1b20a1774021cdcb07303801d55b7ca3fa6cff09
braney
  Wed Jan 8 05:54:20 2025 -0800
fix up chop functions so they don't call ArraySize with NULL

diff --git src/hg/hgPhyloPlace/phyloPlace.c src/hg/hgPhyloPlace/phyloPlace.c
index 1314d28..bae73ed 100644
--- src/hg/hgPhyloPlace/phyloPlace.c
+++ src/hg/hgPhyloPlace/phyloPlace.c
@@ -516,31 +516,31 @@
 struct seqInfo *seqInfoList = NULL;
 struct slName *sampleIds = NULL;
 struct errCatch *errCatch = errCatchNew();
 if (errCatchStart(errCatch))
     {
     char *line;
     int lineSize;
     int sampleCount = 0;
     while (lineFileNext(lf, &line, &lineSize))
         {
         if (startsWith("#CHROM\t", line))
             {
             //#*** TODO: if the user uploads a sample with the same ID as one already in the
             //#*** saved assignment file, then usher will ignore it!
             //#*** Better check for that and warn the user.
-            int colCount = chopTabs(line, NULL);
+            int colCount = chopTabsLen(line);
             if (colCount == 1)
                 {
                 lineFileAbort(lf, "VCF requires tab-separated columns, but no tabs found");
                 }
             sampleCount = colCount - VCF_NUM_COLS_BEFORE_GENOTYPES;
             if (sampleCount < 1 || sampleCount > maxGenotypes)
                 {
                 if (sampleCount < 1)
                     lineFileAbort(lf, "VCF header #CHROM line has %d columns; expecting at least %d "
                                   "columns including sample IDs for genotype columns",
                                   colCount, 10);
                 else
                     lineFileAbort(lf, "VCF header #CHROM line defines %d samples but only up to %d "
                                   "are supported",
                                   sampleCount, maxGenotypes);
@@ -570,31 +570,31 @@
             fputs(line, f);
             fputc('\n', f);
             }
         else if (line[0] == '#')
             {
             fputs(line, f);
             fputc('\n', f);
             }
         else
             {
             if (sampleCount < 1)
                 {
                 lineFileAbort(lf, "VCF header did not include #CHROM line defining sample IDs for "
                               "genotype columns");
                 }
-            int colCount = chopTabs(line, NULL);
+            int colCount = chopTabsLen(line);
             int genotypeCount = colCount - VCF_NUM_COLS_BEFORE_GENOTYPES;
             if (genotypeCount != sampleCount)
                 {
                 lineFileAbort(lf, "VCF header defines %d samples but there are %d genotype columns",
                               sampleCount, genotypeCount);
                 }
             char *words[colCount];
             chopTabs(line, words);
             //#*** TODO: check that POS is sorted
             int pos = strtol(words[1], NULL, 10);
             if (pos > refGenome->size)
                 {
                 lineFileAbort(lf, "VCF POS value %d exceeds size of reference sequence (%d)",
                               pos, refGenome->size);
                 }