Fix issues with large VCF files not displaying in v4.0.4 (#5432)

Author: cmdcolin

packages/core/package.json

@@ -152,7 +152,7 @@
     "@emotion/utils": "^1.4.2",
     "@floating-ui/react": "^0.27.16",
     "@gmod/abortable-promise-cache": "^3.0.4",
-    "@gmod/bgzf-filehandle": "^6.0.10",
+    "@gmod/bgzf-filehandle": "^6.0.12",
     "@gmod/http-range-fetcher": "^5.0.7",
     "@jbrowse/jexl": "^3.0.1",
     "@jbrowse/mobx-state-tree": "^5.5.0",

plugins/gtf/package.json

@@ -31,7 +31,7 @@
   },
   "dependencies": {
     "@flatten-js/interval-tree": "^2.0.3",
-    "@gmod/bgzf-filehandle": "^6.0.10",
+    "@gmod/bgzf-filehandle": "^6.0.12",
     "@jbrowse/core": "workspace:^",
     "@jbrowse/mobx-state-tree": "^5.5.0",
     "@jbrowse/plugin-linear-genome-view": "workspace:^",

pnpm-lock.yaml

@@ -4119,7 +4119,6 @@
         "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/hg002/HG002_ONTrel2_16x_RG_HP10xtrioRTG.bam"
       }
     },
-
     {
       "type": "AlignmentsTrack",
       "trackId": "hg002_cram",
@@ -5035,6 +5034,26 @@
         "uri": "https://hgdownload.gi.ucsc.edu/gbdb/hg19/bbi/hic/GSE63525_HMEC_combined.hic"
       },
       "assemblyNames": ["hg19"]
+    },
+    {
+      "type": "VariantTrack",
+      "trackId": "freq.vcf",
+      "name": "freq.vcf",
+      "adapter": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "https://ftp.ncbi.nih.gov/snp/population_frequency/latest_release/freq.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "https://ftp.ncbi.nih.gov/snp/population_frequency/latest_release/freq.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      },
+      "assemblyNames": ["hg38"]
     }
   ],
   "connections": [],