@gmod/cram 6.0.0 → 7.0.0

package/src/htscodecs/fqzcomp.ts

@@ -1,394 +0,0 @@
-/* eslint-disable no-var */
-// @ts-nocheck
-
-/*
- * 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.
- */
-
-import RangeCoder from './arith_sh.ts'
-import ByteModel from './byte_model.ts'
-import IOStream from './iostream.ts'
-
-// ----------------------------------------------------------------------
-// Main arithmetic entry function: decodes a compressed src and
-// returns the uncompressed buffer.
-
-function read_array(src, tab, size) {
-  let j = 0 // array value
-  let z = 0 // array index: tab[j]
-  let last = -1
-
-  // Remove first level of run-length encoding
-  const R = new Array(1024) // runs
-  while (z < size) {
-    const run = src.ReadByte()
-    R[j++] = run
-    z += run
-
-    if (run == last) {
-      let 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
-  let i = 0
-  j = 0
-  z = 0
-  while (z < size) {
-    let 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) {
-  let 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) {
-  const 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()
-
-  let 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) {
-  const gparams = {
-    max_sym: 0,
-  }
-
-  // Check fqz format version
-  const vers = src.ReadByte()
-  if (vers != 5) {
-    console.error('Invalid FQZComp version number')
-    return
-  }
-
-  const gflags = src.ReadByte()
-  const nparam = gflags & GFLAG_MULTI_PARAM ? src.ReadByte() : 1
-  let max_sel = gflags.nparam > 1 ? gflags.nparam - 1 : 0 // Note max_sel, not num_sel
-
-  const 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 (let 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) {
-  const 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
-  state.s = gparams.max_sel > 0 ? model.sel.ModelDecode(src, rc) : 0
-  state.x = gparams.stab[state.s]
-
-  const 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: IOStream, q_lens: number) {
-  // Decode parameter block
-  const n_out = src.ReadUint7()
-  const gparams = decode_fqz_params(src)
-  if (!gparams) {
-    return
-  }
-  var params = gparams.params
-  const rev = new Array(q_lens.length)
-
-  // Create initial models
-  const model = fqz_create_models(gparams)
-
-  // Create our entropy encoder and output buffers
-  const rc = new RangeCoder(src)
-  rc.RangeStartDecode(src)
-  const output = new Uint8Array(n_out)
-
-  // Internal FQZ state
-  const 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
-  let 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 (let 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)
-    const 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) {
-  let rec = 0
-  let i = 0
-  while (i < qual_len) {
-    if (rev[rec]) {
-      let j = 0
-      let k = len[rec] - 1
-      while (j < k) {
-        const tmp = qual[i + j]
-        qual[i + j] = qual[i + k]
-        qual[i + k] = tmp
-        j++
-        k--
-      }
-    }
-
-    i += len[rec++]
-  }
-}
-
-export function decode(src: Uint8Array, q_lens) {
-  const stream = new IOStream(src)
-
-  return decode_fqz(stream, q_lens)
-}

package/src/htscodecs/iostream.ts

@@ -1,159 +0,0 @@
-// @ts-nocheck
-
-/*
- * 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.
- */
-
-// Turn a buffer into a fake stream with get / put commands.
-// This enables up to closely match the published pseudocode.
-export default class IOStream {
-  buf: Uint8Array
-  length: number
-  pos: number
-  dataView: DataView
-
-  constructor(buf: Uint8Array, start_pos = 0, size = 0) {
-    if (size !== 0) {
-      this.buf = new Uint8Array(size)
-      this.length = size
-    } else {
-      this.buf = buf
-      this.length = buf.length
-    }
-    this.dataView = new DataView(this.buf.buffer)
-    this.pos = start_pos
-  }
-
-  // ----------
-  // Reading
-  EOF() {
-    return this.pos >= this.length
-  }
-
-  ReadData(len: number) {
-    const A = this.buf.slice(this.pos, this.pos + len)
-    this.pos += len
-    return A
-  }
-
-  ReadByte() {
-    const b = this.buf[this.pos]!
-    this.pos++
-    return b
-  }
-
-  ReadChar() {
-    const b = this.buf[this.pos]!
-    this.pos++
-    return String.fromCharCode(b)
-  }
-
-  ReadUint16() {
-    let i = this.ReadByte()
-    i |= this.ReadByte() << 8
-    return i
-  }
-
-  ReadUint32() {
-    const i = this.dataView.getInt32(this.pos, true)
-    this.pos += 4
-    return i
-  }
-
-  // nul terminated string
-  ReadString() {
-    let s = ''
-    let b: number
-    do {
-      b = this.buf[this.pos++]!
-      if (b) {
-        s += String.fromCharCode(b)
-      }
-    } while (b)
-    return s
-  }
-
-  ReadUint7() {
-    // Variable sized unsigned integers
-    let i = 0
-    let c: number
-    do {
-      c = this.ReadByte()
-      i = (i << 7) | (c & 0x7f)
-    } while (c & 0x80)
-
-    return i
-  }
-
-  ReadITF8() {
-    let i = this.buf[this.pos]!
-    this.pos++
-
-    // process.stderr.write("i="+i+"\n");
-
-    if (i >= 0xf0) {
-      // 1111xxxx => +4 bytes
-      i = (i & 0x0f) << 28
-      i +=
-        (this.buf[this.pos + 0]! << 20) +
-        (this.buf[this.pos + 1]! << 12) +
-        (this.buf[this.pos + 2]! << 4) +
-        (this.buf[this.pos + 3]! >> 4)
-      this.pos += 4
-      // process.stderr.write("  4i="+i+"\n");
-    } else if (i >= 0xe0) {
-      // 1110xxxx => +3 bytes
-      i = (i & 0x0f) << 24
-      i +=
-        (this.buf[this.pos + 0]! << 16) +
-        (this.buf[this.pos + 1]! << 8) +
-        (this.buf[this.pos + 2]! << 0)
-      this.pos += 3
-      // process.stderr.write("  3i="+i+"\n");
-    } else if (i >= 0xc0) {
-      // 110xxxxx => +2 bytes
-      i = (i & 0x1f) << 16
-      i += (this.buf[this.pos + 0]! << 8) + (this.buf[this.pos + 1]! << 0)
-      this.pos += 2
-      // process.stderr.write("  2i="+i+"\n");
-    } else if (i >= 0x80) {
-      // 10xxxxxx => +1 bytes
-      i = (i & 0x3f) << 8
-      i += this.buf[this.pos]!
-      this.pos++
-    } else {
-      // 0xxxxxxx => +0 bytes
-    }
-
-    return i
-  }
-}