genoverse 3.2.0 → 4.0.0-beta1

package/js/lib/dalliance/js/bam.js

@@ -1,494 +0,0 @@
-/* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */
-
-//
-// Dalliance Genome Explorer
-// (c) Thomas Down 2006-2011
-//
-// bam.js: indexed binary alignments
-//
-var BAM_MAGIC = 21840194;
-var BAI_MAGIC = 21578050;
-
-function BamFile() {}
-
-function Vob(b, o) {
-  this.block = b;
-  this.offset = o;
-}
-
-Vob.prototype.toString = function() {
-  return '' + this.block + ':' + this.offset;
-}
-
-function Chunk(minv, maxv) {
-  this.minv = minv;
-  this.maxv = maxv;
-}
-
-function makeBam(data, bai, callback) {
-  var bam = new BamFile();
-  bam.data = data;
-  bam.bai = bai;
-
-  bam.data.slice(0, 65536).fetch(function(r) {
-    if (!r) {
-      return dlog("Couldn't access BAM");
-    }
-
-    var unc = unbgzf(r);
-    var uncba = new Uint8Array(unc);
-
-    var magic = readInt(uncba, 0);
-    var headLen = readInt(uncba, 4);
-    var header = '';
-    for (var i = 0; i < headLen; ++i) {
-      header += String.fromCharCode(uncba[i + 8]);
-    }
-
-    var nRef = readInt(uncba, headLen + 8);
-    var p = headLen + 12;
-
-    bam.chrToIndex = {};
-    bam.indexToChr = [];
-    for (var i = 0; i < nRef; ++i) {
-      var lName = readInt(uncba, p);
-      var name = '';
-      for (var j = 0; j < lName - 1; ++j) {
-        name += String.fromCharCode(uncba[p + 4 + j]);
-      }
-      var lRef = readInt(uncba, p + lName + 4);
-      // dlog(name + ': ' + lRef);
-      bam.chrToIndex[name] = i;
-      if (name.indexOf('chr') == 0) {
-        bam.chrToIndex[name.substring(3)] = i;
-      } else {
-        bam.chrToIndex['chr' + name] = i;
-      }
-      bam.indexToChr.push(name);
-
-      p = p + 8 + lName;
-    }
-
-    if (bam.indices) {
-      return callback(bam);
-    }
-  });
-
-  bam.bai.fetch(function(header) { // Do we really need to fetch the whole thing? :-(
-    if (!header) {
-      return dlog("Couldn't access BAI");
-    }
-
-    var uncba = new Uint8Array(header);
-    var baiMagic = readInt(uncba, 0);
-    if (baiMagic != BAI_MAGIC) {
-      return dlog('Not a BAI file');
-    }
-
-    var nref = readInt(uncba, 4);
-
-    bam.indices = [];
-
-    var p = 8;
-    for (var ref = 0; ref < nref; ++ref) {
-      var blockStart = p;
-      var nbin = readInt(uncba, p);
-      p += 4;
-      for (var b = 0; b < nbin; ++b) {
-        var bin = readInt(uncba, p);
-        var nchnk = readInt(uncba, p + 4);
-        p += 8 + (nchnk * 16);
-      }
-      var nintv = readInt(uncba, p);
-      p += 4;
-      p += (nintv * 8);
-      if (nbin > 0) {
-        bam.indices[ref] = new Uint8Array(header, blockStart, p - blockStart);
-      }
-    }
-    if (bam.chrToIndex) {
-      return callback(bam);
-    }
-  });
-}
-
-
-
-BamFile.prototype.blocksForRange = function(refId, min, max) {
-  var index = this.indices[refId];
-  if (!index) {
-    return [];
-  }
-
-  var intBinsL = reg2bins(min, max);
-  var intBins = [];
-  for (var i = 0; i < intBinsL.length; ++i) {
