@jbrowse/plugin-alignments 2.1.7 → 2.2.0

package/src/AlignmentsFeatureDetail/__snapshots__/index.test.js.snap

@@ -29,7 +29,7 @@ exports[`open up a widget 1`] = `
       >
         <svg
           aria-hidden="true"
-          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium tss-rb1zhf-expandIcon css-i4bv87-MuiSvgIcon-root"
+          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-125qixp-MuiSvgIcon-root-expandIcon"
           data-testid="ExpandMoreIcon"
           focusable="false"
           viewBox="0 0 24 24"
@@ -55,7 +55,7 @@ exports[`open up a widget 1`] = `
             role="region"
           >
             <div
-              class="MuiAccordionDetails-root tss-1g973hk-expansionPanelDetails css-15v22id-MuiAccordionDetails-root"
+              class="MuiAccordionDetails-root css-rqrb7m-MuiAccordionDetails-root-expansionPanelDetails"
             >
               <p
                 class="MuiTypography-root MuiTypography-body1 css-ahj2mt-MuiTypography-root"
@@ -63,15 +63,15 @@ exports[`open up a widget 1`] = `
                 Core details
               </p>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                 >
                   Position
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     ctgA:3..102 (+)
@@ -79,15 +79,15 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                 >
                   Name
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     ctgA_3_555_0:0:0_2:0:0_102d
@@ -95,15 +95,15 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                 >
                   Length
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     100
@@ -111,15 +111,15 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                 >
                   Type
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     match
@@ -135,16 +135,16 @@ exports[`open up a widget 1`] = `
                 Attributes
               </p>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   seq
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     TTGTTGCGGAGTTGAACAACGGCATTAGGAACACTTCCGTCTCTCACTTTTATACGATTATGATTGGTTCTTTAGCCTTGGTTTAGATTGGTAGTAGTAG
@@ -152,16 +152,16 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   score
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     37
@@ -169,16 +169,16 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   qual
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <button
                     type="button"
@@ -196,16 +196,16 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   MQ
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     37
@@ -213,16 +213,16 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   CIGAR
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     100M
@@ -230,16 +230,16 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   length_on_ref
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     100
@@ -247,16 +247,16 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   template_length
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     0
@@ -264,16 +264,16 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1m8nxnb-field"
+                class="css-1m8nxnb-field"
               >
                 <div
-                  class="tss-1y9c7n2-fieldName"
+                  class="css-1y9c7n2-fieldName"
                   style="width: 96px;"
                 >
                   seq_length
                 </div>
                 <div
-                  class="tss-1omt041-fieldValue"
+                  class="css-1omt041-fieldValue"
                 >
                   <div>
                     100
@@ -281,7 +281,7 @@ exports[`open up a widget 1`] = `
                 </div>
               </div>
               <div
-                class="tss-1upvn7b-container2"
+                class="css-1upvn7b-container2"
               >
                 <button
                   class="MuiButtonBase-root MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium MuiButton-root MuiButton-contained MuiButton-containedPrimary MuiButton-sizeMedium MuiButton-containedSizeMedium css-sghohy-MuiButtonBase-root-MuiButton-root"
@@ -294,7 +294,7 @@ exports[`open up a widget 1`] = `
                   />
                 </button>
                 <div
-                  class="MuiFormControl-root tss-1x17dzq-formControl css-1nrlq1o-MuiFormControl-root"
+                  class="MuiFormControl-root css-147opmv-MuiFormControl-root-formControl"
                 >
                   <button
                     class="MuiButtonBase-root MuiIconButton-root MuiIconButton-sizeMedium css-78trlr-MuiButtonBase-root-MuiIconButton-root"
@@ -349,7 +349,7 @@ exports[`open up a widget 1`] = `
       >
         <svg
           aria-hidden="true"
-          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium tss-rb1zhf-expandIcon css-i4bv87-MuiSvgIcon-root"
+          class="MuiSvgIcon-root MuiSvgIcon-fontSizeMedium css-125qixp-MuiSvgIcon-root-expandIcon"
           data-testid="ExpandMoreIcon"
           focusable="false"
           viewBox="0 0 24 24"
@@ -375,7 +375,7 @@ exports[`open up a widget 1`] = `
             role="region"
           >
             <div
-              class="MuiAccordionDetails-root tss-1g973hk-expansionPanelDetails css-15v22id-MuiAccordionDetails-root"
+              class="MuiAccordionDetails-root css-rqrb7m-MuiAccordionDetails-root-expansionPanelDetails"
             >
               <div
                 class="MuiFormGroup-root css-dmmspl-MuiFormGroup-root"
@@ -384,7 +384,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -418,7 +418,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -452,7 +452,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -486,7 +486,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -520,7 +520,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -554,7 +554,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -588,7 +588,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -622,7 +622,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -656,7 +656,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -690,7 +690,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -724,7 +724,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"
@@ -758,7 +758,7 @@ exports[`open up a widget 1`] = `
                   class="MuiFormControlLabel-root MuiFormControlLabel-labelPlacementEnd css-j204z7-MuiFormControlLabel-root"
                 >
                   <span
-                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary tss-18u5im4-compact css-12wnr2w-MuiButtonBase-root-MuiCheckbox-root"
+                    class="MuiButtonBase-root MuiCheckbox-root MuiCheckbox-colorPrimary PrivateSwitchBase-root MuiCheckbox-root MuiCheckbox-colorPrimary MuiCheckbox-root MuiCheckbox-colorPrimary css-1r7hq7f-MuiButtonBase-root-MuiCheckbox-root-compact"
                   >
                     <input
                       class="PrivateSwitchBase-input css-1m9pwf3"

package/src/AlignmentsTrack/index.ts

@@ -5,28 +5,34 @@ import {
   createBaseTrackConfig,
   createBaseTrackModel,
 } from '@jbrowse/core/pluggableElementTypes/models'
+
+/**
+ * #config AlignmentsTrack
+ * has very little config; most config and state logic is on the display
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
 function configSchemaFactory(pluginManager: PluginManager) {
   return ConfigurationSchema(
     'AlignmentsTrack',
     {},
-    { baseConfiguration: createBaseTrackConfig(pluginManager) },
+    {
+      /**
+       * #baseConfiguration
+       */
+      baseConfiguration: createBaseTrackConfig(pluginManager),
+    },
   )
 }
-export default function register(pluginManager: PluginManager) {
-  pluginManager.addTrackType(() => {
-    const configSchema = configSchemaFactory(pluginManager)
+export default function register(pm: PluginManager) {
+  pm.addTrackType(() => {
+    const configSchema = configSchemaFactory(pm)
     const track = new TrackType({
       name: 'AlignmentsTrack',
       configSchema,
-      stateModel: createBaseTrackModel(
-        pluginManager,
-        'AlignmentsTrack',
-        configSchema,
-      ),
+      stateModel: createBaseTrackModel(pm, 'AlignmentsTrack', configSchema),
     })
-    const linearAlignmentsDisplay = pluginManager.getDisplayType(
-      'LinearAlignmentsDisplay',
-    )
+    const linearAlignmentsDisplay = pm.getDisplayType('LinearAlignmentsDisplay')
     // Add LinearAlignmentsDisplay here so that it has priority over the other
     // linear displays (defaults to order the displays are added, but we have
     // to add the Pileup and SNPCoverage displays first).

package/src/BamAdapter/BamAdapter.ts

@@ -9,7 +9,6 @@ import { openLocation } from '@jbrowse/core/util/io'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
 import { Feature } from '@jbrowse/core/util/simpleFeature'
 import { toArray } from 'rxjs/operators'
-import { readConfObject } from '@jbrowse/core/configuration'
 import BamSlightlyLazyFeature from './BamSlightlyLazyFeature'
 
 interface Header {
@@ -21,51 +20,52 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
   private samHeader?: Header
 
   private setupP?: Promise<Header>
-
-  protected configured?: Promise<{
+  private configureP?: Promise<{
     bam: BamFile
     sequenceAdapter?: BaseFeatureDataAdapter
   }>
 
   // derived classes may not use the same configuration so a custom
   // configure method allows derived classes to override this behavior
-  protected async configure() {
-    if (!this.configured) {
-      const bamLocation = readConfObject(this.config, 'bamLocation')
-      const location = readConfObject(this.config, ['index', 'location'])
-      const indexType = readConfObject(this.config, ['index', 'indexType'])
-      const bam = new BamFile({
-        bamFilehandle: openLocation(bamLocation, this.pluginManager),
-        csiFilehandle:
-          indexType === 'CSI'
-            ? openLocation(location, this.pluginManager)
-            : undefined,
-        baiFilehandle:
-          indexType !== 'CSI'
-            ? openLocation(location, this.pluginManager)
-            : undefined,
-
-        // chunkSizeLimit and fetchSizeLimit are more troublesome than
-        // helpful, and have given overly large values on the ultra long
-        // nanopore reads even with 500MB limits, so disabled with infinity
-        chunkSizeLimit: Infinity,
-        fetchSizeLimit: Infinity,
-        yieldThreadTime: Infinity,
-      })
+  protected async configurePre() {
+    const bamLocation = this.getConf('bamLocation')
+    const location = this.getConf(['index', 'location'])
+    const indexType = this.getConf(['index', 'indexType'])
+    const pm = this.pluginManager
+    const csi = indexType === 'CSI'
+    const bam = new BamFile({
+      bamFilehandle: openLocation(bamLocation, pm),
+      csiFilehandle: csi ? openLocation(location, pm) : undefined,
+      baiFilehandle: !csi ? openLocation(location, pm) : undefined,
+
+      // chunkSizeLimit and fetchSizeLimit are more troublesome than
+      // helpful, and have given overly large values on the ultra long
+      // nanopore reads even with 500MB limits, so disabled with infinity
+      chunkSizeLimit: Infinity,
+      fetchSizeLimit: Infinity,
+      yieldThreadTime: Infinity,
+    })
 
