198c9b8daecc44fbda6a6494c566c723920f030a
lrnassar
  Wed Mar 11 18:25:21 2026 -0700
Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM.

diff --git src/hg/affyTransciptome/maxTranscriptomeExps.c src/hg/affyTransciptome/maxTranscriptomeExps.c
index fd4a3c90a9a..725c46b2971 100644
--- src/hg/affyTransciptome/maxTranscriptomeExps.c
+++ src/hg/affyTransciptome/maxTranscriptomeExps.c
@@ -1,94 +1,94 @@
 /* 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 "sample.h"
 
 
 
 void usage()
 {
-errAbort("maxTranscriptomeExps - cycle through a list of of affy transcriptome\n"
+errAbort("maxTranscriptomeExps - cycle through a list of affy transcriptome\n"
 	 "experiments and select the max for each position.\n"
 	 "usage:\n\t"
 	 "maxTranscriptomeExps <outputfile> <trackName> <list of input files>\n");
 }
 
 
 void fillInMaxVals(struct sample *samp, struct sample **pSampList, int sampCount, int index)
 {
 int i,j;
 struct sample *s1 = NULL;
 for(i=0;i<sampCount; i++)
     {
     s1 = slElementFromIx(pSampList[i], index);
     for(j=0;j<samp->sampleCount; j++)
 	{
 	if(!(s1->samplePosition[j] == samp->samplePosition[j]))
 	    errAbort("maxTranscriptomeExps::fillInMaxVales() - for probe %s:%d-%d positions at index %i don't agree. %d, %d", 
 		     samp->chrom, samp->chromStart, samp->chromEnd, i, samp->samplePosition[j], s1->samplePosition[j]);
 	samp->sampleHeight[j] = max(samp->sampleHeight[j], s1->sampleHeight[j]);
 	}
     }
 }
 
 
 void maxTranscriptomeExps(char *files[], int numFiles, char *outputFile, char *trackName)
 {
 struct sample **pSampList = NULL;
 struct sample *s1;
 struct sample *maxListSamp  = NULL;
 struct sample *maxSamp = NULL;
 int i;
 int count =0;
 FILE *out = NULL;
 AllocArray(pSampList, numFiles);
 for(i=0;i<numFiles; i++)
  {
  warn("Reading %s.", files[i]);
  pSampList[i] = sampleLoadAll(files[i]);
  }
 
 warn("Calculating Maxes.");
 count = slCount(pSampList[0]);
 for(i=0;i<count;i++)
     {
     AllocVar(maxSamp);
     s1 = slElementFromIx(pSampList[0], i);
     maxSamp->chrom = cloneString(s1->chrom);
     maxSamp->chromStart = s1->chromStart;
     maxSamp->chromEnd = s1->chromEnd;
     maxSamp->name = cloneString(trackName);
     snprintf(maxSamp->strand, sizeof(maxSamp->strand), "%s", s1->strand);
     maxSamp->sampleCount = s1->sampleCount;
     maxSamp->samplePosition = CloneArray(s1->samplePosition, maxSamp->sampleCount);
     AllocArray(maxSamp->sampleHeight, maxSamp->sampleCount);
     fillInMaxVals(maxSamp, pSampList, numFiles, i);
     slAddHead(&maxListSamp, maxSamp);
     }
 slReverse(&maxListSamp);
 warn("Saving Maxes");
 out = mustOpen(outputFile, "w");
 for(maxSamp = maxListSamp; maxSamp != NULL; maxSamp = maxSamp->next)
     {
     sampleTabOut(maxSamp, out);
     }
 carefulClose(&out);
 warn("Cleaning up");
 sampleFreeList(&maxListSamp);
 for(i=0;i<numFiles; i++)
     sampleFreeList(&pSampList[i]);
 freez(&pSampList);
 warn("Done.");
 }
 
 int main(int argc, char *argv[])
 {
 if(argc < 4)
     usage();
 else
     maxTranscriptomeExps(argv+3, argc-3, argv[1], argv[2]);
 return 0;
 }