Add HiCT/Cooler export/import options, reinforce implementation, increase performance

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

@@ -196,6 +196,7 @@ class StartConversionJobRequest implements HiCTAPIRequest {
       readonly assemblyFilename?: string;
       readonly useCurrentAssembly?: boolean;
       readonly direction?: string;
+      readonly outputFilename?: string;
       readonly overwrite?: boolean;
       readonly resolutions?: string;
       readonly compression?: number;
@@ -205,6 +206,8 @@ class StartConversionJobRequest implements HiCTAPIRequest {
       readonly exportMode?: string;
       readonly exportAllResolutions?: boolean;
       readonly buildResolutionPyramid?: boolean;
+      readonly balanceInputCoolers?: boolean;
+      readonly balanceExportedCoolers?: boolean;
       readonly binTableFilename?: string;
       readonly chromSizesFilename?: string;
       readonly binSize?: number;
@@ -232,6 +235,8 @@ class StartBatchConversionJobsRequest implements HiCTAPIRequest {
       readonly exportMode?: string;
       readonly exportAllResolutions?: boolean;
       readonly buildResolutionPyramid?: boolean;
+      readonly balanceInputCoolers?: boolean;
+      readonly balanceExportedCoolers?: boolean;
       readonly binTableFilename?: string;
       readonly chromSizesFilename?: string;
       readonly binSize?: number;

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

@@ -505,6 +505,7 @@ class StartConversionJobRequestDTO extends HiCTAPIRequestDTO<StartConversionJobR
       assemblyFilename: this.entity.options.assemblyFilename,
       useCurrentAssembly: this.entity.options.useCurrentAssembly,
       direction: this.entity.options.direction,
+      outputFilename: this.entity.options.outputFilename,
       overwrite: this.entity.options.overwrite,
       resolutions: this.entity.options.resolutions,
       compression: this.entity.options.compression,
@@ -514,6 +515,8 @@ class StartConversionJobRequestDTO extends HiCTAPIRequestDTO<StartConversionJobR
       exportMode: this.entity.options.exportMode,
       exportAllResolutions: this.entity.options.exportAllResolutions,
       buildResolutionPyramid: this.entity.options.buildResolutionPyramid,
+      balanceInputCoolers: this.entity.options.balanceInputCoolers,
+      balanceExportedCoolers: this.entity.options.balanceExportedCoolers,
       binTableFilename: this.entity.options.binTableFilename,
       chromSizesFilename: this.entity.options.chromSizesFilename,
       binSize: this.entity.options.binSize,
@@ -539,6 +542,8 @@ class StartBatchConversionJobsRequestDTO extends HiCTAPIRequestDTO<StartBatchCon
       exportMode: this.entity.options.exportMode,
       exportAllResolutions: this.entity.options.exportAllResolutions,
       buildResolutionPyramid: this.entity.options.buildResolutionPyramid,
+      balanceInputCoolers: this.entity.options.balanceInputCoolers,
+      balanceExportedCoolers: this.entity.options.balanceExportedCoolers,
       binTableFilename: this.entity.options.binTableFilename,
       chromSizesFilename: this.entity.options.chromSizesFilename,
       binSize: this.entity.options.binSize,

