few extra %'s */ for (s = line; s != NULL && s[0] != 0; s = e) { e = strchr(s, '%'); if (e != NULL) { /* Assume percentage is at end of number. Put * percentage in front of number too. */ char *p = e-1, c; for (;;) { c = *p; if (c != '.' && !isdigit(c)) break; --p; } *p = '%'; e += 1; } } /* Now parse more fully. */ wordCount = chopByChar(line, '%', words, ArraySize(words)); if (wordCount != 5) errAbort("Malformed line %d of %s", lf->lineIx, lf->fileName); for (i=0; i<wordCount; ++i) words[i] = trimSpaces(words[i]); catName = words[0]; if (!hashLookup(catHash, catName)) { struct slName *cat = newSlName(catName); slAddHead(pCatList, cat); hashAdd(catHash, catName, cat); } AllocVar(stat); hashAdd(hash, catName, stat); parseRatio(words[2], &stat->basesPainted, &stat->basesTotal, lf->fileName, lf->lineIx); parseRatio(words[4], &stat->hits, &stat->features, lf->fileName, lf->lineIx); } return hash; } struct hash *readRun(char *fileName, struct hash *allChromHash, struct chrom **pAllChromList, struct hash *catHash, struct slName **pCatList) /* Read a knownVsBlat file into a hash filled with chromosomes. */ { struct hash *chromHash = newHash(6); struct chrom *chrom; struct lineFile *lf = lineFileOpen(fileName, TRUE); char *line; char *chromName; while (lineFileNext(lf, &line, NULL)) { char *e; if ((e = stringIn(" stats:", line)) != NULL) { *e = 0; chromName = trimSpaces(line); if (!hashLookup(allChromHash, chromName)) { AllocVar(chrom); slAddHead(pAllChromList, chrom); hashAddSaveName(allChromHash, chromName, chrom, &chrom->name); } AllocVar(chrom); hashAddSaveName(chromHash, chromName, chrom, &chrom->name); chrom->statHash = readChromStats(lf, catHash, pCatList); } } lineFileClose(&lf); return chromHash; } void kvsSummary(char *outName, int inCount, char *inNames[]) /* kvsSummary - Summarize output of a bunch of knownVsBlats. */ { int i; struct hash *catHash = newHash(8); /* Catagory hash */ struct slName *catList = NULL, *cat; /* Catagory list. */ struct hash *allChromHash = newHash(0); /* Chromosome hash. */ struct chrom *chromList = NULL, *chrom; /* Chromosome list. */ struct hash *runHash = newHash(0); /* Which run this is in. */ struct run *runList = NULL, *run; /* Info about a run. */ -char runNameBuf[64], *runName; +char *runName; +char ext[FILEEXT_LEN]; +char fileName[FILENAME_LEN]; FILE *f = mustOpen(outName, "w"); /* Read input files into a bunch of hashes. */ for (i=0; i<inCount; ++i) { char *inName = inNames[i]; /* Figure out name of run from fileName - prefer suffix. */ - runName = runNameBuf; - runName[0] = 0; - splitPath(inName, NULL, NULL, runNameBuf); - if (runNameBuf[0] == 0) - splitPath(inName, NULL, runNameBuf, NULL); + ext[0] = 0; + splitPath(inName, NULL, NULL, ext); + if (ext[0] == 0) + { + splitPath(inName, NULL, fileName, NULL); + runName = fileName; + } else + { + runName = ext; runName += 1; + } AllocVar(run); slAddHead(&runList, run); hashAddSaveName(runHash, runName, run, &run->name); run->chromHash = readRun(inName, allChromHash, &chromList, catHash, &catList); } slReverse(&chromList); slReverse(&runList); slReverse(&catList); /* Write output. */ for (chrom = chromList; chrom != NULL; chrom = chrom->next) { /* Print header. */ fprintf(f, ">>>>==== %s totals ====<<<<\n", chrom->name); fprintf(f, "%-15s", "region"); for (run = runList; run != NULL; run = run->next) fprintf(f, " %10s", run->name); fprintf(f, "\n"); fprintf(f, "---------------"); for (run = runList; run != NULL; run = run->next) fprintf(f, "-----------"); fprintf(f, "\n"); /* Print fields. */ for (cat = catList; cat != NULL; cat = cat->next) { char *catName = cat->name; struct oneStat *stat; fprintf(f, "%-15s", catName); /* Print all runs on this field. */ for (run = runList; run != NULL; run = run->next) { struct chrom *c; boolean printed = FALSE; if ((c = hashFindVal(run->chromHash, chrom->name)) != NULL) { if ((stat = hashFindVal(c->statHash, cat->name)) != NULL) { char buf[16]; sprintf(buf, "%4.1f%%", divAsPercent(stat->basesPainted, stat->basesTotal)); fprintf(f, " %10s", buf); printed = TRUE; } } if (!printed) fprintf(f, " %10s", "n/a"); } fprintf(f, "\n"); } fprintf(f, "\n"); } } int main(int argc, char *argv[]) /* Process command line. */ { cgiSpoof(&argc, argv); if (argc < 3) usage(); kvsSummary(argv[1], argc-2, argv+2); return 0; }