@gmod/cram 3.0.6 → 4.0.0

package/esm/htscodecs/fqzcomp.js

@@ -0,0 +1,325 @@
+"use strict";
+/*
+ * Copyright (c) 2019 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+const IOStream = require('./iostream');
+const ByteModel = require('./byte_model');
+const RangeCoder = require('./arith_sh');
+//----------------------------------------------------------------------
+// Main arithmetic entry function: decodes a compressed src and
+// returns the uncompressed buffer.
+function read_array(src, tab, size) {
+    var j = 0; // array value
+    var z = 0; // array index: tab[j]
+    var last = -1;
+    // Remove first level of run-length encoding
+    var R = new Array(1024); // runs
+    while (z < size) {
+        var run = src.ReadByte();
+        R[j++] = run;
+        z += run;
+        if (run == last) {
+            var copy = src.ReadByte();
+            z += run * copy;
+            while (copy--)
+                R[j++] = run;
+        }
+        last = run;
+    }
+    // Now expand runs in R to tab, noting 255 is max run
+    var i = 0;
+    j = 0;
+    z = 0;
+    while (z < size) {
+        var run_len = 0;
+        do {
+            var part = R[j++];
+            run_len += part;
+        } while (part == 255);
+        while (run_len--)
+            tab[z++] = i;
+        i++;
+    }
+}
+const QMAX = 256;
+const FLAG_DEDUP = 2;
+const FLAG_FLEN = 4;
+const FLAG_SEL = 8; // whether selector is used in context
+const FLAG_QMAP = 16;
+const FLAG_PTAB = 32;
+const FLAG_DTAB = 64;
+const FLAG_QTAB = 128;
+const GFLAG_MULTI_PARAM = 1;
+const GFLAG_HAVE_STAB = 2;
+const GFLAG_DO_REV = 4;
+// Compute a new context from our current state and qual q
+function fqz_update_ctx(params, state, q) {
+    var last = params.context;
+    state.qctx = (state.qctx << params.qshift) + params.qtab[q]; // >>> 0
+    last += (state.qctx & ((1 << params.qbits) - 1)) << params.qloc; // >>> 0
+    if (params.do_pos)
+        last += params.ptab[Math.min(state.p, 1023)] << params.ploc;
+    if (params.do_delta) {
+        last += params.dtab[Math.min(state.delta, 255)] << params.dloc;
+        // Is it better to use q here or qtab[q]?
+        // If qtab[q] we can map eg [a-z0-9A-Z]->0 ,->1 and have
+        // delta being a token number count into comma separated lists?
+        state.delta += state.prevq != q ? 1 : 0;
+        state.prevq = q;
+    }
+    if (params.do_sel)
+        last += state.s << params.sloc;
+    state.p--;
+    return last & 0xffff;
+}
+function decode_fqz_single_param(src) {
+    var p = {}; // params
+    // Load FQZ parameters
+    p.context = src.ReadUint16();
+    p.pflags = src.ReadByte();
+    p.do_dedup = p.pflags & FLAG_DEDUP;
+    p.fixed_len = p.pflags & FLAG_FLEN;
+    p.do_sel = p.pflags & FLAG_SEL;
+    p.do_qmap = p.pflags & FLAG_QMAP;
+    p.do_pos = p.pflags & FLAG_PTAB;
+    p.do_delta = p.pflags & FLAG_DTAB;
+    p.do_qtab = p.pflags & FLAG_QTAB;
+    p.max_sym = src.ReadByte();
+    var x = src.ReadByte();
+    p.qbits = x >> 4;
+    p.qshift = x & 15;
+    x = src.ReadByte();
+    p.qloc = x >> 4;
+    p.sloc = x & 15;
+    x = src.ReadByte();
+    p.ploc = x >> 4;
+    p.dloc = x & 15;
+    // Qual map, eg to "unbin" Illumina qualities
+    p.qmap = new Array(256);
+    if (p.pflags & FLAG_QMAP) {
+        for (var i = 0; i < p.max_sym; i++)
+            p.qmap[i] = src.ReadByte();
+    }
+    else {
