c81011d4a8f57db347e15aa1248c501b2c8a6fea lrnassar Mon Jun 1 13:16:15 2026 -0700 QA fixes for the lrSv long-read SV supertrack: labels and description cleanups. refs #36258 Trim six subtrack longLabels to the 85-char limit (ga4kSv, hprc2Sv, hgsvc2Sv, chirmade101Sv, cpc1Sv, and lrSvAll; the lrSvAll change is also made in the lrSvMergeAll.py generator so a re-run reproduces it). Standardize the APR dataset name to "Arab Pangenome Reference (APR)" across lrSv.ra, lrSv.html, aprSv.html, and the makeDoc comment (was a mix of "Arabic" and "UAE UPR"). lrSv1kgOnt.html: state per-assembly SV counts (hg38 lifted 148,375 vs hs1 native 161,332, each with its own type breakdown) and encode non-ASCII author names as numeric entities. hgsvc3Sv.html: correct the hg38 counts to match the served bigBed (176,231 DEL+INS, 176,531 total). colorsDbSv.html: use $db in the hgdownload path so it resolves on hs1 as well as hg38. cpc1Sv.html: encode a Unicode minus sign as a numeric entity. diff --git src/hg/makeDb/trackDb/human/cpc1Sv.html src/hg/makeDb/trackDb/human/cpc1Sv.html index b5d40795e95..d4d9ec3d216 100644 --- src/hg/makeDb/trackDb/human/cpc1Sv.html +++ src/hg/makeDb/trackDb/human/cpc1Sv.html @@ -45,31 +45,31 @@ by strand arrows, e.g. <tt>>2541>2547</tt>). It is stable across the graph but has no meaning outside the CPC pangenome graph file.</p> <h2>Collapsing of Multi-allelic Sites</h2> <p> The source VCF was decomposed with <tt>bcftools norm -m -any</tt>, so each graph snarl appears as one VCF row per alternative allele (a single bubble in the graph may have 2-20+ alt paths). For this track we first compute the CPC-only allele count per alt, drop any alt that no CPC sample carries, then collapse all remaining alts sharing the same snarl ID into one track item:</p> <ul> <li><b>SV type</b> is the common class of all alts, or <tt>MIXED</tt> if they disagree (for example one alt is a DEL and another is an INS).</li> - <li><b>SV length</b> is the maximum |len(ALT) − len(REF)| across alts.</li> + <li><b>SV length</b> is the maximum |len(ALT) − len(REF)| across alts.</li> <li><b>Allele count</b> is the sum of the per-alt allele counts.</li> <li><b>Number of alts</b> records how many alternative alleles were merged.</li> </ul> <h2>Filters</h2> <p>Available filters:</p> <ul> <li><b>SV type</b>: any combination of INS, DEL, CPX, MIXED.</li> <li><b>SV length</b>: maximum allele-length difference.</li> <li><b>Allele frequency</b> and <b>allele count</b> across the combined 105 samples.</li> </ul> <h2>Methods</h2>