genoverse 3.2.0 → 4.0.1

package/js/lib/VCFReader.js

@@ -1,286 +0,0 @@
-(function () {
-  var tabi_fmt = {
-    string0: function (size) {
-      return this.parse(['string', size]).replace(/\0+$/, '');
-    },
-    header: {
-      magic   : ['string', 4],
-      n_ref   : 'int32',
-      format  : 'int32',
-      col_seq : 'int32',
-      col_beg : 'int32',
-      col_end : 'int32',
-      meta    : 'int32',
-      skip    : 'int32',
-      l_nm    : 'int32',
-      names   : ['string0', function () { return this.current.l_nm; }]
-    },
-    chunk: {
-      cnk_beg: 'uint64',
-      cnk_end: 'uint64'
-    },
-    bin: {
-      bin      : 'uint32',
-      n_chunk  : 'int32',
-      chunkseq : ['array', 'chunk', function () { return this.current.n_chunk; }]
-    },
-    index: {
-      n_bin     : 'int32',
-      binseq    : ['array', 'bin', function () { return this.current.n_bin; }],
-      n_intv    : 'int32',
-      intervseq : ['array', 'uint64', function () { return this.current.n_intv; }]
-    },
-    tabix: {
-      head     : 'header',
-      indexseq : ['array', 'index', function () { return this.current.head.n_ref; }]
-    }
-  };
-
-  var bgzf_hd_fmt = {
-    header: {
-      id1   : 'uint8',
-      id2   : 'uint8',
-      cm    : 'uint8',
-      flg   : 'uint8',
-      mtime : 'uint32',
-      xfl   : 'uint8',
-      os    : 'uint8',
-      xlen  : 'uint16'
-    },
-    subheader: {
-      si1   : 'uint8',
-      si2   : 'uint8',
-      slen  : 'uint16',
-      bsize : 'uint16'
-    },
-    bgzfHd: { head: 'header', subhead: 'subheader' }
-  };
-
-  var hdSize  = 18;
-  var inflate = dallianceLib.inflateBuffer;
-  var _2p16   = 1 << 16;
-
-  var VCFReader = function (vcf, tbi) {
-    this.vcf_data = vcf;
-    this.tbi_data = tbi;
-  };
-
-  VCFReader.prototype.readTabix = function (cb) {
-    var bins2hash = function (binseq) {
-      var hash = {};
-      var i    = 0;
-      var b;
-
-      for (var x in binseq) {
-        b       = binseq[x].bin;
-        hash[b] = i;
-        i++;
-      }
-
-      return hash;
-    };
-
-    var parse_tabix = function (tabix_buffer) {
-      var tabix = new jParser(tabix_buffer, tabi_fmt).parse('tabix');
-
-      tabix.head.names = tabix.head.names.split('\0');
-      tabix.bhash = {};
-
-      for (var i = 0; i < tabix.head.n_ref; i++){
-        tabix.bhash[i] = bins2hash(tabix.indexseq[i].binseq);
-      }
-
-      cb(tabix);
-    };
-
-    this.inflateRegion(this.tbi_data, 0, 100000000, parse_tabix);
-  };
-
-  VCFReader.prototype.getRecords = function (ref, beg, end, callback) {
-    var records = [];
-    var chunks  = this.getChunks(ref, beg, end);
-    var vcfThis = this;
-
-    if (chunks == -1) {
-      return callback([]);
-    }
-
-    (function loop(x) {
-      if (x < chunks.length) {
-        vcfThis.inflateRegion(vcfThis.vcf_data, chunks[x].start, chunks[x].end, function (record, ebsz) {
-          var last = record.byteLength - ebsz + chunks[x].inner_end;
-          record = vcfThis.buffer2String(record).slice(chunks[x].inner_start, last);
-
-          if (record.length > 0) {
-            record = record.split('\n').filter(function (rec) {
-              if (rec.length > 0) {
-                var n = parseInt(rec.split('\t')[1]);
-                return ((beg <= n) && (n <= end));
-              }
-            }).join('\n');
-
-            records.push(record);
-          }
-
-          loop(++x);
-        });
-      } else {
-        callback(records.join('\n'));
-      }
-    })(0);
-  };
-
-  VCFReader.prototype.getChunks = function (ref, beg, end) {
-    var tbi     = this.tabix;
-    var vcfThis = this;
-
-    ref = tbi.head.names.indexOf(ref.toString());
-
-    if (ref == -1) {
-      return -1;
-    }
-
-    var bids  = this.reg2bins(beg, end + 1).filter(function (x) { return typeof tbi.bhash[ref][x] != 'undefined'; });
-    var bcnks = bids.map(function (x) { return vcfThis.bin2Ranges(tbi, ref, x); });