+        // Useful optimisation to speed up main loop
+        for (var i = 0; i < 256; i++)
+            p.qmap[i] = i; // NOP
+    }
+    // Read tables
+    p.qtab = new Array(1024);
+    if (p.qbits > 0 && p.pflags & FLAG_QTAB) {
+        read_array(src, p.qtab, 256);
+    }
+    else {
+        // Useful optimisation to speed up main loop
+        for (var i = 0; i < 256; i++)
+            p.qtab[i] = i; // NOP
+    }
+    p.ptab = new Array(1024);
+    if (p.pflags & FLAG_PTAB)
+        read_array(src, p.ptab, 1024);
+    p.dtab = new Array(256);
+    if (p.pflags & FLAG_DTAB)
+        read_array(src, p.dtab, 256);
+    return p;
+}
+function decode_fqz_params(src) {
+    var gparams = {
+        max_sym: 0,
+    };
+    // Check fqz format version
+    var vers = src.ReadByte();
+    if (vers != 5) {
+        console.error('Invalid FQZComp version number');
+        return;
+    }
+    var gflags = src.ReadByte();
+    var nparam = gflags & GFLAG_MULTI_PARAM ? src.ReadByte() : 1;
+    var max_sel = gflags.nparam > 1 ? gflags.nparam - 1 : 0; // Note max_sel, not num_sel
+    var stab = new Array(256);
+    if (gflags & GFLAG_HAVE_STAB) {
+        max_sel = src.ReadByte();
+        read_array(src, stab, 256);
+    }
+    else {
+        for (var i = 0; i < nparam; i++)
+            stab[i] = i;
+        for (; i < 256; i++)
+            stab[i] = nparam - 1;
+    }
+    gparams.do_rev = gflags & GFLAG_DO_REV;
+    gparams.stab = stab;
+    gparams.max_sel = max_sel;
+    gparams.params = new Array(gparams.nparam);
+    for (var p = 0; p < nparam; p++) {
+        gparams.params[p] = decode_fqz_single_param(src);
+        if (gparams.max_sym < gparams.params[p].max_sym)
+            gparams.max_sym = gparams.params[p].max_sym;
+    }
+    return gparams;
+}
+function fqz_create_models(gparams) {
+    var model = {};
+    model.qual = new Array(1 << 16);
+    for (var i = 0; i < 1 << 16; i++)
+        model.qual[i] = new ByteModel(gparams.max_sym + 1); // +1 as max value not num. values
+    model.len = new Array(4);
+    for (var i = 0; i < 4; i++)
+        model.len[i] = new ByteModel(256);
+    model.rev = new ByteModel(2);
+    model.dup = new ByteModel(2);
+    if (gparams.max_sel > 0)
+        model.sel = new ByteModel(gparams.max_sel + 1); // +1 as max value not num. values
+    return model;
+}
+// Initialise a new record, updating state.
+// Returns 1 if dup, otherwise 0
+function decode_fqz_new_record(src, rc, gparams, model, state, rev) {
+    // Parameter selector
+    if (gparams.max_sel > 0) {
+        state.s = model.sel.ModelDecode(src, rc);
+    }
+    else {
+        state.s = 0;
+    }
+    state.x = gparams.stab[state.s];
+    var params = gparams.params[state.x];
+    // Reset contexts at the start of each new record
+    if (params.fixed_len >= 0) {
+        // Not fixed or fixed but first record
+        var len = model.len[0].ModelDecode(src, rc);
+        len |= model.len[1].ModelDecode(src, rc) << 8;
+        len |= model.len[2].ModelDecode(src, rc) << 16;
+        len |= model.len[3].ModelDecode(src, rc) << 24;
+        if (params.fixed_len > 0)
+            params.fixed_len = -len;
+    }
+    else {
+        len = -params.fixed_len;
+    }
+    state.len = len;
+    if (gparams.do_rev)
+        rev[state.rec] = model.rev.ModelDecode(src, rc);
+    state.is_dup = 0;
+    if (params.pflags & FLAG_DEDUP) {
+        if (model.dup.ModelDecode(src, rc))
