353a34ac7e7638457db3f55e57452069113d860b braney Sun Sep 6 13:34:28 2026 -0700 Add a bigNet track type, a net of alignments in a bigBed, refs #20824 Track hubs have had no way to show a real net. The usual stand-in is a net rendered as a maf, which loses the level structure that makes a net useful for establishing orthologous sequence. bigNet holds the netAlign columns in a bigBed, so a hub can carry the net itself. The format is bed6+20: the target in chrom/chromStart/chromEnd, the query sequence in name, the query strand in strand, then level and the rest of the netAlign fields. The trackDb line is type bigNet <targetDb> <chainTrack> mirroring type netAlign. chainTrack is the plain trackDb name of the bigChain track in the same hub; hgc adds the hub prefix itself. chainNetLoadRangeHub() builds a chainNet from a bigBed range query and hands it to the same helpToNet() the SQL path uses, so the nesting is rebuilt the same way. netDraw picks its loader off tg->isBigBed and the drawing code below that is untouched. genericNetClick does the same for the details page and follows the named chain track for the alignment. Also bounds the level walk in helpToNet() by help->maxDepth. It could read one past the end of the levels array. netToBigNet converts a net file to bedToBigBed input. It writes the tab line itself rather than calling bigNetTabOut, because autoSql prints a double with %g and that drops digits off a chain score. diff --git src/hg/utils/netToBigNet/tests/expected/simpleTest.bigNet src/hg/utils/netToBigNet/tests/expected/simpleTest.bigNet new file mode 100644 index 00000000000..36eb62c542c --- /dev/null +++ src/hg/utils/netToBigNet/tests/expected/simpleTest.bigNet @@ -0,0 +1,14 @@ +chr22 11474667 11479535 chr9 1000 + 1 88449095 88454102 23550 2697 75185.0 top -1 -1 3069 0 0 854 2910 -1 -1 -1 -1 1600 553 +chr22 11474911 11474928 chr9 1000 + 2 88449345 88449345 0 0 0.0 gap -1 -1 -1 0 0 0 0 -1 -1 -1 -1 0 0 +chr22 11475306 11475318 chr9 1000 + 2 88449713 88449713 0 0 0.0 gap -1 -1 -1 0 0 0 0 -1 -1 -1 -1 0 0 +chr22 11475444 11475471 chr9 1000 + 2 88449826 88449826 0 0 0.0 gap -1 -1 -1 0 0 0 0 -1 -1 -1 -1 0 0 +chr22 11475503 11477149 chr9 1000 + 2 88449858 88450640 0 0 0.0 gap -1 -1 -1 0 0 854 502 -1 -1 -1 -1 0 0 +chr22 11475503 11477149 chr11 1000 + 3 58769938 58770722 56275 115 2236.0 nonSyn -1 -1 80 0 0 854 40 -1 -1 -1 -1 0 0 +chr22 11475573 11477104 chr11 1000 + 4 58770018 58770677 0 0 0.0 gap -1 -1 -1 0 0 854 40 -1 -1 -1 -1 0 0 +chr22 11477657 11477669 chr9 1000 + 2 88451155 88451155 0 0 0.0 gap -1 -1 -1 0 0 0 0 -1 -1 -1 -1 0 0 +chr22 11478751 11478917 chr9 1000 + 2 88452236 88453333 0 0 0.0 gap -1 -1 -1 0 0 0 862 -1 -1 -1 -1 166 0 +chr22 11478751 11478917 chr11 1000 - 3 58780620 58780786 45179 166 4743.0 nonSyn -1 -1 166 0 0 0 114 -1 -1 -1 -1 166 0 +chr22 11479115 11479238 chr9 1000 + 2 88453526 88453910 0 0 0.0 gap -1 -1 -1 0 0 0 337 -1 -1 -1 -1 123 0 +chr22 11479115 11479238 chr11 1000 + 3 58751189 58751305 46828 115 2574.0 nonSyn -1 -1 116 0 0 0 0 -1 -1 -1 -1 123 0 +chr22 11479296 11479395 chr9 1000 + 2 88453968 88453968 0 0 0.0 gap -1 -1 -1 0 0 0 0 -1 -1 -1 -1 41 0 +chr22 11479296 11479395 chr11 1000 + 3 58751359 58751472 46828 95 2126.0 nonSyn -1 -1 113 0 0 0 0 -1 -1 -1 -1 41 0