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&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>