-    var cnks  = bcnks.reduce(function (V, ranges) {
-      ranges.forEach(function (item) { V.push(item); });
-      return V;
-    }, []);
-
-    cnks = this.remove_duplicates(cnks);
-
-    return cnks;
-  };
-
-  VCFReader.prototype.inflateRegion = function (d, beg, end, cbfn) {
-    var blocks  = [];
-    var vcfThis = this;
-
-    var cb = function (block, nextBlockOffset) {
-      blocks.push(block);
-
-      if (nextBlockOffset == -1) {
-        cbfn(vcfThis.appendBuffers(blocks), blocks[blocks.length - 1].byteLength);
-      } else if (nextBlockOffset <= end) {
-        vcfThis.inflateBlock(d, nextBlockOffset, cb);
-      } else {
-        cbfn(vcfThis.appendBuffers(blocks), blocks[blocks.length - 1].byteLength);
-      }
-    };
-
-    this.inflateBlock(d, beg, cb);
-  };
-
-  VCFReader.prototype.inflateBlock = function (d, blockOffset, cbfn) {
-    var cb2 = function (hdobj) {
-      d.slice(blockOffset, hdobj.subhead.bsize + 1).fetch(function (block) {
-        var inflated_block  = inflate(block, hdSize, block.byteLength - hdSize);
-        var nextBlockOffset = blockOffset + hdobj.subhead.bsize + 1;
-
-        if (hdobj.subhead.bsize == 27) {
-          nextBlockOffset = -1; // last bgzf block
-        }
-
-        cbfn(inflated_block, nextBlockOffset);
-      });
-    };
-
-    this.getBGZFHD(d, blockOffset, cb2);
-  };
-
-  VCFReader.prototype.getBGZFHD = function (d, offset, cbfn) {
-    d.slice(offset, hdSize + 1).fetch(function (buf) {
-      var parser = new jParser(buf, bgzf_hd_fmt);
-      var hdobj  = parser.parse('bgzfHd');
-      cbfn(hdobj);
-    });
-  };
-
-  VCFReader.prototype.appendBuffers = function (bufferVec) {
-    var totalSize = 0;
-
-    for (var i = 0; i < bufferVec.length; i++) {
-      totalSize = totalSize + bufferVec[i].byteLength;
-    }
-
-    var tmp    = new Uint8Array(totalSize);
-    var offset = 0;
-
-    for (i = 0; i < bufferVec.length; i++) {
-      tmp.set(new Uint8Array(bufferVec[i]), offset);
-      offset = offset + bufferVec[i].byteLength;
-    }
-
-    return tmp.buffer;
-  };
-
-  VCFReader.prototype.buffer2String = function (resultBuffer) {
-    var s        = '';
-    var resultBB = new Uint8Array(resultBuffer);
-
-    for (var i = 0; i < resultBB.length; ++i) {
-      s += String.fromCharCode(resultBB[i]);
-    }
-
-    return s;
-  };
-
-  VCFReader.prototype.remove_duplicates = function (objectsArray) {
-    var usedObjects = {};
-
-    for (var i = objectsArray.length - 1; i >= 0; i--) {
-      var so = JSON.stringify(objectsArray[i]);
-
-      if (usedObjects[so]) {
-        objectsArray.splice(i, 1);
-      } else {
-        usedObjects[so] = true;
-      }
-    }
-
-    return objectsArray;
-  };
-
-  VCFReader.prototype.bin2Ranges = function (tbi, ref, binid) {
-    var ranges = [];
-    var bs     = tbi.indexseq[ref].binseq;
-    var cnkseq = bs[tbi.bhash[ref][binid]].chunkseq;
-    var cnk;
-
-    for (var i = 0; i < cnkseq.length; i++) {
-      cnk = cnkseq[i];
-
-      ranges.push({
-        start       : Math.floor(cnk.cnk_beg / _2p16),
-        inner_start : cnk.cnk_beg % _2p16,
-        end         : Math.floor(cnk.cnk_end / _2p16),
-        inner_end   : cnk.cnk_end % _2p16
-      });
-    }
-
-    return ranges;
-  };
-
-  VCFReader.prototype.reg2bins = function (beg, end) {
-    var list = [];
-    var i;
-
-    --end;
-
-    list.push(0);
-
-    for (i = 1    + (beg >> 26); i <= 1    + (end >> 26); ++i) { list.push(i); }
-    for (i = 9    + (beg >> 23); i <= 9    + (end >> 23); ++i) { list.push(i); }
-    for (i = 73   + (beg >> 20); i <= 73   + (end >> 20); ++i) { list.push(i); }
-    for (i = 585  + (beg >> 17); i <= 585  + (end >> 17); ++i) { list.push(i); }
-    for (i = 4681 + (beg >> 14); i <= 4681 + (end >> 14); ++i) { list.push(i); }
-
-    return list;
-  };
-
-  window.VCFReader = VCFReader;
-
-  if (typeof module === 'object' && typeof module.exports === 'object') {
-    module.exports = VCFReader;
-  }
-})();