bionode-bwa - npm Package Compare versions

Comparing version 0.0.2 to 0.0.4

package.json

 {
   "name": "bionode-bwa",
   "description": "A Node.js wrapper for the Burrow-Wheeler Aligner (BWA).",
-  "version": "0.0.2",
+  "version": "0.0.4",
   "homepage": "http://github.com/bionode/bionode-bwa",
@@ -21,14 +21,17 @@ "repository": {
   "devDependencies": {
-    "mocha": "~1.21.3",
-    "mocha-lcov-reporter": "0.0.1",
-    "should": "~4.0.4",
+    "async": "~0.9.0",
+    "coveralls": "~2.11.1",
+    "docco": "~0.6.3",
     "istanbul": "~0.3.0",
-    "coveralls": "~2.11.1",
-    "async": "~0.9.0",
     "request": "~2.39.0",
-    "tool-stream": "0.0.1",
+    "tap-spec": "^1.0.0",
+    "tape": "^3.0.0",
+    "testling": "^1.7.1",
     "through2": "~0.5.1",
-    "docco": "~0.6.3"
+    "tool-stream": "0.0.1"
   },
   "keywords": [
+    "bio",
+    "biology",
+    "bionode",
     "bioinformatics",
@@ -47,3 +50,3 @@ "aligner",
     "preinstall": "git clone https://github.com/lh3/bwa.git; cd bwa; git checkout 0.7.10; make",
-    "test": "mocha --reporter spec; rm test/reference.*; rm test/reads.*; rm test/alignment.sam",
+    "test": "node test/bionode-bwa.js | tap-spec && rm test/reference.* && rm test/reads.* && rm test/alignment.sam",
     "build-docs": "docco ./lib/bionode-bwa.js",
@@ -50,0 +53,0 @@ "coverage": "istanbul cover ./node_modules/.bin/_mocha --report lcovonly -- -R spec && rm -rf ./coverage; rm test/reference.*; rm test/reads.*; rm test/alignment.sam",

test/bionode-bwa.js

@@ -5,32 +5,28 @@ var bwa = require('../')
 var request = require('request')
-var should = require('should')
 var tool = require('tool-stream')
 var through = require('through2')
 var async = require('async')
+var test = require('tape')
 
-require('mocha')
-
-describe("Align reads to reference with BWA", function() {
-  this.timeout(6000000);
+test("Align reads to reference with BWA", function (t) {
+  t.plan(2)
   var referencePath = 'test/reference.fasta.gz'
   var readsPath = 'test/reads.fastq.gz'
   var alignmentPath = 'test/alignment.sam'
+  var referenceURL = 'http://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/protozoa/Guillardia_theta/Guith1/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz'
+  var readsURL = 'http://ftp.sra.ebi.ac.uk//vol1/fastq/SRR070/SRR070675/SRR070675.fastq.gz'
 
-  it("should take paths for reference, reads and aligment. Reference should be indexed first.", function(done) {
-    var referenceURL = 'http://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/protozoa/Guillardia_theta/Guith1/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz'
-    var readsURL = 'http://ftp.sra.ebi.ac.uk//vol1/fastq/SRR070/SRR070675/SRR070675.fastq.gz'
-    var downloads = [
-      download(referenceURL, referencePath),
-      download(readsURL, readsPath)
-    ]
-    async.parallel(downloads, alignReadsToRef)
+  var downloads = [
+    download(referenceURL, referencePath),
+    download(readsURL, readsPath)
+  ]
+  async.parallel(downloads, alignReadsToRef)
 
-    function alignReadsToRef() {
-      var mem = bwa() // default to mem
-      mem([referencePath, readsPath, alignmentPath])
-      .on('data', function(data) { checksum(data, '3dae171586e8f5fda2737795ff2e39df711701cb', done) })
-    }
-  })
+  function alignReadsToRef() {
+    var msg = "should take paths for reference, reads and aligment. Reference should be indexed first."
+    var mem = bwa() // default to mem
+    mem([referencePath, readsPath, alignmentPath])
+    .on('data', function(data) { checksum(data, '3dae171586e8f5fda2737795ff2e39df711701cb', msg, t) })
 
-  it("should align using a Stream that takes arrays of paths for reference and reads.", function(done) {
+    var msg = "should align using a Stream that takes arrays of paths for reference and reads."
     var mem = bwa('mem -x pacbio')
@@ -40,4 +36,4 @@ var memStream = mem() // we will pass arguments with write
     memStream.end()
-    memStream.on('data', function(data) { checksum(data, 'a2ac465ac0d9e0879a9f9a43108e36b682f2e018', done) })
-  })
+    memStream.on('data', function(data) { checksum(data, 'a2ac465ac0d9e0879a9f9a43108e36b682f2e018', msg, t) })
+  }
 })
@@ -56,3 +52,3 @@
 
-function checksum(data, hash, cb) {
+function checksum(data, hash, msg, t) {
   if (['index', 'aln'].indexOf(data.operation) === -1 && data.status === 'finished') {
@@ -64,6 +60,5 @@ var alignmentFile = fs.createReadStream(data.sam)
       var sha1 = shasum.digest('hex');
-      sha1.should.eql(hash)
-      cb()
+      t.equal(sha1, hash, msg)
     })
   }
 }

Fixed alerts

Copyleft License

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Found 1 instance in 1 package

Mixed license

License

(Experimental) Package contains multiple licenses.

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Non-permissive License

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(Experimental) A license not known to be considered permissive was found.

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Improved metrics

Number of low license alerts

0

decreased by-100%

License quality

100

increased by42.86%

Worsened metrics

Total package byte prevSize

401359

decreased by-65.48%

Number of package files

21

decreased by-74.7%

Lines of code

1015

decreased by-39.08%

No dependency changes