+            state.is_dup = 1;
+    }
+    state.p = len; // number of remaining bytes in this record
+    state.delta = 0;
+    state.qctx = 0;
+    state.prevq = 0;
+    state.rec++;
+}
+function decode_fqz(src, q_lens) {
+    // Decode parameter block
+    var n_out = src.ReadUint7();
+    var gparams = decode_fqz_params(src);
+    if (!gparams)
+        return;
+    var params = gparams.params;
+    var rev = new Array(q_lens.length);
+    // Create initial models
+    var model = fqz_create_models(gparams);
+    // Create our entropy encoder and output buffers
+    var rc = new RangeCoder(src);
+    rc.RangeStartDecode(src);
+    var output = new Uint8Array(n_out);
+    // Internal FQZ state
+    var state = {
+        qctx: 0, // Qual-only sub-context
+        prevq: 0, // Previous quality value
+        delta: 0, // Running delta (q vs prevq)
+        p: 0, // Number of bases left in current record
+        s: 0, // Current parameter selector value (0 if unused)
+        x: 0, // "stab" tabulated copy of s
+        len: 0, // Length of current string
+        is_dup: 0, // This string is a duplicate of last
+        rec: 0, // Record number
+    };
+    // The main decode loop itself
+    var i = 0; // position in output buffer
+    while (i < n_out) {
+        if (state.p == 0) {
+            decode_fqz_new_record(src, rc, gparams, model, state, rev);
+            if (state.is_dup > 0) {
+                if (model.dup.ModelDecode(src, rc)) {
+                    // Duplicate of last line
+                    for (var x = 0; x < len; x++)
+                        output[i + x] = output[i + x - state.len];
+                    i += state.len;
+                    state.p = 0;
+                    continue;
+                }
+            }
+            q_lens.push(state.len);
+            var params = gparams.params[state.x];
+            var last = params.context;
+        }
+        // Decode the current quality (possibly mapped via qmap)
+        var Q = model.qual[last].ModelDecode(src, rc);
+        //if (params.do_qmap)
+        //    output[i++] = params.qmap[Q];
+        //else
+        //    output[i++] = Q
+        output[i++] = params.qmap[Q]; // optimised version of above
+        last = fqz_update_ctx(params, state, Q);
+    }
+    if (gparams.do_rev)
+        reverse_qualities(output, n_out, rev, q_lens);
+    return output;
+}
+function reverse_qualities(qual, qual_len, rev, len) {
+    var rec = 0;
+    var i = 0;
+    while (i < qual_len) {
+        if (rev[rec]) {
+            var j = 0;
+            var k = len[rec] - 1;
+            while (j < k) {
+                var tmp = qual[i + j];
+                qual[i + j] = qual[i + k];
+                qual[i + k] = tmp;
+                j++;
+                k--;
+            }
+        }
+        i += len[rec++];
+    }
+}
+function decode(src, q_lens) {
+    var stream = new IOStream(src);
+    //var n_out = stream.ReadUint32(); stream.ReadUint32(); // move to main
+    return decode_fqz(stream, q_lens);
+}
+module.exports = { decode };
+//# sourceMappingURL=fqzcomp.js.map

