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/splitFaIntoContigs/splitFaIntoContigs.c src/hg/splitFaIntoContigs/splitFaIntoContigs.c
index 810ef98..35aec33 100644
--- src/hg/splitFaIntoContigs/splitFaIntoContigs.c
+++ src/hg/splitFaIntoContigs/splitFaIntoContigs.c
@@ -440,39 +440,39 @@
 int sequenceNum = 0;
 
 do
     {
     endAgpData = nextAgpEntryToSplitOn(agpFile, dnaSize, &startAgpData);
     /* Point the end of the previous loop iteration's linked list at
        the start of this new one */
     if (NULL != prevAgpData)
 	{
 	prevAgpData->next = startAgpData;
 	startAgpData->prev = prevAgpData;
 	}
     prevAgpData = endAgpData;
 
     sequenceNum++;
-    sprintf(contigDir, "%s/%s_%d", destDir, startAgpData->data.pGap->chrom, sequenceNum);
+    safef(contigDir, sizeof contigDir, "%s/%s_%d", destDir, startAgpData->data.pGap->chrom, sequenceNum);
     makeDir(contigDir);
 
     sprintf(startAgpData->contigName, "%s_%d", startAgpData->data.pGap->chrom, sequenceNum);
 
-    sprintf(filename, "%s/%s_%d.fa", contigDir, startAgpData->data.pGap->chrom, sequenceNum);
+    safef(filename, sizeof filename, "%s/%s_%d.fa", contigDir, startAgpData->data.pGap->chrom, sequenceNum);
     writeSuperContigFaFile(dna, startAgpData, endAgpData, filename, sequenceNum);
 
-    sprintf(filename, "%s/%s_%d.agp", contigDir, startAgpData->data.pGap->chrom, sequenceNum);
+    safef(filename, sizeof filename, "%s/%s_%d.agp", contigDir, startAgpData->data.pGap->chrom, sequenceNum);
     writeSuperContigAgpFile(startAgpData, endAgpData, filename, sequenceNum);
 
     /* Save the start of the whole chromosome */
     if (NULL == startChromAgpData)
 	{
 	startChromAgpData = startAgpData;
 	}
     } while (endAgpData->data.pGap->chromEnd < dnaSize);
 
 return startChromAgpData;
 }
 
 void splitFaIntoContigs(char *agpFile, char *faFile)
 /* 
 splitFaIntoContigs - read the .agp file the .fa file. and split each
@@ -495,31 +495,31 @@
 /* For each chromosome entry */
 while (faMixedSpeedReadNext(lfFa, &dna, &dnaSize, &chromName))
     {
     printf("\nProcessing data for Chromosome: %s, size: %d\n", chromName, dnaSize);
 
     /* Make the output directory. Strip off the leading "chr" prefix.
        output filename = outputDir/chromName/chromFrag/chromFrag.xxx
        example:
        outputDir = "output"
        chromName = "chr1" - we strip off the "chr"
        chromFrag = "chr1_1"
        result    = "output/1/chr1_1/chr1_1.fa"
      */
 
 
-    sprintf(destDir, "%s/%s", outputDir, &chromName[3]);
+    safef(destDir, sizeof destDir, "%s/%s", outputDir, &chromName[3]);
     makeDir(destDir);
 
     startAgpData = makeSuperContigs(lfAgp, dna, dnaSize, destDir);
     writeChromFaFile(chromName, dna, dnaSize, destDir);
     writeChromAgpFile(chromName, startAgpData, destDir);
     writeLiftFiles(chromName, dnaSize, startAgpData, destDir);
 
     printf("Done processing chromosome %s\n", chromName);
     }
 
 printf("Done processing agpFile %s and fasta file %s, with nonbridged split boundaries of %d, bridged split boundaries of %d, absolute split boundaries of %d  bases\n", agpFile, faFile, _nSize, _bSize, _aSize);
 }
 
 int main(int argc, char *argv[])
 /*