@gmod/cram 1.5.9 → 1.6.2

package/dist/cramFile/sectionParsers.js

@@ -1,51 +1,64 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime-corejs3/helpers/interopRequireDefault");
-
-var _keys = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/keys"));
-
-var _forEach = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/instance/for-each"));
-
-var _assign = _interopRequireDefault(require("@babel/runtime-corejs3/core-js-stable/object/assign"));
-
-var _require = require('@gmod/binary-parser'),
-    Parser = _require.Parser;
-
-var singleItf8 = new Parser().itf8();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getSectionParsers = exports.cramFileDefinition = void 0;
+var binary_parser_1 = require("@gmod/binary-parser");
+var singleItf8 = new binary_parser_1.Parser().itf8();
 var cramFileDefinition = {
-  parser: new Parser().string('magic', {
-    length: 4
-  }).uint8('majorVersion').uint8('minorVersion').string('fileId', {
-    length: 20,
-    stripNull: true
-  }),
-  maxLength: 26
+    parser: new binary_parser_1.Parser()
+        .string('magic', { length: 4 })
+        .uint8('majorVersion')
+        .uint8('minorVersion')
+        .string('fileId', { length: 20, stripNull: true }),
+    maxLength: 26,
 };
+exports.cramFileDefinition = cramFileDefinition;
 var cramBlockHeader = {
-  parser: new Parser().uint8('compressionMethod', {
-    formatter:
-    /* istanbul ignore next */
-    function formatter(b) {
-      var method = ['raw', 'gzip', 'bzip2', 'lzma', 'rans'][b];
-      if (!method) throw new Error("compression method number ".concat(b, " not implemented"));
-      return method;
-    }
-  }).uint8('contentType', {
-    formatter:
-    /* istanbul ignore next */
-    function formatter(b) {
-      var type = ['FILE_HEADER', 'COMPRESSION_HEADER', 'MAPPED_SLICE_HEADER', 'UNMAPPED_SLICE_HEADER', // < only used in cram v1
-      'EXTERNAL_DATA', 'CORE_DATA'][b];
-      if (!type) throw new Error("invalid block content type id ".concat(b));
-      return type;
-    }
-  }).itf8('contentId').itf8('compressedSize').itf8('uncompressedSize'),
-  maxLength: 17
+    parser: new binary_parser_1.Parser()
+        .uint8('compressionMethod', {
+        formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ b) {
+            var method = [
+                'raw',
+                'gzip',
+                'bzip2',
+                'lzma',
+                'rans',
+                'rans4x16',
+                'arith',
+                'fqzcomp',
+                'tok3',
+            ][b];
+            if (!method) {
+                throw new Error("compression method number ".concat(b, " not implemented"));
+            }
+            return method;
+        },
+    })
+        .uint8('contentType', {
+        formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ b) {
+            var type = [
+                'FILE_HEADER',
+                'COMPRESSION_HEADER',
+                'MAPPED_SLICE_HEADER',
+                'UNMAPPED_SLICE_HEADER',
+                'EXTERNAL_DATA',
+                'CORE_DATA',
+            ][b];
+            if (!type) {
+                throw new Error("invalid block content type id ".concat(b));
+            }
+            return type;
+        },
+    })
+        .itf8('contentId')
+        .itf8('compressedSize')
+        .itf8('uncompressedSize'),
+    maxLength: 17,
 };
 var cramBlockCrc32 = {
-  parser: new Parser().uint32('crc32'),
-  maxLength: 4
-}; // const ENCODING_NAMES = [
+    parser: new binary_parser_1.Parser().uint32('crc32'),
+    maxLength: 4,
+};
+// const ENCODING_NAMES = [
 //   'NULL', // 0
 //   'EXTERNAL', // 1
 //   'GOLOMB', // 2
@@ -57,334 +70,283 @@ var cramBlockCrc32 = {
 //   'GOLOMB_RICE', // 8
 //   'GAMMA', // 9
 // ]
-
-var cramTagDictionary = new Parser().itf8('size').buffer('ents', {
-  length: 'size',
-  formatter:
-  /* istanbul ignore next */
-  function formatter(buffer) {
-    function makeTagSet(stringStart, stringEnd) {
-      var str = buffer.toString('utf8', stringStart, stringEnd);