package/esm/htscodecs/fqzcomp.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"fqzcomp.js","sourceRoot":"","sources":["../../src/htscodecs/fqzcomp.js"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,MAAM,QAAQ,GAAG,OAAO,CAAC,YAAY,CAAC,CAAA;AACtC,MAAM,SAAS,GAAG,OAAO,CAAC,cAAc,CAAC,CAAA;AACzC,MAAM,UAAU,GAAG,OAAO,CAAC,YAAY,CAAC,CAAA;AAExC,wEAAwE;AACxE,+DAA+D;AAC/D,mCAAmC;AAEnC,SAAS,UAAU,CAAC,GAAG,EAAE,GAAG,EAAE,IAAI;IAChC,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,cAAc;IACxB,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,sBAAsB;IAChC,IAAI,IAAI,GAAG,CAAC,CAAC,CAAA;IAEb,4CAA4C;IAC5C,IAAI,CAAC,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,CAAA,CAAC,OAAO;IAC/B,OAAO,CAAC,GAAG,IAAI,EAAE,CAAC;QAChB,IAAI,GAAG,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;QACxB,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,CAAA;QACZ,CAAC,IAAI,GAAG,CAAA;QAER,IAAI,GAAG,IAAI,IAAI,EAAE,CAAC;YAChB,IAAI,IAAI,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;YACzB,CAAC,IAAI,GAAG,GAAG,IAAI,CAAA;YACf,OAAO,IAAI,EAAE;gBAAE,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,GAAG,CAAA;QAC7B,CAAC;QACD,IAAI,GAAG,GAAG,CAAA;IACZ,CAAC;IAED,qDAAqD;IACrD,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,CAAC,GAAG,CAAC,CAAA;IACL,CAAC,GAAG,CAAC,CAAA;IACL,OAAO,CAAC,GAAG,IAAI,EAAE,CAAC;QAChB,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,GAAG,CAAC;YACF,IAAI,IAAI,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAA;YACjB,OAAO,IAAI,IAAI,CAAA;QACjB,CAAC,QAAQ,IAAI,IAAI,GAAG,EAAC;QAErB,OAAO,OAAO,EAAE;YAAE,GAAG,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAA;QAC9B,CAAC,EAAE,CAAA;IACL,CAAC;AACH,CAAC;AAED,MAAM,IAAI,GAAG,GAAG,CAAA;AAEhB,MAAM,UAAU,GAAG,CAAC,CAAA;AACpB,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,QAAQ,GAAG,CAAC,CAAA,CAAC,sCAAsC;AACzD,MAAM,SAAS,GAAG,EAAE,CAAA;AACpB,MAAM,SAAS,GAAG,EAAE,CAAA;AACpB,MAAM,SAAS,GAAG,EAAE,CAAA;AACpB,MAAM,SAAS,GAAG,GAAG,CAAA;AAErB,MAAM,iBAAiB,GAAG,CAAC,CAAA;AAC3B,MAAM,eAAe,GAAG,CAAC,CAAA;AACzB,MAAM,YAAY,GAAG,CAAC,CAAA;AAEtB,0DAA0D;AAC1D,SAAS,cAAc,CAAC,MAAM,EAAE,KAAK,EAAE,CAAC;IACtC,IAAI,IAAI,GAAG,MAAM,CAAC,OAAO,CAAA;IACzB,KAAK,CAAC,IAAI,GAAG,CAAC,KAAK,CAAC,IAAI,IAAI,MAAM,CAAC,MAAM,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,QAAQ;IACpE,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,GAAG,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,MAAM,CAAC,IAAI,CAAA,CAAC,QAAQ;IAExE,IAAI,MAAM,CAAC,MAAM;QAAE,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,IAAI,CAAC,CAAC,IAAI,MAAM,CAAC,IAAI,CAAA;IAE9E,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;QACpB,IAAI,IAAI,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAC,IAAI,MAAM,CAAC,IAAI,CAAA;QAC9D,yCAAyC;QACzC,wDAAwD;QACxD,+DAA+D;QAC/D,KAAK,CAAC,KAAK,IAAI,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QACvC,KAAK,CAAC,KAAK,GAAG,CAAC,CAAA;IACjB,CAAC;IAED,IAAI,MAAM,CAAC,MAAM;QAAE,IAAI,IAAI,KAAK,CAAC,CAAC,IAAI,MAAM,CAAC,IAAI,CAAA;IAEjD,KAAK,CAAC,CAAC,EAAE,CAAA;IAET,OAAO,IAAI,GAAG,MAAM,CAAA;AACtB,CAAC;AAED,SAAS,uBAAuB,CAAC,GAAG;IAClC,IAAI,CAAC,GAAG,EAAE,CAAA,CAAC,SAAS;IAEpB,sBAAsB;IACtB,CAAC,CAAC,OAAO,GAAG,GAAG,CAAC,UAAU,EAAE,CAAA;IAC5B,CAAC,CAAC,MAAM,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAEzB,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,MAAM,GAAG,UAAU,CAAA;IAClC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;IAClC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,GAAG,QAAQ,CAAA;IAC9B,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;IAChC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;IAC/B,CAAC,CAAC,QAAQ,GAAG,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;IACjC,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,MAAM,GAAG,SAAS,CAAA;IAEhC,CAAC,CAAC,OAAO,