54f465e316441236c128491e53c0e5464c0e672c
lrnassar
  Tue Sep 29 11:40:49 2026 -0700
Fiber-seq: bring the fiberSeqTrackDb.py docstrings back in line with the
three-value sampleClass, and stop the Compendium intro from keeping a running
tally of where the lymphoblastoid lines came from.  readSamples still said the
five GM lines were common cell lines and writeMetadata still said there were
two classes, both a few lines from the SAMPLE_CLASS_COLORS entry that added
the third.  writeMetadata also still had "Common Cell Line" in the old Title
Case, which yesterday's rename missed because the string is wrapped across two
source lines and a line oriented sed cannot see it; worth remembering for the
next rename.  The intro sentence had grown a breakdown that did not add up, 20
HPRC plus 5 rare disease against 27 lymphoblastoid lines, leaving GM12878 and
HG002 unaccounted; it now points at the Sample class filter instead of
counting, since the lab has said more rare disease samples are coming and the
tally would go stale again.  While in there, the claim that accession order
keeps each class together is softened to what the data actually does: the
common cell lines fall in two runs either side of the HPRC block.  Generated
output is unchanged; the .ra, the metadata TSV and the colors JSON all
regenerate byte identical.  Caught by Claude review of 10f0f6d516.
refs #36210

diff --git src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html
index 3a0b84c7f99..56947a9046b 100644
--- src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html
+++ src/hg/makeDb/trackDb/human/hg38/fiberSeqCompendium.html
@@ -1,22 +1,22 @@
 <h2>Description</h2>
 
 <p>
 This track is part of the <a href="hgTrackUi?db=hg38&amp;g=fiberSeq">Fiber-seq</a> collection. It holds the
-full Fiber-seq data for 41 samples: 14 cell lines and 27 lymphoblastoid lines, 20 of them from
-individuals sequenced by the Human Pangenome Reference Consortium and five from rare disease
-cases. Chromatin accessibility and CpG methylation are read from the same
+full Fiber-seq data for 41 samples: 14 cell lines and 27 lymphoblastoid lines. The Sample class
+filter below splits them by where they came from. Chromatin accessibility and CpG methylation
+are read from the same
 molecules in the same experiment, so both are kept in one table here and can be compared without
 worrying about differences in cell preparation or sequencing depth. Six kinds of data are
 available for each sample:
 </p>
 
 <ul>
   <li><b>Percent accessible</b>: the fraction of Fiber-seq molecules on which a position was
       called accessible, combining both chromosomes.</li>
   <li><b>FIRE peaks</b>: the accessible regulatory elements called from that signal, with a
       score and a false discovery rate.</li>
   <li><b>Haplotype accessibility</b>: the percent-accessible signal computed separately for the
       two parental chromosomes and drawn as an overlay, which makes elements that are open on
       one chromosome but not the other visible directly.</li>
   <li><b>CpG methylation</b>: percent of reads methylated at each CpG, over both
       chromosomes.</li>