-      var tags = [];
-
-      for (var _i = 0; _i < str.length; _i += 3) {
-        tags.push(str.substr(_i, 3));
-      }
-
-      return tags;
-    }
-    /* eslint-disable */
-
-
-    var tagSets = [];
-    var stringStart = 0;
-    var i;
-    /* eslint-enable */
-
-    for (i = 0; i < buffer.length; i += 1) {
-      if (!buffer[i]) {
-        tagSets.push(makeTagSet(stringStart, i));
-        stringStart = i + 1;
-      }
-    }
-
-    if (i > stringStart) tagSets.push(makeTagSet(stringStart, i));
-    return tagSets;
-  }
-}); // const cramPreservationMapKeys = 'XX RN AP RR SM TD'.split(' ')
-
-var parseByteAsBool = new Parser().uint8(null, {
-  formatter:
-  /* istanbul ignore next */
-  function formatter(val) {
-    return !!val;
-  }
-});
-var cramPreservationMap = new Parser().itf8('mapSize').itf8('mapCount').array('ents', {
-  length: 'mapCount',
-  type: new Parser().string('key', {
-    length: 2,
-    stripNull: false // formatter: val => cramPreservationMapKeys[val] || 0,
-
-  }).choice('value', {
-    tag: 'key',
-    choices: {
-      MI: parseByteAsBool,
-      UI: parseByteAsBool,
-      PI: parseByteAsBool,
-      RN: parseByteAsBool,
-      AP: parseByteAsBool,
-      RR: parseByteAsBool,
-      SM: new Parser().array(null, {
-        type: 'uint8',
-        length: 5
-      }),
-      TD: new Parser().nest(null, {
-        type: cramTagDictionary,
-        formatter:
-        /* istanbul ignore next */
-        function formatter(data) {
-          return data.ents;
+var cramTagDictionary = new binary_parser_1.Parser().itf8('size').buffer('ents', {
+    length: 'size',
+    formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ buffer) {
+        function makeTagSet(stringStart, stringEnd) {
+            var str = buffer.toString('utf8', stringStart, stringEnd);
+            var tags = [];
+            for (var i_1 = 0; i_1 < str.length; i_1 += 3) {
+                tags.push(str.substr(i_1, 3));
+            }
+            return tags;
         }
-      })
-    }
-  })
+        /* eslint-disable */
+        var tagSets = [];
+        var stringStart = 0;
+        var i;
+        /* eslint-enable */
+        for (i = 0; i < buffer.length; i += 1) {
+            if (!buffer[i]) {
+                tagSets.push(makeTagSet(stringStart, i));
+                stringStart = i + 1;
+            }
+        }
+        if (i > stringStart) {
+            tagSets.push(makeTagSet(stringStart, i));
+        }
+        return tagSets;
+    },
+});
+// const cramPreservationMapKeys = 'XX RN AP RR SM TD'.split(' ')
+var parseByteAsBool = new binary_parser_1.Parser().uint8(null, {
+    formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ val) { return !!val; },
+});
+var cramPreservationMap = new binary_parser_1.Parser()
+    .itf8('mapSize')
+    .itf8('mapCount')
+    .array('ents', {
+    length: 'mapCount',
+    type: new binary_parser_1.Parser()
+        .string('key', {
+        length: 2,
+        stripNull: false,
+        // formatter: val => cramPreservationMapKeys[val] || 0,
+    })
+        .choice('value', {
+        tag: 'key',
+        choices: {
+            MI: parseByteAsBool,
+            UI: parseByteAsBool,
+            PI: parseByteAsBool,
+            RN: parseByteAsBool,
+            AP: parseByteAsBool,
+            RR: parseByteAsBool,
+            SM: new binary_parser_1.Parser().array(null, { type: 'uint8', length: 5 }),
+            TD: new binary_parser_1.Parser().nest(null, {
+                type: cramTagDictionary,
+                formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ data) { return data.ents; },
+            }),
+        },
+    }),
 });
 /* istanbul ignore next */
-
 function formatMap(data) {
-  var map = {};
-
-  for (var i = 0; i < data.ents.length; i += 1) {
-    var _data$ents$i = data.ents[i],
-        key = _data$ents$i.key,
-        value = _data$ents$i.value;
-    if (map[key]) console.warn("duplicate key ".concat(key, " in map"));
-    map[key] = value;
-  }
-
-  return map;
+    var map = {};
