@gmod/cram - npm Package Compare versions

Comparing version 1.2.0 to 1.3.0

dist/cramFile/codecs/index.js

@@ -11,10 +11,5 @@ 'use strict';
 var BetaCodec = require('./beta');
+var GammaCodec = require('./gamma');
+var SubexpCodec = require('./subexp');
 
-// class GolombCodec extends CramCodec {}
-// class ByteArrayLengthCodec extends CramCodec {}
-// class BetaCodec extends CramCodec {}
-// class SubexpCodec extends CramCodec {}
-// class GolombRiceCodec extends CramCodec {}
-// class GammaCodec extends CramCodec {}
-
 var codecClasses = {
@@ -26,6 +21,6 @@ 1: ExternalCodec,
   5: ByteArrayStopCodec,
-  6: BetaCodec
-  // 7: SubexpCodec,
+  6: BetaCodec,
+  7: SubexpCodec,
   // 8: GolombRiceCodec,
-  // 9: GammaCodec,
+  9: GammaCodec
 };
@@ -32,0 +27,0 @@

dist/cramFile/sectionParsers.js

@@ -221,3 +221,3 @@ 'use strict';
         6: new Parser().itf8('offset').itf8('length'), // BETA
-        7: new Parser().itf8('offset').itf8('K'),
+        7: new Parser().itf8('offset').itf8('K'), // SUBEXP
         8: new Parser().itf8('offset').itf8('log2m'), // GOLOMB_RICE
@@ -224,0 +224,0 @@ 9: new Parser().itf8('offset') // GAMMA

dist/cramFile/slice/decodeRecord.js

@@ -7,2 +7,6 @@ 'use strict';
 
+var _toConsumableArray2 = require('babel-runtime/helpers/toConsumableArray');
+
+var _toConsumableArray3 = _interopRequireDefault(_toConsumableArray2);
+
 var _parseInt = require('babel-runtime/core-js/number/parse-int');
@@ -160,2 +164,17 @@
 
+function thingToString(thing) {
+  if (thing instanceof Buffer) {
+    return readNullTerminatedStringFromBuffer(thing);
+  } else if (thing.length && thing.indexOf) {
+    // array-like
+    if (!thing[thing.length - 1]) {
+      // trim zeroes off the end if necessary
+      var termIndex = thing.indexOf(0);
+      return String.fromCharCode.apply(String, (0, _toConsumableArray3.default)(thing.slice(0, termIndex)));
+    }
+    return String.fromCharCode.apply(String, (0, _toConsumableArray3.default)(thing));
+  }
+  return String(thing);
+}
+
 function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, recordNumber) {
@@ -180,3 +199,3 @@ var cramRecord = new CramRecord();
 
-  if (compressionScheme.readNamesIncluded) cramRecord.readName = decodeDataSeries('RN').toString('utf8'); // new String(readNameCodec.readData(), charset)
+  if (compressionScheme.readNamesIncluded) cramRecord.readName = thingToString(decodeDataSeries('RN'));
 
@@ -188,3 +207,5 @@ // mate record
     mate.flags = decodeDataSeries('MF');
-    if (!compressionScheme.readNamesIncluded) cramRecord.mate.readName = decodeDataSeries('RN'); // new String(readNameCodec.readData(), charset)
+    if (!compressionScheme.readNamesIncluded) {
+      mate.readName = thingToString(decodeDataSeries('RN'));
+    }
     mate.sequenceId = decodeDataSeries('NS');
@@ -191,0 +212,0 @@ mate.alignmentStart = decodeDataSeries('NP');

dist/cramFile/slice/index.js

@@ -107,3 +107,4 @@ 'use strict';
     sequenceId: mateRecord.sequenceId,
-    alignmentStart: mateRecord.alignmentStart
+    alignmentStart: mateRecord.alignmentStart,
+    uniqueId: mateRecord.uniqueId
   };
@@ -118,3 +119,4 @@ if (mateRecord.readName) thisRecord.mate.readName = mateRecord.readName;
       sequenceId: thisRecord.sequenceId,
-      alignmentStart: thisRecord.alignmentStart
+      alignmentStart: thisRecord.alignmentStart,
+      uniqueId: thisRecord.uniqueId
     };
@@ -588,2 +590,3 @@ if (thisRecord.readName) mateRecord.mate.readName = thisRecord.readName;
                   if (!codec) throw new CramMalformedError('no codec defined for ' + dataSeriesName + ' data series');
+                  // console.log(dataSeriesName, Object.getPrototypeOf(codec))
                   return codec.decode(_this, coreDataBlock, blocksByContentId, cursors);
@@ -604,3 +607,3 @@ };
                 records[i] = decodeRecord(this, decodeDataSeries, compressionScheme, sliceHeader, coreDataBlock, blocksByContentId, cursors, majorVersion, i);
-                records[i].uniqueId = sliceHeader.content.recordCounter + i;
+                records[i].uniqueId = sliceHeader.content.recordCounter + i + 1;
                 _context7.next = 45;
@@ -607,0 +610,0 @@ break;

package.json

 {
   "name": "@gmod/cram",
-  "version": "1.2.0",
+  "version": "1.3.0",
   "description": "read CRAM files with pure Javascript",
@@ -30,3 +30,3 @@ "license": "MIT",
     "build": "babel src -d dist",
-    "built-tests": "rm -rf built-tests; babel test -d built-tests; ln -s ../test/data built-tests/data; mocha built-tests",
+    "built-tests": "rm -rf built-tests; mkdir built-tests; ln -s ../test/data built-tests/data; babel test -d built-tests; mocha built-tests",
     "watch": "npm-watch",
@@ -33,0 +33,0 @@ "prepublishOnly": "npm test && npm run build && cp dist/errors.js errors.js",

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Improved metrics

Total package byte prevSize

241672

increased by2.14%

Number of package files

40

increased by5.26%

Lines of code

5326

increased by1.99%

No dependency changes