a8694a3b22d43f0536c02101e9f3b56b5339b4dc
max
  Wed Sep 9 05:47:17 2026 -0700
hubtools: add "import igv" and "splitHap", and the bTaeGut7 zebra finch hub

import igv builds a hub from an IGV session XML. Every Track element becomes a
track, in session order, with the IGV display attributes translated to trackDb
settings. Files the browser can read over the network are linked where they are;
bed, gff, gtf, wig and bedGraph are downloaded and converted, which needs
chrom.sizes and gets them from --chromSizes, from the UCSC assembly, or from a
bigWig of the session itself, the only source there is for a custom assembly.
The BED cleaner exists because real files are not to spec: reversed start/end,
scores over 1000, "#rrggbb" colours, names past 255 characters, and columns that
are not the BED field they sit in, such as trf writing the repeat motif where
thickStart belongs.

splitHap turns a hub built on a diploid assembly into one hub with a genome per
haplotype, reading both assemblies' chrom.sizes and chromAlias from GenArk and
sending each record to whichever assembly has its sequence. It writes
splitHap.report.txt with the records per track per haplotype, the sequences
neither assembly has, and the records reaching past a sequence end, and checks
every track as it goes: records read must equal records matched plus records
with no sequence, and every match must produce an output record or a drop. A
track that does not add up stops the run rather than being written up as a
finding.

Two conversion fixes that came out of the zebra finch data. GFF3 requires unique
IDs, but an annotation of a phased assembly often gives both haplotypes the same
ID; gff3ToGenePred then merges the two copies into one transcript spanning two
chromosomes and discards it, which was losing 31 of 182 retrocopies. IDs that
occur on more than one sequence are now made unique per sequence first. And a
feature name is now taken from the first non-numeric attribute, so a
RepeatMasker GFF gives Motif:Tgut716A rather than the running number in ID=.

genark addContrib gains --tier alpha|beta|public. It edits only betaGenArk.txt
and publicGenArk.txt; beta.hub.txt and public.hub.txt are generated from those
lists and shipped by quickPush.pl, so writing them by hand would push content
outside the normal flow and lose it at the next clade build. The default alpha
tier leaves the lists untouched, so re-running an install cannot demote a
collection that is already promoted.

doc/contrib/bTaeGut7 and trackDb/contrib/bTaeGut7 are the zebra finch
telomere-to-telomere hub built with the above, from the IGV session the authors
ship with the annotations on GenomeArk (Formenti et al, Cell 2026, PMID
42561917). 21 tracks in 6 collections plus 3 standalone, 27 description pages,
and a makeDoc recording where every record went.

diff --git src/hg/makeDb/doc/contrib/bTaeGut7/sourceTracks.tsv src/hg/makeDb/doc/contrib/bTaeGut7/sourceTracks.tsv
new file mode 100644
index 00000000000..56ce7259767
--- /dev/null
+++ src/hg/makeDb/doc/contrib/bTaeGut7/sourceTracks.tsv
@@ -0,0 +1,24 @@
+# track name in trackDb.txt <tab> name that 'hubtools import igv' gives it
+# the second column comes from the file names in the IGV session; when the
+# authors change the session, this is the file that has to be updated
+gcPercent	bTaeGut7v04_MT_rDNATeloscopegcbw_1
+seqEntropy	bTaeGut7v04_MT_rDNATeloscopeentropybw_2
+nonBdna	bTaeGut7v04_MT_rDNAgfa2BQuadronsortedv01bed_15
+covHifi	dip_hifi_Cov_5
+covOnt	dip_ont_Cov_6
+covClr	bTaeGut14_CLRcovbw_4
+egapx	bTaeGut7v04_MT_rDNAEGAPxv01gtfgz_7
+retrocopies	bTaeGut7v04_MT_rDNARCPediav01gff_8
+transposons	bTaeGut7v04_MT_rDNAEDTA2v02gtfgz_9
+tandemRepeats	bTaeGut7v04_MT_rDNAtrfsortedv01bed_13
+satellome	bTaeGut7v04_MT_rDNAsatellomev01bed_14
+centroSat	bTaeGut7v04_MT_rDNARMTakki2022v01coloredmergedgff_10
+centroCores	bTaeGut7v04_MT_rDNAcentromere_detectorv01gff_12
+centroMarkers	bTaeGut7v04_MT_rDNABLASTKnief2016v02bed_11
+telomeres	bTaeGut7v04_MT_rDNATeloscopeterminalbed_16
+itsRepeats	bTaeGut7v04_MT_rDNAteloscopev03itsmerged200bed_17
+newRegions	bTaeGut7v04_MT_rDNAPURfastgav01bed_3
+largeSv	bTaeGut7v04_MT_rDNAlarge_SVsv01bed_19
+methyl5mC	bTaeGut7v04_MT_rDNAPBmethylationv01bw_18
+compartE1	bTaeGut7v04_MT_rDNACooltoolsE1200kbpflippeddipcollatedv01bw_20
+compartAB	bTaeGut7v04_MT_rDNACooltoolsE1200kbpflippeddipcollatedv01bed_21