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