2ae817bcd648f2a3184bb4b118840e65749fea2d
max
  Thu Sep 24 04:15:20 2026 -0700
problematic.txt/html: reconcile Panmask Easy/Difficult coverage to 87.8%/12.2%, one decimal place, refs #38375

diff --git src/hg/makeDb/doc/hg38/problematic.txt src/hg/makeDb/doc/hg38/problematic.txt
index 78730657ba0..002af6626f8 100644
--- src/hg/makeDb/doc/hg38/problematic.txt
+++ src/hg/makeDb/doc/hg38/problematic.txt
@@ -133,21 +133,23 @@
 # Anna pointed out that a track called "Panmask" under a "Problematic Regions" container is
 # confusing, since it marks the easy regions, not the problematic ones. Rather than changing
 # the released Panmask Easy track, we add a second track with the inverse regions, for use in
 # the Problematic Regions Recommended Track Set. Checked the source first: Zenodo record
 # 16755940 is still at v1.4 (Aug 6 2025, finalized Sep 22 2025), same version already in use,
 # and the local file's MD5 matches the file on Zenodo, so no re-download was needed.
 cd /hive/data/genomes/hg38/bed/problematic/panmask
 # Panmask covers only the 24 main chromosomes (no chrM, no alts/randoms/fixes), so restrict
 # the complement to that same set rather than the full 711-sequence chrom.sizes, and exclude
 # assembly gaps from the complement with the !gap idiom, so centromeric N-runs don't get
 # double-counted as "hard" on top of the existing Gap track.
 awk '$1 !~ /_/ && $1 != "chrM" {printf "%s\t%s\thg38.2bit\n", $1, $2}' \
     ../../../chrom.sizes > primary24.chrom.sizes
 featureBits hg38 '!/gbdb/hg38/problematic/hg38.pm151b-v3.easy.bb' '!gap' \
     -chromSize=primary24.chrom.sizes -bed=hg38.pm151b-v3.notEasy.bed -minSize=1
-# 359,192,609 bases of 2,937,659,104 (12.227%) -- the complement of Panmask Easy's 87.8%
+# 359,192,609 bases of 2,937,659,104 (12.2%) -- the complement of Panmask Easy's 87.8% on this
+# same primary24/gap-excluded set (checked with featureBits on the Easy bigBed directly, sums
+# to 100% as expected; problematic.html's Easy figure updated to 87.8% to match).
 bedSort hg38.pm151b-v3.notEasy.bed hg38.pm151b-v3.notEasy.bed
 cut -f1-3 hg38.pm151b-v3.notEasy.bed > hg38.pm151b-v3.notEasy.bed3
 bedToBigBed hg38.pm151b-v3.notEasy.bed3 ../../../chrom.sizes hg38.pm151b-v3.notEasy.bb -type=bed3 -tab
 gzip -k hg38.pm151b-v3.notEasy.bed3
 mv hg38.pm151b-v3.notEasy.bed3.gz hg38.pm151b-v3.notEasy.bed.gz