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

@@ -337,13 +337,22 @@
                         Drop all precomputed caches before running the wizard
                       </label>
                     </div>
-                    <div class="form-check form-switch mt-3">
+                    <div v-if="hasSelectedCoolerSource" class="form-check form-switch mt-3">
                       <input id="build-resolution-pyramid" v-model="buildResolutionPyramid" class="form-check-input" type="checkbox" />
                       <label class="form-check-label" for="build-resolution-pyramid">
                         Build optimized resolution pyramid with hictk
                       </label>
                       <div class="form-text">
-                        Enabled by default. HiCT will zoomify and balance converted Cooler inputs before import so sparse or single-resolution files open with a complete set of map resolutions.
+                        Enabled by default. HiCT will zoomify converted Cooler inputs before import so sparse or single-resolution files open with a complete set of map resolutions.
+                      </div>
+                    </div>
+                    <div v-if="hasSelectedCoolerSource" class="form-check form-switch mt-3">
+                      <input id="balance-input-coolers" v-model="balanceInputCoolers" class="form-check-input" type="checkbox" />
+                      <label class="form-check-label" for="balance-input-coolers">
+                        Balance input Coolers with hictk
+                      </label>
+                      <div class="form-text">
+                        Enabled by default for .cool/.mcool inputs. HiCT will run hictk ICE balancing before importing so Cooler weights are available immediately.
                       </div>
                     </div>
                     <div v-if="toolchainStatus && !toolchainStatus.hicConversionAvailable" class="alert alert-warning mt-3 mb-0">
@@ -913,6 +922,7 @@ const precomputeTracks = ref(true);
 const forceTrackPrecompute = ref(false);
 const dropCachesBeforeRun = ref(false);
 const buildResolutionPyramid = ref(true);
+const balanceInputCoolers = ref(true);
 const blendMode = ref<WizardBlendMode>("OVER");
 const topOpacity = ref(0.5);
 const bottomOpacity = ref(1.0);
@@ -1353,6 +1363,16 @@ const isOpenableAssemblyFilename = (name: string): boolean => {
   );
 };
 
+const isCoolerFilename = (name: string): boolean => {
+  const lowered = name.toLowerCase();
+  return lowered.endsWith(".cool") || lowered.endsWith(".mcool");
+};
+
+const hasSelectedCoolerSource = computed(() =>
+  isCoolerFilename(primarySource.filename) ||
+  (requiresSecondarySource.value && isCoolerFilename(secondarySource.filename))
+);
+
 const stripCompressionSuffix = (name: string): string =>
   name.replace(/\.(gz|bgz|xz|zst|zstd|bz2|lz4|lzo)$/i, "");
 
@@ -1749,8 +1769,13 @@ const ensureOpenedFilename = async (source: SourceDraft): Promise<string> => {
   if (!resolution) {
     throw new Error(`Failed to resolve source ${source.filename}`);
   }
+  const forceCoolerPreparation =
+    isCoolerFilename(source.filename) &&
+    canConvertSource(source) &&
+    (buildResolutionPyramid.value || balanceInputCoolers.value);
   if (
     (!(source.forceConversion && canConvertSource(source))) &&
+    !forceCoolerPreparation &&
     (resolution.action === "OPEN_DIRECT" || resolution.action === "REUSE_CONVERTED")
   ) {
     return resolution.resolvedFilename;
@@ -1770,6 +1795,7 @@ const ensureOpenedFilename = async (source: SourceDraft): Promise<string> => {
       binSize: source.binSize ?? undefined,
       countAsFloat: source.countAsFloat || undefined,
       buildResolutionPyramid: buildResolutionPyramid.value,
+      balanceInputCoolers: balanceInputCoolers.value,
     })
   );
   const finishedJob = await waitForConversionJob(started.jobId);

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

@@ -25,7 +25,7 @@
     <div class="modal-dialog modal-lg modal-dialog-centered modal-dialog-scrollable">
       <div class="modal-content">
         <div class="modal-header">
-          <h5 class="modal-title">Export matrix to .mcool</h5>
+          <h5 class="modal-title">Export matrix to Cooler</h5>
           <button type="button" class="btn-close" @click="emit('dismissed')"></button>
         </div>
         <div class="modal-body">
@@ -85,6 +85,20 @@
             </div>
           </div>
 
+          <div class="mb-3">
+            <label class="form-label">Output Cooler filename</label>
+            <input
+              v-model="outputFilename"
+              class="form-control"
+              type="text"
+              placeholder="matrix.mcool"
+              @input="outputFilenameTouched = true"
+            />
+            <small class="text-muted">
+              Relative to the HiCT data directory. Use .cool for one selected resolution, or .mcool for multiple resolutions.
+            </small>
+          </div>
+
           <div class="mb-3">
             <div class="form-check form-switch">
               <input
@@ -169,6 +183,22 @@
             Disabled by default: only the finest resolution is exported, so you can zoomify later if needed.
           </small>
 