-    intBins[intBinsL[i]] = true;
-  }
-  var leafChunks = [],
-    otherChunks = [];
-
-  var nbin = readInt(index, 0);
-  var p = 4;
-  for (var b = 0; b < nbin; ++b) {
-    var bin = readInt(index, p);
-    var nchnk = readInt(index, p + 4);
-    //        dlog('bin=' + bin + '; nchnk=' + nchnk);
-    p += 8;
-    if (intBins[bin]) {
-      for (var c = 0; c < nchnk; ++c) {
-        var cs = readVob(index, p);
-        var ce = readVob(index, p + 8);
-        (bin < 4681 ? otherChunks : leafChunks).push(new Chunk(cs, ce));
-        p += 16;
-      }
-    } else {
-      p += (nchnk * 16);
-    }
-  }
-  //    dlog('leafChunks = ' + miniJSONify(leafChunks));
-  //    dlog('otherChunks = ' + miniJSONify(otherChunks));
-  var nintv = readInt(index, p);
-  var lowest = null;
-  var minLin = Math.min(min >> 14, nintv - 1),
-    maxLin = Math.min(max >> 14, nintv - 1);
-  for (var i = minLin; i <= maxLin; ++i) {
-    var lb = readVob(index, p + 4 + (i * 8));
-    if (!lb) {
-      continue;
-    }
-    if (!lowest || lb.block < lowest.block || lb.offset < lowest.offset) {
-      lowest = lb;
-    }
-  }
-  // dlog('Lowest LB = ' + lowest);
-  var prunedOtherChunks = [];
-  if (lowest != null) {
-    for (var i = 0; i < otherChunks.length; ++i) {
-      var chnk = otherChunks[i];
-      if (chnk.maxv.block >= lowest.block && chnk.maxv.offset >= lowest.offset) {
-        prunedOtherChunks.push(chnk);
-      }
-    }
-  }
-  // dlog('prunedOtherChunks = ' + miniJSONify(prunedOtherChunks));
-  otherChunks = prunedOtherChunks;
-
-  var intChunks = [];
-  for (var i = 0; i < otherChunks.length; ++i) {
-    intChunks.push(otherChunks[i]);
-  }
-  for (var i = 0; i < leafChunks.length; ++i) {
-    intChunks.push(leafChunks[i]);
-  }
-
-  intChunks.sort(function(c0, c1) {
-    var dif = c0.minv.block - c1.minv.block;
-    if (dif != 0) {
-      return dif;
-    } else {
-      return c0.minv.offset - c1.minv.offset;
-    }
-  });
-  var mergedChunks = [];
-  if (intChunks.length > 0) {
-    var cur = intChunks[0];
-    for (var i = 1; i < intChunks.length; ++i) {
-      var nc = intChunks[i];
-      if (nc.minv.block == cur.maxv.block /* && nc.minv.offset == cur.maxv.offset */ ) { // no point splitting mid-block
-        cur = new Chunk(cur.minv, nc.maxv);
-      } else {
-        mergedChunks.push(cur);
-        cur = nc;
-      }
-    }
-    mergedChunks.push(cur);
-  }
-  //    dlog('mergedChunks = ' + miniJSONify(mergedChunks));
-  return mergedChunks;
-}
-
-BamFile.prototype.fetch = function(chr, min, max, callback) {
-  var thisB = this;
-
-  var chrId = this.chrToIndex[chr];
-  var chunks;
-  if (chrId === undefined) {
-    chunks = [];
-  } else {
-    chunks = this.blocksForRange(chrId, min, max);
-    if (!chunks) {
-      callback(null, 'Error in index fetch');
-    }
-  }
-
-  var records = [];
-  var index = 0;
-  var data;
-
-  function tramp() {
-    if (index >= chunks.length) {
-      return callback(records);
-    } else if (!data) {