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAE1B,IAAI,CAAC,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IACtB,CAAC,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;IAChB,CAAC,CAAC,MAAM,GAAG,CAAC,GAAG,EAAE,CAAA;IACjB,CAAC,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAClB,CAAC,CAAC,IAAI,GAAG,CAAC,IAAI,CAAC,CAAA;IACf,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,CAAA;IACf,CAAC,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAClB,CAAC,CAAC,IAAI,GAAG,CAAC,IAAI,CAAC,CAAA;IACf,CAAC,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,CAAA;IAEf,6CAA6C;IAC7C,CAAC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACvB,IAAI,CAAC,CAAC,MAAM,GAAG,SAAS,EAAE,CAAC;QACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,OAAO,EAAE,CAAC,EAAE;YAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAChE,CAAC;SAAM,CAAC;QACN,4CAA4C;QAC5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE;YAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA,CAAC,MAAM;IACpD,CAAC;IAED,cAAc;IACd,CAAC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,IAAI,CAAC,CAAC,MAAM,GAAG,SAAS,EAAE,CAAC;QACxC,UAAU,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;IAC9B,CAAC;SAAM,CAAC;QACN,4CAA4C;QAC5C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE;YAAE,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA,CAAC,MAAM;IACpD,CAAC;IAED,CAAC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,IAAI,CAAC,CAAA;IACxB,IAAI,CAAC,CAAC,MAAM,GAAG,SAAS;QAAE,UAAU,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;IAEvD,CAAC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACvB,IAAI,CAAC,CAAC,MAAM,GAAG,SAAS;QAAE,UAAU,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,EAAE,GAAG,CAAC,CAAA;IAEtD,OAAO,CAAC,CAAA;AACV,CAAC;AAED,SAAS,iBAAiB,CAAC,GAAG;IAC5B,IAAI,OAAO,GAAG;QACZ,OAAO,EAAE,CAAC;KACX,CAAA;IAED,2BAA2B;IAC3B,IAAI,IAAI,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IACzB,IAAI,IAAI,IAAI,CAAC,EAAE,CAAC;QACd,OAAO,CAAC,KAAK,CAAC,gCAAgC,CAAC,CAAA;QAC/C,OAAM;IACR,CAAC;IAED,IAAI,MAAM,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;IAC3B,IAAI,MAAM,GAAG,MAAM,GAAG,iBAAiB,CAAC,CAAC,CAAC,GAAG,CAAC,QAAQ,EAAE,CAAC,CAAC,CAAC,CAAC,CAAA;IAC5D,IAAI,OAAO,GAAG,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA,CAAC,4BAA4B;IAEpF,IAAI,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACzB,IAAI,MAAM,GAAG,eAAe,EAAE,CAAC;QAC7B,OAAO,GAAG,GAAG,CAAC,QAAQ,EAAE,CAAA;QACxB,UAAU,CAAC,GAAG,EAAE,IAAI,EAAE,GAAG,CAAC,CAAA;IAC5B,CAAC;SAAM,CAAC;QACN,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE;YAAE,IAAI,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QAC5C,OAAO,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE;YAAE,IAAI,CAAC,CAAC,CAAC,GAAG,MAAM,GAAG,CAAC,CAAA;IAC3C,CAAC;IACD,OAAO,CAAC,MAAM,GAAG,MAAM,GAAG,YAAY,CAAA;IACtC,OAAO,CAAC,IAAI,GAAG,IAAI,CAAA;IACnB,OAAO,CAAC,OAAO,GAAG,OAAO,CAAA;IAEzB,OAAO,CAAC,MAAM,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;IAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QAChC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,uBAAuB,CAAC,GAAG,CAAC,CAAA;QAChD,IAAI,OAAO,CAAC,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,OAAO;YAC7C,OAAO,CAAC,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,OAAO,CAAA;IAC/C,CAAC;IAED,OAAO,OAAO,CAAA;AAChB,CAAC;AAED,SAAS,iBAAiB,CAAC,OAAO;IAChC,IAAI,KAAK,GAAG,EAAE,CAAA;IAEd,KAAK,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;IAC/B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