+          <div class="form-check form-switch mb-2">
+            <input
+              id="export-balance-coolers"
+              v-model="balanceExportedCoolers"
+              class="form-check-input"
+              type="checkbox"
+              role="switch"
+            />
+            <label class="form-check-label" for="export-balance-coolers">
+              Balance exported Cooler with hictk
+            </label>
+          </div>
+          <small class="text-muted d-block mb-3">
+            Enabled by default. Auto and hictk-assisted modes run ICE balancing so downstream Cooler tools can use generated weights.
+          </small>
+
           <div class="form-check mb-3">
             <input
               id="export-overwrite"
@@ -177,7 +207,7 @@
               type="checkbox"
             />
             <label class="form-check-label" for="export-overwrite">
-              Overwrite existing .mcool next to source
+              Overwrite existing output
             </label>
           </div>
 
@@ -198,7 +228,7 @@
             @click="startExport"
           >
             <span v-if="submitting" class="spinner-border spinner-border-sm me-2"></span>
-            Export .mcool
+            Export Cooler
           </button>
         </div>
       </div>
@@ -242,6 +272,9 @@ const compression = ref(6);
 const parallelism = ref(Math.max(1, navigator.hardwareConcurrency || 1));
 const exportMode = ref("auto");
 const exportAllResolutions = ref(false);
+const balanceExportedCoolers = ref(true);
+const outputFilename = ref("");
+const outputFilenameTouched = ref(false);
 const selectorKind = ref<"source" | "agp" | null>(null);
 const submitting = ref(false);
 const errorMessage = ref("");
@@ -258,6 +291,16 @@ watch(
   }
 );
 
+watch(
+  [sourceFilename, exportAllResolutions],
+  () => {
+    if (!outputFilenameTouched.value) {
+      outputFilename.value = defaultOutputFilename(sourceFilename.value, exportAllResolutions.value);
+    }
+  },
+  { immediate: true }
+);
+
 function isHictFilename(filename: string): boolean {
   return filename.toLowerCase().endsWith(".hict.hdf5");
 }
@@ -269,12 +312,26 @@ function isAgpFilename(filename: string): boolean {
 function onFileSelected(filename: string): void {
   if (selectorKind.value === "source") {
     sourceFilename.value = filename;
+    if (!outputFilenameTouched.value) {
+      outputFilename.value = defaultOutputFilename(filename, exportAllResolutions.value);
+    }
   } else if (selectorKind.value === "agp") {
     customAgpFilename.value = filename;
   }
   selectorKind.value = null;
 }
 
+function defaultOutputFilename(filename: string, allResolutions: boolean): string {
+  if (!filename) {
+    return "";
+  }
+  const extension = allResolutions ? ".mcool" : ".cool";
+  const stripped = filename
+    .replace(/\.hict\.hdf5$/i, "")
+    .replace(/\.hict$/i, "");
+  return `${stripped}${extension}`;
+}
+
 function loadConversionJobs(): void {
   jobsLoading.value = true;
   props.networkManager.requestManager
@@ -309,6 +366,7 @@ async function startExport(): Promise<void> {
       new StartConversionJobRequest({
         filename: sourceFilename.value,
         direction: "hict-to-mcool",
+        outputFilename: outputFilename.value || defaultOutputFilename(sourceFilename.value, exportAllResolutions.value),
         useCurrentAssembly: useCurrentAssembly.value,
         assemblyFilename: useCurrentAssembly.value ? undefined : customAgpFilename.value || undefined,
         overwrite: overwrite.value,
@@ -317,6 +375,7 @@ async function startExport(): Promise<void> {
         parallelism: parallelism.value,
         exportMode: exportMode.value,
         exportAllResolutions: exportAllResolutions.value,
+        balanceExportedCoolers: balanceExportedCoolers.value,
       })
     );
     jobId.value = response.jobId;