+    for (var i = 0; i < data.ents.length; i += 1) {
+        var _a = data.ents[i], key = _a.key, value = _a.value;
+        if (map[key]) {
+            console.warn("duplicate key ".concat(key, " in map"));
+        }
+        map[key] = value;
+    }
+    return map;
 }
-
 var unversionedParsers = {
-  cramFileDefinition: cramFileDefinition,
-  cramBlockHeader: cramBlockHeader,
-  cramBlockCrc32: cramBlockCrc32
-}; // each of these is a function of the major and minor version
-
+    cramFileDefinition: cramFileDefinition,
+    cramBlockHeader: cramBlockHeader,
+    cramBlockCrc32: cramBlockCrc32,
+};
+// each of these is a function of the major and minor version
 var versionedParsers = {
-  // assemble a section parser for the unmapped slice header, with slight
-  // variations depending on the major version of the cram file
-  cramUnmappedSliceHeader: function cramUnmappedSliceHeader(majorVersion) {
-    var maxLength = 0;
-    var parser = new Parser().itf8('numRecords');
-    maxLength += 5; // recordCounter is itf8 in a CRAM v2 file, absent in CRAM v1
-
-    if (majorVersion >= 3) {
-      parser = parser.ltf8('recordCounter');
-      maxLength += 9;
-    } else if (majorVersion === 2) {
-      parser = parser.itf8('recordCounter');
-      maxLength += 5;
-    }
-
-    parser = parser.itf8('numBlocks').itf8('numContentIds').array('contentIds', {
-      type: singleItf8,
-      length: 'numContentIds'
-    });
-    maxLength += 5 * 2; // + numContentIds*5
-    // the md5 sum is missing in cram v1
-
-    if (majorVersion >= 2) {
-      parser = parser.array('md5', {
-        type: 'uint8',
-        length: 16
-      });
-      maxLength += 16;
-    }
-
-    var maxLengthFunc = function maxLengthFunc(numContentIds) {
-      return maxLength + numContentIds * 5;
-    };
-
-    return {
-      parser: parser,
-      maxLength: maxLengthFunc
-    }; // : p, maxLength: numContentIds => 5 + 9 + 5 * 2 + 5 * numContentIds + 16 }
-  },
-  // assembles a section parser for the unmapped slice header, with slight
-  // variations depending on the major version of the cram file
-  cramMappedSliceHeader: function cramMappedSliceHeader(majorVersion) {
-    var parser = new Parser().itf8('refSeqId').itf8('refSeqStart').itf8('refSeqSpan').itf8('numRecords');
-    var maxLength = 5 * 4;
-
-    if (majorVersion >= 3) {
-      parser = parser.ltf8('recordCounter');
-      maxLength += 9;
-    } else if (majorVersion === 2) {
-      parser = parser.itf8('recordCounter');
-      maxLength += 5;
-    }
-
-    parser = parser.itf8('numBlocks').itf8('numContentIds').array('contentIds', {
-      type: singleItf8,
-      length: 'numContentIds'
-    }).itf8('refBaseBlockId');
-    maxLength += 5 * 3; // the md5 sum is missing in cram v1
-
-    if (majorVersion >= 2) {
-      parser = parser.array('md5', {
-        type: 'uint8',
-        length: 16
-      });
-      maxLength += 16;
-    }
-
-    var maxLengthFunc = function maxLengthFunc(numContentIds) {
-      return maxLength + numContentIds * 5;
-    };
-
-    return {
-      parser: parser,
-      maxLength: maxLengthFunc
-    };
-  },
-  cramEncoding: function cramEncoding(majorVersion) {
-    var parser = new Parser().namely('cramEncoding').itf8('codecId').itf8('parametersBytes').choice('parameters', {
-      tag: 'codecId',
-      choices: {
-        0: new Parser(),
-        // NULL
-        1: new Parser().itf8('blockContentId'),
-        // EXTERNAL
-        2: new Parser().itf8('offset').itf8('M'),
-        // GOLOMB,
-        // HUFFMAN_INT
-        3: Parser.start().itf8('numCodes').array('symbols', {
-          length: 'numCodes',
-          type: singleItf8
-        }).itf8('numLengths').array('bitLengths', {
-          length: 'numLengths',
-          type: singleItf8
-        }),
-        4: Parser.start() // BYTE_ARRAY_LEN
-        .nest('lengthsEncoding', {
-          type: 'cramEncoding'
-        }).nest('valuesEncoding', {
-          type: 'cramEncoding'
-        }),
-        // BYTE_ARRAY_STOP is a little different for CRAM v1
