@nanalogue/node 0.1.4 → 0.2.0

package/README.md

@@ -97,7 +97,8 @@ The output is a JSON object for the first read:
   "reference_end": 17,
   "alignment_length": 8,
   "alignment_type": "primary_forward",
-  "mod_count": "T+T:0;(probabilities >= 0.5020, PHRED base qual >= 0)"
+  "mod_count": "T+T:0;(probabilities >= 0.5020, PHRED base qual >= 0)",
+  "mapq": 255
 }
 ```
 <!-- TEST OUTPUT: END readInfo -->
@@ -158,7 +159,8 @@ The output is a JSON object for the first read. The `data` arrays contain
     }
   ],
   "read_id": "5d10eb9a-aae1-4db8-8ec6-7ebb34d32575",
-  "seq_len": 8
+  "seq_len": 8,
+  "mapq": 255
 }
 ```
 <!-- TEST OUTPUT: END bamMods -->
@@ -171,12 +173,11 @@ Compute windowed modification densities across reads.
 ```typescript
 import { windowReads } from '@nanalogue/node';
 
-const json = await windowReads({
+const entries = await windowReads({
   bamPath: 'tests/data/examples/example_1.bam',
   win: 2,
   step: 1
 });
-const entries = JSON.parse(json);
 console.log(JSON.stringify(entries[0], null, 2));
 ```
 <!-- TEST CODE: END windowReads -->

package/index.d.ts

@@ -24,6 +24,7 @@ export interface MappedReadInfo {
   alignment_length: number;
   alignment_type: 'primary_forward' | 'primary_reverse' | 'secondary_forward' | 'secondary_reverse' | 'supplementary_forward' | 'supplementary_reverse';
   mod_count: string;
+  mapq: number;
 }
 
 export interface UnmappedReadInfo {
@@ -31,6 +32,7 @@ export interface UnmappedReadInfo {
   sequence_length: number;
   alignment_type: 'unmapped';
   mod_count: string;
+  mapq: number;
 }
 
 export type ReadInfoRecord = MappedReadInfo | UnmappedReadInfo;
@@ -146,6 +148,7 @@ export interface MappedBamModRecord {
   mod_table: ModTableEntry[];
   read_id: string;
   seq_len: number;
+  mapq: number;
 }
 
 export interface UnmappedBamModRecord {
@@ -153,12 +156,43 @@ export interface UnmappedBamModRecord {
   mod_table: ModTableEntry[];
   read_id: string;
   seq_len: number;
+  mapq: number;
 }
 
 export type BamModRecord = MappedBamModRecord | UnmappedBamModRecord;
 
 export declare function bamMods(options: ReadOptions): Promise<BamModRecord[]>;
 
+// Window output types
+export interface WindowModTableEntry {
+  base: string;
+  is_strand_plus: boolean;
+  mod_code: string;
+  data: [number, number, number, number, number, number][];
+}
+
+export interface MappedWindowReadEntry {
+  alignment_type: 'primary_forward' | 'primary_reverse' | 'secondary_forward' | 'secondary_reverse' | 'supplementary_forward' | 'supplementary_reverse';
+  alignment: {
+    start: number;
+    end: number;
+    contig: string;
+    contig_id: number;
+  };
+  mod_table: WindowModTableEntry[];
+  read_id: string;
+  seq_len: number;
+}
+
+export interface UnmappedWindowReadEntry {
+  alignment_type: 'unmapped';
+  mod_table: WindowModTableEntry[];
+  read_id: string;
+  seq_len: number;
+}
+
+export type WindowReadEntry = MappedWindowReadEntry | UnmappedWindowReadEntry;
+
 // Base options shared by WindowOptions (excluding region/fullRegion)
 interface BaseWindowOptionsCore {
   /** Path to the BAM file (local path or URL). */
@@ -246,6 +280,6 @@ interface WindowOptionsWithoutRegion extends BaseWindowOptionsCore {
  */
 export type WindowOptions = WindowOptionsWithRegion | WindowOptionsWithoutRegion;
 
-export declare function windowReads(options: WindowOptions): Promise<string>;
+export declare function windowReads(options: WindowOptions): Promise<WindowReadEntry[]>;
 
 export declare function seqTable(options: ReadOptions): Promise<string>;

