61dc7885a5f1001e2bc189501379088f2b53379d
galt
  Mon Feb 23 15:42:36 2026 -0800
fixes things found automated codereview. for bigBedCmdSupport lib moved slAddHead, removed stray debugmsg and fixed comment and added static keyword. fixed bigChainToChain chromFound = FALSE, removed stray test makefile, fixed existing typo "tines", and added a missing space after issing space before optionMultiVal(). refs #37146

diff --git src/hg/utils/bigMafToMaf/bigMafToMaf.c src/hg/utils/bigMafToMaf/bigMafToMaf.c
index d9117bea71f..90c0847d0ed 100644
--- src/hg/utils/bigMafToMaf/bigMafToMaf.c
+++ src/hg/utils/bigMafToMaf/bigMafToMaf.c
@@ -1,181 +1,181 @@
 /* bigMafToMaf - convert bigMaf to maf file. */
 #include "common.h"
 #include "linefile.h"
 #include "hash.h"
 #include "bigBed.h"
 #include "basicBed.h"
 #include "options.h"
 #include "udc.h"
 #include "hdb.h"
 #include "bigBedCmdSupport.h"
 
 char *clChrom = NULL;
 int clStart = -1;
 int clEnd = -1;
 char *clBed = NULL;
 char *clPos = NULL;
 struct slName *clRange = NULL;
 struct hash *chromHash = NULL;
 boolean skipChromCheck = FALSE;
 
 struct lm *lm = NULL;
 
 void usage()
 /* Explain usage and exit. */
 {
 errAbort(
   "bigMafToMaf - convert bigMaf to maf file\n"
   "usage:\n"
   "   bigMafToMaf file.bigMaf file.maf\n"
   "options:\n"
   "   -chrom=chr1 - if set restrict output to given chromosome\n"
   "   -start=N - if set, restrict output to only that over start 0 based coordinate\n"
   "   -end=N - if set, restrict output to only that under end\n"
   "   -range=\"chrom start end\" - if set, restrict output to only that within range from start to end. \n"
   "          This range start is a half-open 0-based coordinate like used in BED files. \n"
   "   -range=chrom:start-end - if set, restrict output to only that within range from start to end. \n"
   "          This range start is a 1-based start position. \n"
   "    Do not use range with chrom, start, and/or end options. \n"
   "   -range may be specified multiple times for multiple ranges. \n"
   "   -bed=in.bed - restrict output to all regions in a BED file\n"
   "   -positions=in.pos - restrict output to all regions in a position file with 1-based start\n"
   "   -udcDir=/dir/to/cache - place to put cache for remote bigBed/bigWigs\n"
   "   -skipChromCheck - skip checking chrom name.\n"
   );
 }
 
 /* chunking keeps memory down */
 static int chunkSizeBases = 1048576;
 
 /* Command line validation table. */
 static struct optionSpec options[] = {
    {"chrom", OPTION_STRING},
    {"start", OPTION_INT},
    {"end", OPTION_INT},
    {"bed", OPTION_STRING},
    {"range", OPTION_STRING|OPTION_MULTI},
    {"positions", OPTION_STRING},
    {"udcDir", OPTION_STRING},
    {"skipChromCheck", OPTION_BOOLEAN},
    {NULL, 0},
 };
 
 static void writeMafAli(char *ptr, FILE *f)
 /* output one block, change ';'  back to newline */
 {
 for(; *ptr; ptr++)
     {
     if (*ptr == ';')
         fputc('\n', f);
     else
         fputc(*ptr, f);
     }
 fputc('\n', f);
 
 }
 
 static void processChromChunk(struct bbiFile *bbi, char *chrom,
                               int start, int end, char *bedName, FILE *f)
 /* Output one chunk.  Only blocks where start is in the range will be written
- * to avoid outputting a block multiple tines.  */
+ * to avoid outputting a block multiple times.  */
 {
 struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom,
                                                     start, end, 0, lm);
 for(; bbList; bbList = bbList->next)
     {
     if ((start <= bbList->start) && (bbList->start < end))
         writeMafAli(bbList->rest, f);
     }
 }
 
 void processChrom(struct bbiFile *bbi, struct bbiChromInfo *chrom,
                          FILE *f)
 /* output MAF blocks from one chrom */
 {
 int start = 0, end = chrom->size;
 if (clStart >= 0)
     {
     start = clStart;
     }
 if (clEnd >= 0)
     {
     end = clEnd;
     if (end > chrom->size)
 	end = chrom->size;
     }
 if (start > end)
     errAbort("invalid range, start=%d > end=%d", start, end);
 while (start < end)
     {
     int chunkEnd = min(start + chunkSizeBases, end);
     processChromChunk(bbi, chrom->name, start, chunkEnd, NULL, f);
     start = chunkEnd;
     }
 }
 
 static void bigMafToMaf(char *bigBed, char *mafFile)
 /* bigMafToMaf - convert bigMaf to maf file. */
 {
 struct bbiFile *bbi = bigBedFileOpen(bigBed);
 FILE *f = mustOpen(mafFile, "w");
 struct bbiChromInfo *chrom, *chromList = bbiChromList(bbi);
 if (!skipChromCheck)
     chromHash = makeChromHash(chromList);
 fprintf(f, "##maf version=1\n");
 
 if (clBed != NULL)
     {
     genericBigToNonBigFromBed(bbi, chromHash, clBed, f, &processChromChunk);
     }
 else if (clPos != NULL)
     {
     genericBigToNonBigFromPos(bbi, chromHash, clPos, f, &processChromChunk);
     }
 else if (clRange != NULL)
     {
     genericBigToNonBigFromRange(bbi, chromHash, f, clRange, &processChromChunk);
     }
 else
     {
     boolean chromFound = FALSE;
     for (chrom = chromList; chrom != NULL; chrom = chrom->next)
 	{
 	if (clChrom != NULL && !sameString(clChrom, chrom->name))
 	    continue;
 	chromFound = TRUE;
 	processChrom(bbi, chrom, f);
 	}
     if (clChrom && !chromFound && !skipChromCheck)
 	errAbort("specified chrom %s not found in bigMaf", clChrom);
     }
 bbiChromInfoFreeList(&chromList);
 carefulClose(&f);
 bbiFileClose(&bbi);
 }
 
 int main(int argc, char *argv[])
 /* Process command line. */
 {
 lm = lmInit(0);
 optionInit(&argc, argv, options);
 if (argc != 3)
     usage();
 udcSetDefaultDir(optionVal("udcDir", udcDefaultDir()));
 clChrom = optionVal("chrom", clChrom);
 clStart = optionInt("start", clStart);
 clEnd = optionInt("end", clEnd);
 clBed = optionVal("bed", clBed);
 clRange = optionMultiVal("range", clRange);
 clPos = optionVal("positions", clPos);
 skipChromCheck = optionExists("skipChromCheck");
 
 if ((clBed || clPos || clRange) && (clChrom || (clStart >= 0) || (clEnd >= 0)))
     errAbort("-bed or -positions or -range can not be used with -chrom -start or -end options");
 if ((clBed && clPos) || (clBed && clRange) || (clPos && clRange))
     errAbort("-bed, -positions, and -range can not be used together");
 
 bigMafToMaf(argv[1], argv[2]);
 
 lmCleanup(&lm);
 return 0;
 }