-        5: new Parser().uint8('stopByte')[majorVersion > 1 ? 'itf8' : 'int']('blockContentId'),
-        6: new Parser().itf8('offset').itf8('length'),
-        // BETA
-        7: new Parser().itf8('offset').itf8('K'),
-        // SUBEXP
-        8: new Parser().itf8('offset').itf8('log2m'),
-        // GOLOMB_RICE
-        9: new Parser().itf8('offset') // GAMMA
-
-      }
-    });
-    return {
-      parser: parser
-    };
-  },
-  cramDataSeriesEncodingMap: function cramDataSeriesEncodingMap(majorVersion) {
-    return new Parser().itf8('mapSize').itf8('mapCount').array('ents', {
-      length: 'mapCount',
-      type: new Parser().string('key', {
-        length: 2,
-        stripNull: false
-      }).nest('value', {
-        type: this.cramEncoding(majorVersion).parser
-      })
-    });
-  },
-  cramTagEncodingMap: function cramTagEncodingMap(majorVersion) {
-    return new Parser().itf8('mapSize').itf8('mapCount').array('ents', {
-      length: 'mapCount',
-      type: new Parser().itf8('key', {
-        formatter:
-        /* istanbul ignore next */
-        function formatter(integerRepresentation) {
-          return (
-            /* istanbul ignore next */
-            String.fromCharCode(integerRepresentation >> 16 & 0xff) + String.fromCharCode(integerRepresentation >> 8 & 0xff) + String.fromCharCode(integerRepresentation & 0xff)
-          );
+    // assemble a section parser for the unmapped slice header, with slight
+    // variations depending on the major version of the cram file
+    cramUnmappedSliceHeader: function (majorVersion) {
+        var maxLength = 0;
+        var parser = new binary_parser_1.Parser().itf8('numRecords');
+        maxLength += 5;
+        // recordCounter is itf8 in a CRAM v2 file, absent in CRAM v1
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter');
+            maxLength += 9;
         }
-      }).nest('value', {
-        type: this.cramEncoding(majorVersion).parser
-      })
-    });
-  },
-  cramCompressionHeader: function cramCompressionHeader(majorVersion) {
-    var parser = new Parser(); // TODO: if we want to support CRAM v1, we will need to refactor
-    // compression header into 2 parts to parse the landmarks,
-    // like the container header
-
-    parser = parser.nest('preservation', {
-      type: cramPreservationMap,
-      formatter: formatMap
-    }).nest('dataSeriesEncoding', {
-      type: this.cramDataSeriesEncodingMap(majorVersion),
-      formatter: formatMap
-    }).nest('tagEncoding', {
-      type: this.cramTagEncodingMap(majorVersion),
-      formatter: formatMap
-    });
-    return {
-      parser: parser
-    };
-  },
-  cramContainerHeader1: function cramContainerHeader1(majorVersion) {
-    var parser = new Parser().int32('length') // byte size of the container data (blocks)
-    .itf8('refSeqId') // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
-    .itf8('refSeqStart') // the alignment start position or 0 for unmapped reads
-    .itf8('alignmentSpan') // the length of the alignment or 0 for unmapped reads
-    .itf8('numRecords'); // number of records in the container
-
-    var maxLength = 4 + 5 * 4;
-
-    if (majorVersion >= 3) {
-      parser = parser.ltf8('recordCounter'); // 1-based sequential index of records in the file/stream.
-
-      maxLength += 9;
-    } else if (majorVersion === 2) {
-      parser = parser.itf8('recordCounter');
-      maxLength += 5;
-    }
-
-    if (majorVersion > 1) {
-      parser = parser.ltf8('numBases'); // number of read bases
-
-      maxLength += 9;
-    }
-
-    parser = parser.itf8('numBlocks') // the number of blocks
-    .itf8('numLandmarks'); // the number of landmarks
-
-    maxLength += 5 + 5;
-    return {
-      parser: parser,
-      maxLength: maxLength
-    };
-  },
-  cramContainerHeader2: function cramContainerHeader2(majorVersion) {
-    var parser = new Parser().itf8('numLandmarks') // the number of blocks
-    // Each integer value of this array is a byte offset
-    // into the blocks byte array. Landmarks are used for
-    // random access indexing.