,IAAI,EAAE,EAAE,CAAC,EAAE;QAC9B,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,OAAO,CAAC,OAAO,GAAG,CAAC,CAAC,CAAA,CAAC,kCAAkC;IAEvF,KAAK,CAAC,GAAG,GAAG,IAAI,KAAK,CAAC,CAAC,CAAC,CAAA;IACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE;QAAE,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,SAAS,CAAC,GAAG,CAAC,CAAA;IAE7D,KAAK,CAAC,GAAG,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,CAAA;IAC5B,KAAK,CAAC,GAAG,GAAG,IAAI,SAAS,CAAC,CAAC,CAAC,CAAA;IAE5B,IAAI,OAAO,CAAC,OAAO,GAAG,CAAC;QAAE,KAAK,CAAC,GAAG,GAAG,IAAI,SAAS,CAAC,OAAO,CAAC,OAAO,GAAG,CAAC,CAAC,CAAA,CAAC,kCAAkC;IAE1G,OAAO,KAAK,CAAA;AACd,CAAC;AAED,2CAA2C;AAC3C,gCAAgC;AAChC,SAAS,qBAAqB,CAAC,GAAG,EAAE,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG;IAChE,qBAAqB;IACrB,IAAI,OAAO,CAAC,OAAO,GAAG,CAAC,EAAE,CAAC;QACxB,KAAK,CAAC,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;IAC1C,CAAC;SAAM,CAAC;QACN,KAAK,CAAC,CAAC,GAAG,CAAC,CAAA;IACb,CAAC;IACD,KAAK,CAAC,CAAC,GAAG,OAAO,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IAE/B,IAAI,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;IAEpC,iDAAiD;IACjD,IAAI,MAAM,CAAC,SAAS,IAAI,CAAC,EAAE,CAAC;QAC1B,sCAAsC;QACtC,IAAI,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;QAC3C,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,IAAI,CAAC,CAAA;QAC7C,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,IAAI,EAAE,CAAA;QAC9C,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,IAAI,EAAE,CAAA;QAC9C,IAAI,MAAM,CAAC,SAAS,GAAG,CAAC;YAAE,MAAM,CAAC,SAAS,GAAG,CAAC,GAAG,CAAA;IACnD,CAAC;SAAM,CAAC;QACN,GAAG,GAAG,CAAC,MAAM,CAAC,SAAS,CAAA;IACzB,CAAC;IACD,KAAK,CAAC,GAAG,GAAG,GAAG,CAAA;IAEf,IAAI,OAAO,CAAC,MAAM;QAAE,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;IAEnE,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;IAChB,IAAI,MAAM,CAAC,MAAM,GAAG,UAAU,EAAE,CAAC;QAC/B,IAAI,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC;YAAE,KAAK,CAAC,MAAM,GAAG,CAAC,CAAA;IACtD,CAAC;IAED,KAAK,CAAC,CAAC,GAAG,GAAG,CAAA,CAAC,2CAA2C;IACzD,KAAK,CAAC,KAAK,GAAG,CAAC,CAAA;IACf,KAAK,CAAC,IAAI,GAAG,CAAC,CAAA;IACd,KAAK,CAAC,KAAK,GAAG,CAAC,CAAA;IACf,KAAK,CAAC,GAAG,EAAE,CAAA;AACb,CAAC;AAED,SAAS,UAAU,CAAC,GAAG,EAAE,MAAM;IAC7B,yBAAyB;IACzB,IAAI,KAAK,GAAG,GAAG,CAAC,SAAS,EAAE,CAAA;IAC3B,IAAI,OAAO,GAAG,iBAAiB,CAAC,GAAG,CAAC,CAAA;IACpC,IAAI,CAAC,OAAO;QAAE,OAAM;IACpB,IAAI,MAAM,GAAG,OAAO,CAAC,MAAM,CAAA;IAC3B,IAAI,GAAG,GAAG,IAAI,KAAK,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAElC,wBAAwB;IACxB,IAAI,KAAK,GAAG,iBAAiB,CAAC,OAAO,CAAC,CAAA;IAEtC,gDAAgD;IAChD,IAAI,EAAE,GAAG,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;IAC5B,EAAE,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAA;IACxB,IAAI,MAAM,GAAG,IAAI,UAAU,CAAC,KAAK,CAAC,CAAA;IAElC,qBAAqB;IACrB,IAAI,KAAK,GAAG;QACV,IAAI,EAAE,CAAC,EAAE,wBAAwB;QACjC,KAAK,EAAE,CAAC,EAAE,yBAAyB;QACnC,KAAK,EAAE,CAAC,EAAE,6BAA6B;QACvC,CAAC,EAAE,CAAC,EAAE,yCAAyC;QAC/C,CAAC,EAAE,CAAC,EAAE,iDAAiD;QACvD,CAAC,EAAE,CAAC,EAAE,6BAA6B;QACnC,GAAG,EAAE,CAAC,EAAE,2BAA2B;QACnC,MAAM,EAAE,CAAC,EAAE,qCAAqC;QAChD,GAAG,EAAE,CAAC,EAAE,gBAAgB;KACzB,CAAA;IAED,8BAA8B;IAC9B,IAAI,CAAC,GAAG,CAAC,CAAA,CAAC,4BAA4B;IACtC,OAAO,CAAC,GAAG,KAAK,EAAE,CAAC;QACjB,IAAI,KAAK,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;YACjB,qBAAqB,CAAC,GAAG,EAAE,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;YAC1D,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACrB,IAAI,KAAK,CAAC,GAAG,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