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/htdocs/goldenPath/help/trackDb/trackDbSettings.json src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
index 4cd7823d864..735541ca44e 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.json
@@ -1,25 +1,26 @@
 {
  "version": "v3",
  "categories": [
   "Common Settings",
   "Common Settings - less frequent",
   "bam - Compressed Alignment Track Settings",
   "bigBarChart",
   "bigBed - Item or Region Track Settings",
   "Item or Region Track Settings - less frequent",
   "bigChain - Pairwise Alignments",
+  "bigNet - Alignment Nets",
   "bigGenePred - Gene Annotations",
   "bigInteract",
   "bigMaf - Multiple Alignments",
   "bigNarrowPeak - Peaks",
   "bigPsl - Pairwise Alignments",
   "bigWig - Signal Graphing Track Settings",
   "bigLolly - Lollipop charts",
   "hic - Hi-C contact matrices",
   "halSnake - Multiple Alignments",
   "vcfTabix - Variant Call Format Track Settings",
   "vcfPhasedTrio - Variant Call Format Track Settings",
   "superTrack - Folder Track Settings",
   "Composite Track Settings",
   "Composite - Subgroups Settings",
   "Composite - Views Settings",
@@ -94,30 +95,31 @@
    "key": "bigDataUrl",
    "category": "Common Settings",
    "roles": [
     "super",
     "composite",
     "view",
     "leaf"
    ],
    "types": [
     "bigBarChart",
     "bigBed",
     "bigChain",
     "bigInteract",
     "bigLolly",
     "bigMaf",
+    "bigNet",
     "bigPsl",
     "bigWig",
     "bam",
     "hic",
     "vcfTabix",
     "vcfPhasedTrio"
    ],
    "level": "required",
    "fmt": "bigDataUrl <url/relativePath>",
    "ex": "bigDataUrl http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bb",
    "desc": "The location of a remote data file containing the bulk of the data for the track."
   },
   {
    "key": "html",
    "category": "Common Settings",
@@ -1953,30 +1955,44 @@
     "bed",
     "bigBed",
     "genePred",
     "bigGenePred",
     "psl",
     "bigPsl",
     "chain",
     "bigChain",
     "bam"
    ],
    "level": "full",
    "fmt": "baseColorDefault\n                    <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>",
    "ex": "",
    "desc": "Specifies the default drawing mode."
   },
+  {
+   "key": "bigNet",
+   "category": "bigNet - Alignment Nets",
+   "roles": [
+    "leaf"
+   ],
+   "types": [
+    "bigNet"
+   ],
+   "level": "new",
+   "fmt": "type bigNet targetDb chainTrack",
+   "ex": "",
+   "desc": ""
+  },
   {
    "key": "bigGenePred",
    "category": "bigGenePred - Gene Annotations",
    "roles": [
     "leaf"
    ],
    "types": [
     "bigGenePred"
    ],
    "level": null,
    "fmt": "type bigGenePred",
    "ex": "",
    "desc": ""
   },
   {