-    .array('landmarks', {
-      type: new Parser().itf8(),
-      length: 'numLandmarks'
-    });
-    var crcLength = 0;
-
-    if (majorVersion >= 3) {
-      parser = parser.uint32('crc32');
-      crcLength = 4;
-    }
-
-    return {
-      parser: parser,
-      maxLength: function maxLength(numLandmarks) {
-        return 5 + numLandmarks * 5 + crcLength;
-      }
-    };
-  }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        parser = parser
+            .itf8('numBlocks')
+            .itf8('numContentIds')
+            .array('contentIds', {
+            type: singleItf8,
+            length: 'numContentIds',
+        });
+        maxLength += 5 * 2; // + numContentIds*5
+        // the md5 sum is missing in cram v1
+        if (majorVersion >= 2) {
+            parser = parser.array('md5', { type: 'uint8', length: 16 });
+            maxLength += 16;
+        }
+        var maxLengthFunc = function (numContentIds) { return maxLength + numContentIds * 5; };
+        return { parser: parser, maxLength: maxLengthFunc }; // : p, maxLength: numContentIds => 5 + 9 + 5 * 2 + 5 * numContentIds + 16 }
+    },
+    // assembles a section parser for the unmapped slice header, with slight
+    // variations depending on the major version of the cram file
+    cramMappedSliceHeader: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .itf8('refSeqId')
+            .itf8('refSeqStart')
+            .itf8('refSeqSpan')
+            .itf8('numRecords');
+        var maxLength = 5 * 4;
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter');
+            maxLength += 9;
+        }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        parser = parser
+            .itf8('numBlocks')
+            .itf8('numContentIds')
+            .array('contentIds', {
+            type: singleItf8,
+            length: 'numContentIds',
+        })
+            .itf8('refBaseBlockId');
+        maxLength += 5 * 3;
+        // the md5 sum is missing in cram v1
+        if (majorVersion >= 2) {
+            parser = parser.array('md5', { type: 'uint8', length: 16 });
+            maxLength += 16;
+        }
+        var maxLengthFunc = function (numContentIds) { return maxLength + numContentIds * 5; };
+        return { parser: parser, maxLength: maxLengthFunc };
+    },
+    cramEncoding: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .namely('cramEncoding')
+            .itf8('codecId')
+            .itf8('parametersBytes')
+            .choice('parameters', {
+            tag: 'codecId',
+            choices: {
+                0: new binary_parser_1.Parser(),
+                1: new binary_parser_1.Parser().itf8('blockContentId'),
+                2: new binary_parser_1.Parser().itf8('offset').itf8('M'),
+                // HUFFMAN_INT
+                3: binary_parser_1.Parser.start()
+                    .itf8('numCodes')
+                    .array('symbols', { length: 'numCodes', type: singleItf8 })
+                    .itf8('numLengths')
+                    .array('bitLengths', { length: 'numLengths', type: singleItf8 }),
+                4: binary_parser_1.Parser.start() // BYTE_ARRAY_LEN
+                    .nest('lengthsEncoding', { type: 'cramEncoding' })
+                    .nest('valuesEncoding', { type: 'cramEncoding' }),
+                // BYTE_ARRAY_STOP is a little different for CRAM v1
+                5: new binary_parser_1.Parser()
+                    .uint8('stopByte')[majorVersion > 1 ? 'itf8' : 'int']('blockContentId'),
+                6: new binary_parser_1.Parser().itf8('offset').itf8('length'),
+                7: new binary_parser_1.Parser().itf8('offset').itf8('K'),
+                8: new binary_parser_1.Parser().itf8('offset').itf8('log2m'),
+                9: new binary_parser_1.Parser().itf8('offset'), // GAMMA
+            },
+        });
+        return { parser: parser };
+    },
+    cramDataSeriesEncodingMap: function (majorVersion) {
+        return new binary_parser_1.Parser()
+            .itf8('mapSize')
+            .itf8('mapCount')
+            .array('ents', {
+            length: 'mapCount',
+            type: new binary_parser_1.Parser()
+                .string('key', { length: 2, stripNull: false })
+                .nest('value', { type: this.cramEncoding(majorVersion).parser }),
+        });
+    },
+    cramTagEncodingMap: function (majorVersion) {
