Fix using Color by modifications on BAM/CRAM that need ref renaming (#…

…2128) * Add assemblyName to the modifications rename * Demo files * Sample file * Slightly better types to address lint warning about any
GMOD · Jul 14, 2021 · 5bd7b12 · 5bd7b12
1 parent f0da11b
commit 5bd7b12
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Showing 2 changed files with 71 additions and 2 deletions.
diff --git a/plugins/alignments/src/shared.ts b/plugins/alignments/src/shared.ts
@@ -1,7 +1,10 @@
 import { BlockSet } from '@jbrowse/core/util/blockTypes'
 
 import { getSession } from '@jbrowse/core/util'
-import { getRpcSessionId } from '@jbrowse/core/util/tracks'
+import {
+  getRpcSessionId,
+  getTrackAssemblyNames,
+} from '@jbrowse/core/util/tracks'
 import { IAnyStateTreeNode } from 'mobx-state-tree'
 import { AnyConfigurationModel } from '@jbrowse/core/configuration/configurationSchema'
 
@@ -33,7 +36,9 @@ export async function getUniqueTagValues(
 }
 
 export async function getUniqueModificationValues(
-  self: IAnyStateTreeNode,
+  self: IAnyStateTreeNode & {
+    parentTrack: IAnyStateTreeNode & { configuration: AnyConfigurationModel }
+  },
   adapterConfig: AnyConfigurationModel,
   colorScheme: { type: string; tag?: string },
   blocks: BlockSet,
@@ -53,6 +58,7 @@ export async function getUniqueModificationValues(
       tag: colorScheme.tag,
       sessionId,
       regions: blocks.contentBlocks,
+      assemblyName: getTrackAssemblyNames(self.parentTrack)[0],
       ...opts,
     },
   )

diff --git a/test_data/config_demo.json b/test_data/config_demo.json
@@ -3163,6 +3163,69 @@
           "uri": "https://jbrowse.org/genomes/GRCh38/methylation/modified_bases.5mC.bb"
         }
       }
+    },
+    {
+      "type": "AlignmentsTrack",
+      "trackId": "modbam_test.reference",
+      "name": "Nanopolish modbam_test.reference 20:10000000",
+      "assemblyNames": ["hg38"],
+      "category": ["Methylation"],
+      "adapter": {
+        "type": "BamAdapter",
+        "bamLocation": {
+          "uri": "https://jbrowse.org/genomes/hg19/nanopolish_methylation_test/modbam_test.reference.bam"
+        },
+        "index": {
+          "location": {
+            "uri": "https://jbrowse.org/genomes/hg19/nanopolish_methylation_test/modbam_test.reference.bam.bai"
+          },
+          "indexType": "BAI"
+        },
+        "sequenceAdapter": {
+          "type": "BgzipFastaAdapter",
+          "fastaLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
+          },
+          "faiLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
+          },
+          "gziLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
+          }
+        }
+      }
+    },
+
+    {
+      "type": "AlignmentsTrack",
+      "trackId": "modbam_test.read",
+      "name": "Nanopolish modbam_test.read 20:10000000",
+      "category": ["Methylation"],
+      "assemblyNames": ["hg38"],
+      "adapter": {
+        "type": "BamAdapter",
+        "bamLocation": {
+          "uri": "https://jbrowse.org/genomes/hg19/nanopolish_methylation_test/modbam_test.read.bam"
+        },
+        "index": {
+          "location": {
+            "uri": "https://jbrowse.org/genomes/hg19/nanopolish_methylation_test/modbam_test.read.bam.bai"
+          },
+          "indexType": "BAI"
+        },
+        "sequenceAdapter": {
+          "type": "BgzipFastaAdapter",
+          "fastaLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
+          },
+          "faiLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
+          },
+          "gziLocation": {
+            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
+          }
+        }
+      }
     }
   ],
   "connections": [],