,EAAE,CAAC;oBACnC,yBAAyB;oBACzB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE;wBAC1B,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;oBAC3C,CAAC,IAAI,KAAK,CAAC,GAAG,CAAA;oBACd,KAAK,CAAC,CAAC,GAAG,CAAC,CAAA;oBACX,SAAQ;gBACV,CAAC;YACH,CAAC;YACD,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAA;YAEtB,IAAI,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAA;YACpC,IAAI,IAAI,GAAG,MAAM,CAAC,OAAO,CAAA;QAC3B,CAAC;QAED,wDAAwD;QACxD,IAAI,CAAC,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,WAAW,CAAC,GAAG,EAAE,EAAE,CAAC,CAAA;QAE7C,qBAAqB;QACrB,mCAAmC;QACnC,MAAM;QACN,qBAAqB;QACrB,MAAM,CAAC,CAAC,EAAE,CAAC,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA,CAAC,6BAA6B;QAC1D,IAAI,GAAG,cAAc,CAAC,MAAM,EAAE,KAAK,EAAE,CAAC,CAAC,CAAA;IACzC,CAAC;IAED,IAAI,OAAO,CAAC,MAAM;QAAE,iBAAiB,CAAC,MAAM,EAAE,KAAK,EAAE,GAAG,EAAE,MAAM,CAAC,CAAA;IAEjE,OAAO,MAAM,CAAA;AACf,CAAC;AAED,SAAS,iBAAiB,CAAC,IAAI,EAAE,QAAQ,EAAE,GAAG,EAAE,GAAG;IACjD,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,OAAO,CAAC,GAAG,QAAQ,EAAE,CAAC;QACpB,IAAI,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;YACb,IAAI,CAAC,GAAG,CAAC,CAAA;YACT,IAAI,CAAC,GAAG,GAAG,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;gBACb,IAAI,GAAG,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACrB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;gBACzB,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,GAAG,CAAA;gBACjB,CAAC,EAAE,CAAA;gBACH,CAAC,EAAE,CAAA;YACL,CAAC;QACH,CAAC;QAED,CAAC,IAAI,GAAG,CAAC,GAAG,EAAE,CAAC,CAAA;IACjB,CAAC;AACH,CAAC;AAED,SAAS,MAAM,CAAC,GAAG,EAAE,MAAM;IACzB,IAAI,MAAM,GAAG,IAAI,QAAQ,CAAC,GAAG,CAAC,CAAA;IAE9B,uEAAuE;IAEvE,OAAO,UAAU,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;AACnC,CAAC;AAED,MAAM,CAAC,OAAO,GAAG,EAAE,MAAM,EAAE,CAAA"}

package/esm/htscodecs/index.d.ts

@@ -0,0 +1,5 @@
+export function r4x8_uncompress(inputBuffer: any, outputBuffer: any): Uint8Array<any>;
+export function r4x16_uncompress(inputBuffer: any): any;
+export function arith_uncompress(inputBuffer: any): Uint8Array<any>;
+export function fqzcomp_uncompress(inputBuffer: any): Uint8Array<any> | undefined;
+export function tok3_uncompress(inputBuffer: any): Uint8Array<ArrayBuffer>;

package/esm/htscodecs/index.js

@@ -0,0 +1,70 @@
+"use strict";
+/*
+ * Copyright (c) 2020 Genome Research Ltd.
+ * Author(s): James Bonfield
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ *    1. Redistributions of source code must retain the above copyright notice,
+ *       this list of conditions and the following disclaimer.
+ *
+ *    2. Redistributions in binary form must reproduce the above
+ *       copyright notice, this list of conditions and the following
+ *       disclaimer in the documentation and/or other materials provided
+ *       with the distribution.
+ *
+ *    3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
+ *       Institute nor the names of its contributors may be used to endorse
+ *       or promote products derived from this software without specific
+ *       prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
+ * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
+ * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+// This is an interface to the htscodecs reference implementation of
+// the CRAM 3.1 codecs.
+// This JavaScript file is not part of the reference implementation
+// and is simply and interface to get a consistent interface for cram-js.