+        return new binary_parser_1.Parser()
+            .itf8('mapSize')
+            .itf8('mapCount')
+            .array('ents', {
+            length: 'mapCount',
+            type: new binary_parser_1.Parser()
+                .itf8('key', {
+                formatter: /* istanbul ignore next */ function (/* istanbul ignore next */ integerRepresentation) {
+                    /* istanbul ignore next */
+                    return String.fromCharCode((integerRepresentation >> 16) & 0xff) +
+                        String.fromCharCode((integerRepresentation >> 8) & 0xff) +
+                        String.fromCharCode(integerRepresentation & 0xff);
+                },
+            })
+                .nest('value', { type: this.cramEncoding(majorVersion).parser }),
+        });
+    },
+    cramCompressionHeader: function (majorVersion) {
+        var parser = new binary_parser_1.Parser();
+        // TODO: if we want to support CRAM v1, we will need to refactor
+        // compression header into 2 parts to parse the landmarks,
+        // like the container header
+        parser = parser
+            .nest('preservation', {
+            type: cramPreservationMap,
+            formatter: formatMap,
+        })
+            .nest('dataSeriesEncoding', {
+            type: this.cramDataSeriesEncodingMap(majorVersion),
+            formatter: formatMap,
+        })
+            .nest('tagEncoding', {
+            type: this.cramTagEncodingMap(majorVersion),
+            formatter: formatMap,
+        });
+        return { parser: parser };
+    },
+    cramContainerHeader1: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .int32('length') // byte size of the container data (blocks)
+            .itf8('refSeqId') // reference sequence identifier, -1 for unmapped reads, -2 for multiple reference sequences
+            .itf8('refSeqStart') // the alignment start position or 0 for unmapped reads
+            .itf8('alignmentSpan') // the length of the alignment or 0 for unmapped reads
+            .itf8('numRecords'); // number of records in the container
+        var maxLength = 4 + 5 * 4;
+        if (majorVersion >= 3) {
+            parser = parser.ltf8('recordCounter'); // 1-based sequential index of records in the file/stream.
+            maxLength += 9;
+        }
+        else if (majorVersion === 2) {
+            parser = parser.itf8('recordCounter');
+            maxLength += 5;
+        }
+        if (majorVersion > 1) {
+            parser = parser.ltf8('numBases'); // number of read bases
+            maxLength += 9;
+        }
+        parser = parser
+            .itf8('numBlocks') // the number of blocks
+            .itf8('numLandmarks'); // the number of landmarks
+        maxLength += 5 + 5;
+        return { parser: parser, maxLength: maxLength };
+    },
+    cramContainerHeader2: function (majorVersion) {
+        var parser = new binary_parser_1.Parser()
+            .itf8('numLandmarks') // the number of blocks
+            // Each integer value of this array is a byte offset
+            // into the blocks byte array. Landmarks are used for
+            // random access indexing.
+            .array('landmarks', {
+            type: new binary_parser_1.Parser().itf8(),
+            length: 'numLandmarks',
+        });
+        var crcLength = 0;
+        if (majorVersion >= 3) {
+            parser = parser.uint32('crc32');
+            crcLength = 4;
+        }
+        return {
+            parser: parser,
+            maxLength: function (numLandmarks) { return 5 + numLandmarks * 5 + crcLength; },
+        };
+    },
 };
-
 function getSectionParsers(majorVersion) {
-  var _context;
-
-  var parsers = (0, _assign.default)({}, unversionedParsers);
-  (0, _forEach.default)(_context = (0, _keys.default)(versionedParsers)).call(_context, function (parserName) {
-    parsers[parserName] = versionedParsers[parserName](majorVersion);
-  });
-  return parsers;
+    var parsers = Object.assign({}, unversionedParsers);
+    Object.keys(versionedParsers).forEach(function (parserName) {
+        parsers[parserName] = versionedParsers[parserName](majorVersion);
+    });
+    return parsers;
 }
-
-module.exports = {
-  cramFileDefinition: cramFileDefinition,
-  getSectionParsers: getSectionParsers
-};
+exports.getSectionParsers = getSectionParsers;
+//# sourceMappingURL=sectionParsers.js.map