hic-straw - npm Package Compare versions

Comparing version 0.9.3 to 0.9.4

package.json

 {
   "name": "hic-straw",
-  "version": "0.9.3",
+  "version": "0.9.4",
   "description": "Utilities for reading .files (contact matrix files)",
@@ -28,3 +28,3 @@ "main": "src/index.js",
   "scripts": {
-    "build": "webpack; webpack --config webpack.config.var.js; node wrapper/build.js",
+    "build": "webpack; webpack --config webpack.config.es.js; node wrapper/build.js",
     "test": "mocha -u tdd"
@@ -31,0 +31,0 @@ },

README.md

@@ -105,3 +105,3 @@ # hic-straw
 
-<script src="https://cdn.jsdelivr.net/npm/hic-straw@0.9.3/dist/hic-straw.js"></script>
+<script src="https://cdn.jsdelivr.net/npm/hic-straw@0.9.4/dist/hic-straw.js"></script>
 
@@ -108,0 +108,0 @@ ...

src/hicFile.js

@@ -53,3 +53,3 @@ const zlib = require('zlib')
                 const remoteFile = new RemoteFile(args)
-                if(isGoogle(this.url)) {
+                if(isGoogleDrive(this.url)) {
                     this.file = new ThrottledFile(remoteFile, googleRateLimiter)
@@ -780,4 +780,4 @@ } else {
 
-function isGoogle(url) {
-    return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com") > 0
+function isGoogleDrive(url) {
+    return url.indexOf("drive.google.com") >= 0 || url.indexOf("www.googleapis.com/drive") > 0
 }
@@ -784,0 +784,0 @@

src/io/remoteFile.js

@@ -20,6 +20,6 @@ const fetch = require('cross-fetch')
         let url = this.url.slice()    // slice => copy
-        if(jsEnv.isNode) {
+        if (jsEnv.isNode) {
             headers['User-Agent'] = 'straw'
         } else {
-            if(this.config.oauthToken) {
+            if (this.config.oauthToken) {
                 const token = resolveToken(this.config.oauthToken)
@@ -37,3 +37,3 @@ headers['Authorization'] = `Bearer ${token}`
 
-        if(this.config.apiKey) {
+        if (this.config.apiKey) {
             url = addParameter(url, "key", this.config.apiKey)
@@ -56,4 +56,3 @@ }
             throw err
-        }
-        else {
+        } else {
             return response.arrayBuffer();
@@ -68,3 +67,3 @@ }
         async function resolveToken(token) {
-            if(typeof token === 'function') {
+            if (typeof token === 'function') {
                 return await Promise.resolve(token())    // Normalize the result to a promise, since we don't know what the function returns
@@ -84,2 +83,4 @@ } else {
         return url.replace("//www.dropbox.com", "//dl.dropboxusercontent.com");
+    } else if (url.startsWith("ftp://ftp.ncbi.nlm.nih.gov")) {
+        return url.replace("ftp://", "https://")
     } else {
@@ -92,3 +93,3 @@ return url
 function addParameter(url, name, value) {
-    const  paramSeparator = url.includes("?") ? "&" : "?";
+    const paramSeparator = url.includes("?") ? "&" : "?";
     return url + paramSeparator + name + "=" + value;
@@ -95,0 +96,0 @@ }

src/straw.js

@@ -25,2 +25,12 @@ const HicFile = require("./hicFile")
         const idx2 = this.hicFile.chromosomeIndexMap[chr2]
+
+        if(idx1 === undefined) {
+            console.log("No chromosome named: " + region1.chr)
+            return []
+        }
+        if(idx2 === undefined) {
+            console.log("No chromosome named: " + region2.chr)
+            return []
+        }
+
         const x1 = (region1.start === undefined) ? undefined : region1.start / binsize
@@ -32,2 +42,6 @@ const x2 = (region1.end === undefined) ? undefined : region1.end / binsize
         const matrix = await this.hicFile.readMatrix(idx1, idx2)
+        if(!matrix) {
+            console.log("No matrix for " + region1.chr + "-" + region2.chr)
+            return []
+        }
 
@@ -70,2 +84,6 @@ // Find the requested resolution
 
+        if(!blocks || blocks.length === 0) {
+            return []
+        }
+
         const chr1 = this.hicFile.getFileChrName(region1.chr)
@@ -72,0 +90,0 @@ const chr2 = this.hicFile.getFileChrName(region2.chr)

No alert changes

Improved metrics

Total package byte prevSize

369952

2.64%

Lines of code

2261

1.8%

No dependency changes