-      // dlog('fetching ' + index);
-      var c = chunks[index];
-      var fetchMin = c.minv.block;
-      var fetchMax = c.maxv.block + (1 << 16); // *sigh*
-      thisB.data.slice(fetchMin, fetchMax - fetchMin).fetch(function(r) {
-        data = unbgzf(r, c.maxv.block - c.minv.block + 1);
-        return tramp();
-      });
-    } else {
-      var ba = new Uint8Array(data);
-      thisB.readBamRecords(ba, chunks[index].minv.offset, records, min, max, chrId);
-      data = null;
-      ++index;
-      return tramp();
-    }
-  }
-  tramp();
-}
-
-var SEQRET_DECODER = ['=', 'A', 'C', 'x', 'G', 'x', 'x', 'x', 'T', 'x', 'x', 'x', 'x', 'x', 'x', 'N'];
-var CIGAR_DECODER = ['M', 'I', 'D', 'N', 'S', 'H', 'P', '=', 'X', '?', '?', '?', '?', '?', '?', '?'];
-
-function BamRecord() {}
-
-BamFile.prototype.readBamRecords = function(ba, offset, sink, min, max, chrId) {
-  while (true) {
-    var blockSize = readInt(ba, offset);
-    var blockEnd = offset + blockSize + 4;
-    if (blockEnd >= ba.length) {
-      return sink;
-    }
-
-    var record = new BamRecord();
-
-    var refID = readInt(ba, offset + 4);
-    var pos = readInt(ba, offset + 8);
-
-    var bmn = readInt(ba, offset + 12);
-    var bin = (bmn & 0xffff0000) >> 16;
-    var mq = (bmn & 0xff00) >> 8;
-    var nl = bmn & 0xff;
-
-    var flag_nc = readInt(ba, offset + 16);
-    var flag = (flag_nc & 0xffff0000) >> 16;
-    var nc = flag_nc & 0xffff;
-
-    var lseq = readInt(ba, offset + 20);
-
-    var nextRef = readInt(ba, offset + 24);
-    var nextPos = readInt(ba, offset + 28);
-
-    var tlen = readInt(ba, offset + 32);
-
-    var readName = '';
-    for (var j = 0; j < nl - 1; ++j) {
-      readName += String.fromCharCode(ba[offset + 36 + j]);
-    }
-
-    var p = offset + 36 + nl;
-
-    var cigar = '';
-    for (var c = 0; c < nc; ++c) {
-      var cigop = readInt(ba, p);
-      cigar = cigar + (cigop >> 4) + CIGAR_DECODER[cigop & 0xf];
-      p += 4;
-    }
-    record.cigar = cigar;
-
-    var seq = '';
-    var seqBytes = (lseq + 1) >> 1;
-    for (var j = 0; j < seqBytes; ++j) {
-      var sb = ba[p + j];
-      seq += SEQRET_DECODER[(sb & 0xf0) >> 4];
-      seq += SEQRET_DECODER[(sb & 0x0f)];
-    }
-    p += seqBytes;
-    record.seq = seq;
-
-    var qseq = '';
-    for (var j = 0; j < lseq; ++j) {
-      qseq += String.fromCharCode(ba[p + j]);
-    }
-    p += lseq;
-    record.quals = qseq;
-
-    record.pos = pos;
-    record.mq = mq;
-    record.readName = readName;
-    record.segment = this.indexToChr[refID];
-
-    while (p < blockEnd) {
-      var tag = String.fromCharCode(ba[p]) + String.fromCharCode(ba[p + 1]);
-      var type = String.fromCharCode(ba[p + 2]);
-      var value;
-
-      if (type == 'A') {
-        value = String.fromCharCode(ba[p + 3]);
-        p += 4;
-      } else if (type == 'i' || type == 'I') {
-        value = readInt(ba, p + 3);
-        p += 7;
-      } else if (type == 'c' || type == 'C') {
-        value = ba[p + 3];
-        p += 4;
-      } else if (type == 's' || type == 'S') {
-        value = readShort(ba, p + 3);
-        p += 5;
-      } else if (type == 'f') {
-        throw 'FIXME need floats';
-      } else if (type == 'Z' || type == 'H') {
-        p += 3;
-        value = '';
-        for (;;) {
-          var cc = ba[p++];
-          if (cc == 0) {
-            break;
-          } else {
-            value += String.fromCharCode(cc);
-          }
-        }
-      } else if (type == 'B') {
-        var atype = String.fromCharCode(ba[p + 3]);
-        var alen = readInt(ba, p + 4);
-        var elen;
-        var reader;
-        if (atype == 'i' || atype == 'I' || atype == 'f') {
-          elen = 4;
-          if (atype == 'f') reader = readFloat;
-          else reader = readInt;
-        } else if (atype == 's' || atype == 'S') {
-          elen = 2;
-          reader = readShort;
-        } else if (atype == 'c' || atype == 'C') {
-          elen = 1;
-          reader = readByte;
-        } else {
-          throw 'Unknown array type ' + atype;
-        }
-
-        p += 8;
-        value = [];
-        for (var i = 0; i < alen; ++i) {
-          value.push(reader(ba, p));
-          p += elen;
-        }
-      } else {
-        throw 'Unknown type ' + type;
-      }
-      record[tag] = value;
-    }
-
-    if (!min || record.pos <= max && record.pos + lseq >= min) {
-      if (chrId === undefined || refID == chrId) {
-        sink.push(record);
-      }
-    }
-    offset = blockEnd;
-  }
-
-  // Exits via top of loop.
-};
-
-(function() {
-  var convertBuffer = new ArrayBuffer(8);
-  var ba = new Uint8Array(convertBuffer);
-  var fa = new Float32Array(convertBuffer);
-
-
-  window.readFloat = function(buf, offset) {
-    ba[0] = buf[offset];
-    ba[1] = buf[offset + 1];
-    ba[2] = buf[offset + 2];
-    ba[3] = buf[offset + 3];
-    return fa[0];
-  };
-})();
-
-function readInt64(ba, offset) {
-  return (ba[offset + 7] << 24) | (ba[offset + 6] << 16) | (ba[offset + 5] << 8) | (ba[offset + 4]);
-}
-
-function readInt(ba, offset) {
-  return (ba[offset + 3] << 24) | (ba[offset + 2] << 16) | (ba[offset + 1] << 8) | (ba[offset]);
-}
-
-function readShort(ba, offset) {
-  return (ba[offset + 1] << 8) | (ba[offset]);
-}
-
-function readByte(ba, offset) {
-  return ba[offset];
-}
-
-function readVob(ba, offset) {
-  var block = ((ba[offset + 6] & 0xff) * 0x100000000) + ((ba[offset + 5] & 0xff) * 0x1000000) + ((ba[offset + 4] & 0xff) * 0x10000) + ((ba[offset + 3] & 0xff) * 0x100) + ((ba[offset + 2] & 0xff));
-  var bint = (ba[offset + 1] << 8) | (ba[offset]);
-  if (block == 0 && bint == 0) {
-    return null; // Should only happen in the linear index?
-  } else {
-    return new Vob(block, bint);
-  }
-}
-
-function unbgzf(data, lim) {
-  lim = Math.min(lim || 1, data.byteLength - 100);
-  var oBlockList = [];
-  var ptr = [0];
-  var totalSize = 0;
-
-  while (ptr[0] < lim) {
-    var ba = new Uint8Array(data, ptr[0], 100); // FIXME is this enough for all credible BGZF block headers?
