454b361596ac3494472e4e5dc6950326321e17c0
lrnassar
  Tue Jul 7 17:55:41 2026 -0700
Fix wrong column indices in TP53 Provisional Classification build summary. The post-build console summary read flds[13]/[14] (PS3 and PP3 labels) for the AF and BS2 counts instead of flds[15]/[16] (af_code and bs2), so it mislabeled PS3/BS3 as AF codes and always reported 0 BS2 rows. Emitted bigBed data was unaffected. refs #37399

diff --git src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py
index 88cb7c72196..2557ca05b54 100644
--- src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py
+++ src/hg/makeDb/scripts/tp53/tp53ProvisionalClass.py
@@ -560,32 +560,32 @@
     with open(bed, 'w') as f:
         f.write("\n".join(bed_lines) + "\n")
     lib.run_sort_bed(bed)
     bb = os.path.join(outdir, "TP53ProvisionalClass{}.bb".format(db.capitalize()))
     lib.run_bedToBigBed(bed, as_file, bb, lib.chrom_sizes_path(db), "bed9+9")
     print("  wrote {}".format(bb))
 
     from collections import Counter
     cnt = Counter()
     af_cnt = Counter()
     bs2_cnt = 0
     with open(bed) as f:
         for line in f:
             flds = line.split("\t")
             cnt[flds[9]] += 1
-            af_cnt[flds[13]] += 1
-            if flds[14] == 'BS2':
+            af_cnt[flds[15]] += 1
+            if flds[16] == 'BS2':
                 bs2_cnt += 1
     print("  Class distribution:")
     for k, n in cnt.most_common():
         print("    {}: {}".format(k, n))
     print("  AF code distribution: {}".format(dict(af_cnt)))
     print("  BS2 applied: {} rows".format(bs2_cnt))
 
 
 def main():
     p = argparse.ArgumentParser(description=__doc__)
     p.add_argument('-o', '--output-dir', default=DEFAULT_OUTDIR)
     p.add_argument('--db', action='append', help='hg38 or hg19 (repeat). Default hg38.')
     args = p.parse_args()
     dbs = args.db if args.db else ['hg38']
     for db in dbs: