Utilize .assembly alongside .hic

src/app/core/net/api/RequestManager.ts

@@ -81,6 +81,7 @@ import {
   GetConversionJobRequest,
   GetConversionToolchainStatusRequest,
   SetDotplotAlignerPreferenceRequest,
+  ConvertAssemblyToAgpRequest,
   StopConversionJobRequest,
   RenameContigRequest,
   RenameScaffoldRequest,
@@ -882,6 +883,16 @@ class RequestManager {
     return this.sendRequest(request).then((response) => response.data);
   }
 
+  public async convertAssemblyToAgp(options: {
+    filename: string;
+    outputFilename?: string;
+    overwrite?: boolean;
+  }): Promise<{ status: string; inputFilename: string; outputFilename: string }> {
+    return this.sendRequest(new ConvertAssemblyToAgpRequest(options)).then(
+      (response) => response.data
+    );
+  }
+
   public async startBatchConversionJobs(
     request: StartBatchConversionJobsRequest
   ): Promise<{ status: string; groupId: string; jobIds: string[] }> {

src/app/core/net/api/request.ts

@@ -214,6 +214,18 @@ class StartBatchConversionJobsRequest implements HiCTAPIRequest {
   ) {}
 }
 
+class ConvertAssemblyToAgpRequest implements HiCTAPIRequest {
+  requestPath = "/convert/assembly-to-agp";
+
+  public constructor(
+    public readonly options: {
+      readonly filename: string;
+      readonly outputFilename?: string;
+      readonly overwrite?: boolean;
+    }
+  ) {}
+}
+
 class ListConversionJobsRequest implements HiCTAPIRequest {
   requestPath = "/convert/jobs/list";
 }
@@ -670,6 +682,7 @@ export {
   DropAllCachesRequest,
   StartConversionJobRequest,
   StartBatchConversionJobsRequest,
+  ConvertAssemblyToAgpRequest,
   ListConversionJobsRequest,
   GetConversionJobRequest,
   StopConversionJobRequest,

src/app/core/net/dto/requestDTO.ts

@@ -74,6 +74,7 @@ import {
   StartBatchConversionJobsRequest,
   StartDotplotJobsRequest,
   SetDotplotAlignerPreferenceRequest,
+  ConvertAssemblyToAgpRequest,
   ListDotplotJobsRequest,
   ListConversionJobsRequest,
   GetConversionJobRequest,
@@ -129,6 +130,10 @@ abstract class HiCTAPIRequestDTO<
         return new StartBatchConversionJobsRequestDTO(
           entity as StartBatchConversionJobsRequest
         );
+      case entity instanceof ConvertAssemblyToAgpRequest:
+        return new ConvertAssemblyToAgpRequestDTO(
+          entity as ConvertAssemblyToAgpRequest
+        );
       case entity instanceof StartDotplotJobsRequest:
         return new StartDotplotJobsRequestDTO(
           entity as StartDotplotJobsRequest
@@ -515,6 +520,16 @@ class StartBatchConversionJobsRequestDTO extends HiCTAPIRequestDTO<StartBatchCon
   }
 }
 
+class ConvertAssemblyToAgpRequestDTO extends HiCTAPIRequestDTO<ConvertAssemblyToAgpRequest> {
+  toDTO(): Record<string, unknown> {
+    return {
+      filename: this.entity.options.filename,
+      outputFilename: this.entity.options.outputFilename,
+      overwrite: this.entity.options.overwrite,
+    };
+  }
+}
+
 class StartDotplotJobsRequestDTO extends HiCTAPIRequestDTO<StartDotplotJobsRequest> {
   toDTO(): Record<string, unknown> {
     return {