-    var xlen = (ba[11] << 8) | (ba[10]);
-    // dlog('xlen[' + (ptr[0]) +']=' + xlen);
-    var unc = jszlib_inflate_buffer(data, 12 + xlen + ptr[0], Math.min(65536, data.byteLength - 12 - xlen - ptr[0]), ptr);
-    ptr[0] += 8;
-    totalSize += unc.byteLength;
-    oBlockList.push(unc);
-  }
-
-  if (oBlockList.length == 1) {
-    return oBlockList[0];
-  } else {
-    var out = new Uint8Array(totalSize);
-    var cursor = 0;
-    for (var i = 0; i < oBlockList.length; ++i) {
-      var b = new Uint8Array(oBlockList[i]);
-      arrayCopy(b, 0, out, cursor, b.length);
-      cursor += b.length;
-    }
-    return out.buffer;
-  }
-}
-
-//
-// Binning (transliterated from SAM1.3 spec)
-//
-/* calculate bin given an alignment covering [beg,end) (zero-based, half-close-half-open) */
-function reg2bin(beg, end) {
-  --end;
-  if (beg >> 14 == end >> 14) return ((1 << 15) - 1) / 7 + (beg >> 14);
-  if (beg >> 17 == end >> 17) return ((1 << 12) - 1) / 7 + (beg >> 17);
-  if (beg >> 20 == end >> 20) return ((1 << 9) - 1) / 7 + (beg >> 20);
-  if (beg >> 23 == end >> 23) return ((1 << 6) - 1) / 7 + (beg >> 23);
-  if (beg >> 26 == end >> 26) return ((1 << 3) - 1) / 7 + (beg >> 26);
-  return 0;
-}
-
-/* calculate the list of bins that may overlap with region [beg,end) (zero-based) */
-var MAX_BIN = (((1 << 18) - 1) / 7);
-
-function reg2bins(beg, end) {
-  var i = 0,
-    k, list = [];
-  --end;
-  list.push(0);
-  for (k = 1 + (beg >> 26); k <= 1 + (end >> 26); ++k) list.push(k);
-  for (k = 9 + (beg >> 23); k <= 9 + (end >> 23); ++k) list.push(k);
-  for (k = 73 + (beg >> 20); k <= 73 + (end >> 20); ++k) list.push(k);
-  for (k = 585 + (beg >> 17); k <= 585 + (end >> 17); ++k) list.push(k);
-  for (k = 4681 + (beg >> 14); k <= 4681 + (end >> 14); ++k) list.push(k);
-  return list;
-}

package/js/lib/dalliance/js/bin.js

@@ -1,185 +0,0 @@
-/* -*- mode: javascript; c-basic-offset: 4; indent-tabs-mode: nil -*- */
-
-//
-// Dalliance Genome Explorer
-// (c) Thomas Down 2006-2011
-//
-// bin.js general binary data support
-//
-
-function BlobFetchable(b) {
-    this.blob = b;
-}
-
-BlobFetchable.prototype.slice = function(start, length) {
-    var b;
-
-    if (this.blob.slice) {
-        if (length) {
-            b = this.blob.slice(start, start + length);
-        } else {
-            b = this.blob.slice(start);
-        }
-    } else {
-        if (length) {
-            b = this.blob.webkitSlice(start, start + length);
-        } else {
-            b = this.blob.webkitSlice(start);
-        }
-    }
-    return new BlobFetchable(b);
-}
-
-BlobFetchable.prototype.fetch = function(callback) {
-    var reader = new FileReader();
-    reader.onloadend = function(ev) {
-        callback(bstringToBuffer(reader.result));
-    };
-    reader.readAsBinaryString(this.blob);
-}
-
-function URLFetchable(url, start, end, opts) {
-    if (!opts) {
-        if (typeof start === 'object') {
-            opts = start;
-            start = undefined;
-        } else {
-            opts = {};
-        }
-    }
-
-    this.url = url;
-    this.start = start || 0;
-    if (end) {
-        this.end = end;
-    }
-    this.opts = opts;
-}
-
-URLFetchable.prototype.slice = function(s, l) {
-    if (s < 0) {
-        throw 'Bad slice ' + s;
-    }
-
-    var ns = this.start, ne = this.end;
-    if (ns && s) {
-        ns = ns + s;
-    } else {
-        ns = s || ns;
-    }
-    if (l && ns) {
-        ne = ns + l - 1;
-    } else {
-        ne = ne || l - 1;
-    }
-    return new URLFetchable(this.url, ns, ne, this.opts);
