99eb74885ff5bce42cadafee93274df7039dcab5
braney
  Sat Sep 26 17:34:11 2026 -0700
unit tests for four v503 tickets, refs #38391, #37262, #38120, #38107, #38125, #38154

cgiDecodeTest prints what malformed and cut-short %hh escapes decode to, and
checks that cgiDecode never reads past the length it is given.  udcDotsTest
prints the cache directory udc makes for remote URLs with "." and ".." in
them, including the ones that must abort.  pngWriteTest writes a memGfx image
as a PNG, reads it back with libpng, compares every pixel, and checks the row
filter of every row.  pgSnpManyAllelesTester builds per-allele counts from a
VCF record with 150 ALT alleles.

Each test fails with its fix backed out, except that zlib-ng was not swapped
out for #38125.  The test registry gets a row for each ticket.

diff --git src/hg/lib/tests/pgSnpManyAllelesTester.c src/hg/lib/tests/pgSnpManyAllelesTester.c
new file mode 100644
index 00000000000..e159f1dc28a
--- /dev/null
+++ src/hg/lib/tests/pgSnpManyAllelesTester.c
@@ -0,0 +1,60 @@
+/* pgSnpManyAllelesTester - check the allele counts pgSnp takes from a VCF record with many
+ * alleles.
+ *
+ * pgSnpFromVcfRecord() turns the AN and AC INFO fields into one count per allele.  It used to
+ * collect them in a fixed array of 80, and a repeat site can have hundreds of alleles: the
+ * Japan ToMMo 61k VCF on hg38 crashed hgTracks this way.  This test reads a VCF whose middle
+ * record has 150 ALT alleles, each with its own AC value, and prints the allele count and the
+ * per-allele counts pgSnp builds for every record.  refs #38154 */
+
+/* Copyright (C) 2026 The Regents of the University of California
+ * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
+
+#include "common.h"
+#include "vcf.h"
+#include "pgSnp.h"
+
+static char *vcfFileName = "input/pgSnpManyAlleles/test.vcf";
+
+static void checkCounts(struct vcfRecord *rec, struct pgSnp *pgs)
+/* For a record whose AC values are all present, the counts must be AN minus the sum of AC for
+ * the reference allele, then each AC value in order. */
+{
+struct vcfInfoElement *an = (struct vcfInfoElement *)vcfRecordFindInfo(rec, "AN");
+struct vcfInfoElement *ac = (struct vcfInfoElement *)vcfRecordFindInfo(rec, "AC");
+int i, refCount = an->values[0].datInt;
+for (i = 0; i < ac->count; i++)
+    {
+    if (ac->missingData[i])
+        {
+        printf("    has missing AC values, not compared\n");
+        return;
+        }
+    refCount -= ac->values[i].datInt;
+    }
+struct dyString *dy = dyStringNew(0);
+dyStringPrintf(dy, "%d", refCount);
+for (i = 0; i < ac->count; i++)
+    dyStringPrintf(dy, ",%d", ac->values[i].datInt);
+printf("    counts %s the AN and AC fields\n",
+       sameString(dy->string, pgs->alleleFreq) ? "match" : "DO NOT MATCH");
+dyStringFree(&dy);
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+struct vcfFile *vcff = vcfFileMayOpen(vcfFileName, NULL, 0, 0, 0, -1, TRUE);
+if (vcff == NULL)
+    errAbort("could not open %s", vcfFileName);
+struct vcfRecord *rec;
+for (rec = vcff->records; rec != NULL; rec = rec->next)
+    {
+    struct pgSnp *pgs = pgSnpFromVcfRecord(rec);
+    printf("%s: %d alleles\n", rec->name, pgs->alleleCount);
+    printf("    alleleFreq %s\n", pgs->alleleFreq);
+    checkCounts(rec, pgs);
+    }
+vcfFileFree(&vcff);
+return 0;
+}