+var r4x8 = require('./rans');
+var r4x16 = require('./rans4x16');
+var arith = require('./arith_gen');
+var fqzcomp = require('./fqzcomp');
+var tok3 = require('./tok3');
+function r4x8_uncompress(inputBuffer, outputBuffer) {
+    return r4x8.decode(inputBuffer);
+}
+function r4x16_uncompress(inputBuffer) {
+    return r4x16.decode(inputBuffer);
+}
+function arith_uncompress(inputBuffer) {
+    // fix by @cmdcolin for CRAM 3.1
+    // xref https://github.com/jkbonfield/htscodecs/pull/1/files
+    return new arith().decode(inputBuffer);
+}
+function fqzcomp_uncompress(inputBuffer) {
+    var q_lens = new Array();
+    return fqzcomp.decode(inputBuffer, q_lens);
+}
+function tok3_uncompress(inputBuffer) {
+    // Returns in string form instead of buffer
+    var out = tok3.decode(inputBuffer, 0, '\0');
+    return Uint8Array.from(Array.from(out).map(letter => letter.charCodeAt(0)));
+}
+module.exports = {
+    r4x8_uncompress: r4x8_uncompress,
+    r4x16_uncompress: r4x16_uncompress,
+    arith_uncompress: arith_uncompress,
+    fqzcomp_uncompress: fqzcomp_uncompress,
+    tok3_uncompress: tok3_uncompress,
+};
+//# sourceMappingURL=index.js.map

package/esm/htscodecs/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/htscodecs/index.js"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,oEAAoE;AACpE,uBAAuB;AAEvB,mEAAmE;AACnE,yEAAyE;AAEzE,IAAI,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;AAC5B,IAAI,KAAK,GAAG,OAAO,CAAC,YAAY,CAAC,CAAA;AACjC,IAAI,KAAK,GAAG,OAAO,CAAC,aAAa,CAAC,CAAA;AAClC,IAAI,OAAO,GAAG,OAAO,CAAC,WAAW,CAAC,CAAA;AAClC,IAAI,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,CAAA;AAE5B,SAAS,eAAe,CAAC,WAAW,EAAE,YAAY;IAChD,OAAO,IAAI,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACjC,CAAC;AAED,SAAS,gBAAgB,CAAC,WAAW;IACnC,OAAO,KAAK,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AAClC,CAAC;AAED,SAAS,gBAAgB,CAAC,WAAW;IACnC,gCAAgC;IAChC,4DAA4D;IAC5D,OAAO,IAAI,KAAK,EAAE,CAAC,MAAM,CAAC,WAAW,CAAC,CAAA;AACxC,CAAC;AAED,SAAS,kBAAkB,CAAC,WAAW;IACrC,IAAI,MAAM,GAAG,IAAI,KAAK,EAAE,CAAA;IACxB,OAAO,OAAO,CAAC,MAAM,CAAC,WAAW,EAAE,MAAM,CAAC,CAAA;AAC5C,CAAC;AAED,SAAS,eAAe,CAAC,WAAW;IAClC,2CAA2C;IAC3C,IAAI,GAAG,GAAG,IAAI,CAAC,MAAM,CAAC,WAAW,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAC3C,OAAO,UAAU,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC,EAAE,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AAC7E,CAAC;AAED,MAAM,CAAC,OAAO,GAAG;IACf,eAAe,EAAE,eAAe;IAChC,gBAAgB,EAAE,gBAAgB;IAClC,gBAAgB,EAAE,gBAAgB;IAClC,kBAAkB,EAAE,kBAAkB;IACtC,eAAe,EAAE,eAAe;CACjC,CAAA"}

package/esm/htscodecs/iostream.d.ts

@@ -0,0 +1,27 @@
+export = IOStream;
+declare class IOStream {
+    constructor(buf: any, start_pos?: number, size?: number);
+    buf: any;
+    length: any;
+    dataView: DataView<any>;
+    pos: number;
+    EOF(): boolean;
+    ReadData(len: any): any;
+    ReadByte(): any;
+    ReadChar(): string;
+    ReadUint16(): any;
+    ReadUint32(): number;
+    ReadString(): string;
+    ReadUint7(): number;
+    ReadITF8(): any;
+    WriteByte(b: any): void;
+    WriteChar(b: any): void;
+    WriteString(str: any): void;
+    WriteData(buf: any, len: any): void;
+    WriteStream(stream: any): void;
+    WriteUint16(u: any): void;
+    WriteUint32(u: any): void;
+    WriteUint7(i: any): void;
+    WriteITF8(i: any): void;
+    WriteByteNeg(b: any): void;
+}