src/app/ui/components/upper_ribbon/CoolerConverter.vue

@@ -285,7 +285,7 @@ const batchSelection: Ref<Set<string>> = ref(new Set<string>());
 const batchAssemblyFilename: Ref<string> = ref("");
 const assemblySelectorOpen: Ref<boolean> = ref(false);
 const batchParallelJobs: Ref<number> = ref(2);
-const batchParallelism: Ref<number> = ref(4);
+const batchParallelism: Ref<number> = ref(Math.max(1, navigator.hardwareConcurrency || 4));
 const batchJobIds: Ref<string[]> = ref([]);
 const batchStatusMap: Ref<Map<string, string>> = ref(new Map());
 const batchProgressMap: Ref<Map<string, number>> = ref(new Map());

src/app/ui/components/upper_ribbon/DotplotGenerator.vue

@@ -293,8 +293,8 @@ const sampleBp = ref(250);
 const minAlignmentLength = ref(50);
 const extraMinimap2Args = ref("");
 const alignerPreference = ref("auto");
-const alignmentThreads = ref(Math.max(1, Math.min(12, navigator.hardwareConcurrency || 4)));
-const conversionThreads = ref(Math.max(1, Math.min(12, navigator.hardwareConcurrency || 4)));
+const alignmentThreads = ref(Math.max(1, navigator.hardwareConcurrency || 4));
+const conversionThreads = ref(Math.max(1, navigator.hardwareConcurrency || 4));
 const overwrite = ref(false);
 
 const fastaEntries = computed<FileSelectionTableEntry[]>(() =>

src/app/ui/components/upper_ribbon/FileWizardModal.vue

@@ -312,6 +312,13 @@
                       <div class="input-group">
                         <input class="form-control" type="text" readonly :value="primaryAgp || 'Optional .agp or Juicebox .assembly for primary source'" />
                         <button class="btn btn-outline-secondary" @click="openSelector('primary-agp')">Browse…</button>
+                        <button
+                          v-if="primaryAgp?.toLowerCase().endsWith('.assembly')"
+                          class="btn btn-outline-primary"
+                          @click="convertAssemblySelectionToAgp('primary')"
+                        >
+                          Convert to AGP
+                        </button>
                       </div>
                       <small class="text-muted d-block mt-2">
                         .agp is loaded after opening. .assembly is passed to .hic conversion; for already converted
@@ -327,6 +334,13 @@
                       <div class="input-group">
                         <input class="form-control" type="text" readonly :value="secondaryAgp || 'Optional .agp or Juicebox .assembly for secondary source'" />
                         <button class="btn btn-outline-secondary" @click="openSelector('secondary-agp')">Browse…</button>
+                        <button
+                          v-if="secondaryAgp?.toLowerCase().endsWith('.assembly')"
+                          class="btn btn-outline-primary"
+                          @click="convertAssemblySelectionToAgp('secondary')"
+                        >
+                          Convert to AGP
+                        </button>
                       </div>
                     </div>
                   </div>
@@ -1279,6 +1293,34 @@ const onSelectorPicked = async (filename: string): Promise<void> => {
   }
 };
 
+const convertAssemblySelectionToAgp = async (
+  source: "primary" | "secondary"
+): Promise<void> => {
+  const filename = source === "primary" ? primaryAgp.value : secondaryAgp.value;
+  if (!filename.toLowerCase().endsWith(".assembly")) {
+    return;
+  }
+  const outputFilename = filename.replace(/\.assembly$/i, ".agp");
+  if (
+    !window.confirm(
+      `Convert ${filename} to ${outputFilename}? An existing AGP copy will be overwritten.`
+    )
+  ) {
+    return;
+  }
+  const result = await props.networkManager.requestManager.convertAssemblyToAgp({
+    filename,
+    outputFilename,
+    overwrite: true,
+  });
+  if (source === "primary") {
+    primaryAgp.value = result.outputFilename;
+  } else {
+    secondaryAgp.value = result.outputFilename;
+  }
+  toast.success(`Created ${result.outputFilename}`);
+};
+
 const sleep = (ms: number): Promise<void> =>
   new Promise((resolve) => window.setTimeout(resolve, ms));