package/index.js

@@ -253,48 +253,51 @@ switch (platform) {
         }
         break
       case 'riscv64':
+        if (isMusl()) {
+          throw new Error(`Unsupported architecture on Linux musl: ${arch}`)
+        }
+        localFileExisted = existsSync(
+          join(__dirname, 'nanalogue.linux-riscv64-gnu.node')
+        )
+        try {
+          if (localFileExisted) {
+            nativeBinding = require('./nanalogue.linux-riscv64-gnu.node')
+          } else {
+            nativeBinding = require('@nanalogue/node-linux-riscv64-gnu')
+          }
+        } catch (e) {
+          loadError = e
+        }
+        break
+      case 'ppc64':
         if (isMusl()) {
           localFileExisted = existsSync(
-            join(__dirname, 'nanalogue.linux-riscv64-musl.node')
+            join(__dirname, 'nanalogue.linux-ppc64-musl.node')
           )
           try {
             if (localFileExisted) {
-              nativeBinding = require('./nanalogue.linux-riscv64-musl.node')
+              nativeBinding = require('./nanalogue.linux-ppc64-musl.node')
             } else {
-              nativeBinding = require('@nanalogue/node-linux-riscv64-musl')
+              nativeBinding = require('@nanalogue/node-linux-ppc64-musl')
             }
           } catch (e) {
             loadError = e
           }
         } else {
           localFileExisted = existsSync(
-            join(__dirname, 'nanalogue.linux-riscv64-gnu.node')
+            join(__dirname, 'nanalogue.linux-ppc64-gnu.node')
           )
           try {
             if (localFileExisted) {
-              nativeBinding = require('./nanalogue.linux-riscv64-gnu.node')
+              nativeBinding = require('./nanalogue.linux-ppc64-gnu.node')
             } else {
-              nativeBinding = require('@nanalogue/node-linux-riscv64-gnu')
+              nativeBinding = require('@nanalogue/node-linux-ppc64-gnu')
             }
           } catch (e) {
             loadError = e
           }
         }
         break
-      case 's390x':
-        localFileExisted = existsSync(
-          join(__dirname, 'nanalogue.linux-s390x-gnu.node')
-        )
-        try {
-          if (localFileExisted) {
-            nativeBinding = require('./nanalogue.linux-s390x-gnu.node')
-          } else {
-            nativeBinding = require('@nanalogue/node-linux-s390x-gnu')
-          }
-        } catch (e) {
-          loadError = e
-        }
-        break
       default:
         throw new Error(`Unsupported architecture on Linux: ${arch}`)
     }

package/package.json

@@ -1,12 +1,13 @@
 {
   "name": "@nanalogue/node",
-  "version": "0.1.4",
+  "version": "0.2.0",
   "description": "Node.js bindings for Nanalogue: single-molecule BAM/Mod-BAM analysis",
   "main": "index.js",
   "types": "index.d.ts",
   "files": [
     "index.js",
-    "index.d.ts"
+    "index.d.ts",
+    "README.md"
   ],
   "napi": {
     "binaryName": "nanalogue",
@@ -16,7 +17,12 @@
       "x86_64-unknown-linux-gnu",
       "x86_64-unknown-linux-musl",
       "aarch64-unknown-linux-gnu",
-      "aarch64-unknown-linux-musl"
+      "aarch64-unknown-linux-musl",
+      "armv7-unknown-linux-gnueabihf",
+      "armv7-unknown-linux-musleabihf",
+      "riscv64gc-unknown-linux-gnu",
+      "powerpc64le-unknown-linux-gnu",
+      "powerpc64le-unknown-linux-musl"
     ]
   },
   "engines": {
@@ -30,6 +36,7 @@
     "lint": "biome check .",
     "lint:fix": "biome check --write .",
     "format": "biome format --write .",
+    "prepare": "git config core.hooksPath .githooks || true",
     "prepublishOnly": "napi pre-publish --npm-dir npm --no-gh-release"
   },
   "devDependencies": {
@@ -57,11 +64,16 @@
   },
   "author": "Sathish Thiyagarajan <mail@unintegrable.com>",
   "optionalDependencies": {
-    "@nanalogue/node-darwin-x64": "0.1.4",
-    "@nanalogue/node-darwin-arm64": "0.1.4",
-    "@nanalogue/node-linux-x64-gnu": "0.1.4",
-    "@nanalogue/node-linux-x64-musl": "0.1.4",
-    "@nanalogue/node-linux-arm64-gnu": "0.1.4",
-    "@nanalogue/node-linux-arm64-musl": "0.1.4"
+    "@nanalogue/node-darwin-x64": "0.2.0",
+    "@nanalogue/node-darwin-arm64": "0.2.0",
+    "@nanalogue/node-linux-x64-gnu": "0.2.0",
+    "@nanalogue/node-linux-x64-musl": "0.2.0",
+    "@nanalogue/node-linux-arm64-gnu": "0.2.0",
+    "@nanalogue/node-linux-arm64-musl": "0.2.0",
+    "@nanalogue/node-linux-arm-gnueabihf": "0.2.0",
+    "@nanalogue/node-linux-arm-musleabihf": "0.2.0",
+    "@nanalogue/node-linux-riscv64-gnu": "0.2.0",
+    "@nanalogue/node-linux-ppc64-gnu": "0.2.0",
+    "@nanalogue/node-linux-ppc64-musl": "0.2.0"
   }
 }