-      const adapterConfig = readConfObject(this.config, 'sequenceAdapter')
-      if (adapterConfig && this.getSubAdapter) {
-        this.configured = this.getSubAdapter(adapterConfig).then(
-          ({ dataAdapter }) => ({
-            bam,
-            sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,
-          }),
-        )
-      } else {
-        this.configured = Promise.resolve({ bam })
+    const adapterConfig = this.getConf('sequenceAdapter')
+    if (adapterConfig && this.getSubAdapter) {
+      const { dataAdapter } = await this.getSubAdapter(adapterConfig)
+      return {
+        bam,
+        sequenceAdapter: dataAdapter as BaseFeatureDataAdapter,
       }
+    } else {
+      return { bam }
+    }
+  }
+
+  protected async configure() {
+    if (!this.configureP) {
+      this.configureP = this.configurePre().catch(e => {
+        this.configureP = undefined
+        throw e
+      })
     }
-    return this.configured
+    return this.configureP
   }
 
   async getHeader(opts?: BaseOptions) {
@@ -231,7 +231,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
     // @ts-ignore
     if (bam.index.filehandle !== '?') {
       const bytes = await bytesForRegions(regions, bam)
-      const fetchSizeLimit = readConfObject(this.config, 'fetchSizeLimit')
+      const fetchSizeLimit = this.getConf('fetchSizeLimit')
       return { bytes, fetchSizeLimit }
     } else {
       return super.estimateRegionsStats(regions, opts)
@@ -241,7 +241,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
   freeResources(/* { region } */): void {}
 
   // depends on setup being called before the BAM constructor
-  refIdToName(refId: number): string | undefined {
+  refIdToName(refId: number) {
     return this.samHeader?.idToName[refId]
   }
 }

package/src/BamAdapter/configSchema.ts

@@ -1,37 +1,65 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { types } from 'mobx-state-tree'
 
-export default types.late(() =>
-  ConfigurationSchema(
-    'BamAdapter',
-    {
-      bamLocation: {
-        type: 'fileLocation',
-        defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
+/**
+ * #config BamAdapter
+ * used to configure BAM adapter
+ */
+function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
+
+const configSchema = ConfigurationSchema(
+  'BamAdapter',
+  {
+    /**
+     * #slot
+     */
+    bamLocation: {
+      type: 'fileLocation',
+      defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
+    },
+
+    index: ConfigurationSchema('BamIndex', {
+      /**
+       * #slot index.indexType
+       */
+      indexType: {
+        model: types.enumeration('IndexType', ['BAI', 'CSI']),
+        type: 'stringEnum',
+        defaultValue: 'BAI',
       },
-      index: ConfigurationSchema('BamIndex', {
-        indexType: {
-          model: types.enumeration('IndexType', ['BAI', 'CSI']),
-          type: 'stringEnum',
-          defaultValue: 'BAI',
-        },
-        location: {
-          type: 'fileLocation',
-          defaultValue: {
-            uri: '/path/to/my.bam.bai',
-            locationType: 'UriLocation',
-          },
+      /**
+       * #slot index.location
+       */
+      location: {
+        type: 'fileLocation',
+        defaultValue: {
+          uri: '/path/to/my.bam.bai',
+          locationType: 'UriLocation',
         },
-      }),
-      fetchSizeLimit: {
-        type: 'number',
-        defaultValue: 5_000_000,
-      },
-      sequenceAdapter: {
-        type: 'frozen',
-        defaultValue: null,
       },
+    }),
+    /**
+     * #slot
+     */
+    fetchSizeLimit: {
+      type: 'number',
+      description:
+        'used to determine when to display a warning to the user that too much data will be fetched',
+      defaultValue: 5_000_000,
     },
-    { explicitlyTyped: true },
-  ),
+    /**
+     * #slot
+     * generally refers to the reference genome assembly's sequence adapter
+     * currently needs to be manually added
+     */
+    sequenceAdapter: {
+      type: 'frozen',
+      description:
+        'sequence data adapter, used to calculate SNPs when BAM reads lacking MD tags',
+      defaultValue: null,
+    },
+  },
+  { explicitlyTyped: true },
 )
+
+export default configSchema

package/src/CramAdapter/CramAdapter.test.ts

@@ -4,10 +4,9 @@ import PluginManager from '@jbrowse/core/PluginManager'
 import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
 import Adapter from './CramAdapter'
 import { SequenceAdapter } from './CramTestAdapters'
-import configSchemaF from './configSchema'
+import configSchema from './configSchema'
 
 const pluginManager = new PluginManager()
-const configSchema = pluginManager.load(configSchemaF)
 
 const getVolvoxSequenceSubAdapter: getSubAdapterType = async () => {
   return {