-}
-
-var seed=0;
-var isIOS = navigator.userAgent.indexOf('Safari') >= 0 && navigator.userAgent.indexOf('Chrome') < 0 ;
-
-URLFetchable.prototype.fetchAsText = function(callback) {
-    var req = new XMLHttpRequest();
-    var length;
-    var url = this.url;
-    if (isIOS) {
-        url = url + '?salt=' + (++seed);
-    }
-    req.open('GET', url, true);
-
-    if (this.end) {
-        if (this.end - this.start > 100000000) {
-            throw 'Monster fetch!';
-        }
-        req.setRequestHeader('Range', 'bytes=' + this.start + '-' + this.end);
-        length = this.end - this.start + 1;
-    }
-
-    req.onreadystatechange = function() {
-        if (req.readyState == 4) {
-            if (req.status == 200 || req.status == 206) {
-                return callback(req.responseText);
-            } else {
-                return callback(null);
-            }
-        }
-    };
-    if (this.opts.credentials) {
-        req.withCredentials = true;
-    }
-    req.send('');
-}
-
-URLFetchable.prototype.fetch = function(callback, attempt, truncatedLength) {
-    var thisB = this;
-
-    attempt = attempt || 1;
-    if (attempt > 3) {
-        return callback(null);
-    }
-
-    var req = new XMLHttpRequest();
-    var length;
-    var url = this.url;
-    if (isIOS) {
-        // console.log('Safari hack');
-        url = url + '?salt=' + (++seed);
-    }
-    req.open('GET', url, true);
-    req.overrideMimeType('text/plain; charset=x-user-defined');
-    if (this.end) {
-        if (this.end - this.start > 100000000) {
-            throw 'Monster fetch!';
-        }
-        // console.log('req bytes=' + this.start + '-' + this.end);
-        req.setRequestHeader('Range', 'bytes=' + this.start + '-' + this.end);
-        length = this.end - this.start + 1;
-    }
-    req.responseType = 'arraybuffer';
-    req.onreadystatechange = function() {
-        if (req.readyState == 4) {
-            if (req.status == 200 || req.status == 206) {
-                if (req.response) {
-                    var bl = req.response.byteLength;
-                    // console.log('Got ' + bl + ' expected ' + length);
-                    if (length && length != bl && (!truncatedLength || bl != truncatedLength)) {
-                        return thisB.fetch(callback, attempt + 1, bl);
-                    } else {
-                        return callback(req.response);
-                    }
-                } else if (req.mozResponseArrayBuffer) {
-                    return callback(req.mozResponseArrayBuffer);
-                } else {
-                    var r = req.responseText;
-                    if (length && length != r.length && (!truncatedLength || r.length != truncatedLength)) {
-                        return thisB.fetch(callback, attempt + 1, r.length);
-                    } else {
-                        return callback(bstringToBuffer(req.responseText));
-                    }
-                }
-            } else {
-                return thisB.fetch(callback, attempt + 1);
-            }
-        }
-    };
-    if (this.opts.credentials) {
-        req.withCredentials = true;
-    }
-    req.send('');
-}
-
-function bstringToBuffer(result) {
-    if (!result) {
-        return null;
-    }
-
-//    var before = Date.now();
-    var ba = new Uint8Array(result.length);
-    for (var i = 0; i < ba.length; ++i) {
-        ba[i] = result.charCodeAt(i);
-    }
-//    var after  = Date.now();
-//    dlog('bb took ' + (after - before) + 'ms');
-    return ba.buffer;
-}
-