@gmod/cram 3.0.7 → 4.0.0

package/src/htscodecs/README.md

@@ -1,64 +0,0 @@
-# Reference implementation files
-
-This directory contains javascript implementations of the custom codecs using in
-CRAM 3.1, capable of being run under node.js.
-
-These is not written for speed, but for clarity and as an exercise in checking
-the pseudocode in the CRAM specification. It is written as close to this
-pseudocode as is possible.
-
-Prerequisites: minimist package for command line parsing and bzip2 for part of
-the arith_gen.js code.
-
-    npm install minimist
-    npm install bzip2
-
-## iostream.js
-
-Makes a buffer appear to be a stream with ReadByte, ReadITF8, etc functions.
-
-## rans.js
-
-Implements the order-0 and order-1 rans (4x8) decoder as used in CRAM3.0.
-
-## main_rans.js
-
-A command line tool to exercise the rans.js code, included for debug purposes.
-
-## rans4x16.js, main_rans4x16.js
-
-A 16-bit renormalising variant of rANS above. This also includes transforms for
-RLE, bit-packing and 4-way interleaving.
-
-## arith_sh.js
-
-Arithmetic (range) coding with Schindler carry handling.
-
-## byte_model.js
-
-An adaptive model for keeping track of symbol frequencies.
-
-## arith_gen.js, main_arith_gen.js
-
-Wrapper around arith_sh.js to perform order-0/1 encoding with RLE and
-bit-packing. Plus debug command line tool
-
-## fqzcomp.js, main_fqzcomp.js
-
-Implements the fqzcomp quality compression codec. Plus debug command line tool.
-
-## tok3.js, main_tok3.js
-
-Implements the tokenise_name3 read identifier compression codec. Plus debug
-command line tool.
-
-# Testing
-
-The various main js files can be used for adhoc testing. There is also a
-Makefile which performs checks against known defined data streams and does
-round-trip testing in both Javascript and if compiled the C variant. You can set
-CORPUS make variable to a larger data set such htscodecs-corpus.
-
-eg.
-
-    make check CORPUS=../tests/htscodecs-corpus/

package/src/htscodecs/main_arith_gen.js

@@ -1,96 +0,0 @@
-/*
- * Copyright (c) 2019,2020 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.
- */
-
-// Command line tool to manually test the arith_gen.js code.
-
-var fs = require('fs')
-var RangeCoderGen = require('./arith_gen')
-
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] })
-
-if (argv._.length != 1) {
-  process.stderr.write(
-    'Usage: node main_arith_gen.js [-d] [-o order] input-file > output-file\n',
-  )
-  process.exit(1)
-}
-
-var filein = argv._[0]
-
-var buf = fs.readFileSync(filein)
-var blk_size = 1024 * 1024
-var raw = argv.r
-
-var arith = new RangeCoderGen()
-if (!argv.d) {
-  var order = argv.o != undefined ? argv.o : 0
-  // -o8.4 => 8+(256*4)
-  order += Math.round((order - (order >> 0)) * 10) * 256
-  var pos = 0
-  var out_len = 0
-  if (raw) blk_size = buf.length
-  while (pos < buf.length) {
-    var buf2 = arith.encode(buf.slice(pos, pos + blk_size), order)
-
-    // Compressed buffer size. Used in multi-block format.
-    var csize = new Buffer.allocUnsafe(4)
-    if (!raw) {
-      csize.writeInt32LE(buf2.length, 0)
-      process.stdout.write(csize)
-    }
-
-    // Write compressed buffer itself
-    process.stdout.write(buf2)
-
-    pos += blk_size
-    out_len += buf2.length
-  }
-  process.stderr.write(
-    'Compress order ' + order + ', ' + buf.length + ' => ' + out_len + '\n',
-  )
-} else {
-  var pos = 0
-  var out_len = 0
-  var len = buf.length
-  while (pos < buf.length) {
-    if (!raw) {
-      len = buf.readInt32LE(pos)
-      pos += 4
-    }
-    var buf2 = arith.decode(buf.slice(pos, pos + len))
-    process.stdout.write(buf2)
-    out_len += buf2.length
-    pos += len
-  }
-  process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n')
-}

package/src/htscodecs/main_fqzcomp.js

@@ -1,113 +0,0 @@
-/*
- * Copyright (c) 2019,2020 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.
- */
-
-var fs = require('fs')
-var fqz = require('./fqzcomp')
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] })
-
-if (argv._.length != 1) {
-  process.stderr.write(
-    'Usage: node main_fqzcomp.js [-d] input-file > output-file\n',
-  )
-  process.exit(1)
-}
-
-var filein = argv._[0]
-
-var buf = fs.readFileSync(filein)
-var raw = argv.r
-
-if (!argv.d) {
-  // Line breaks to get sequence length, but then stitch together into
-  // a single non-breaking buffer.
-  var len = 0
-  var j = 0
-  var q_lens = new Array()
-  var q_dirs = new Array()
-  var q_len = 0
-  for (var i = 0; i < buf.length; i++) {
-    if (buf[i] == '\n'.charCodeAt(0) || buf[i] == '\t'.charCodeAt(0)) {
-      q_lens.push(len)
-      if (q_len == 0) q_len = len
-      else if (q_len != len) q_len = -1 // marker for multiple lengths
-      len = 0
-
-      if (buf[i] == '\t'.charCodeAt(0)) {
-        // parse 2nd token for read1/read2 status
-        var dir = ''
-        for (i++; i < buf.length && buf[i] != '\n'.charCodeAt(0); i++)
-          dir += String.fromCharCode(buf[i])
-        q_dirs.push(dir)
-      } else {
-        q_dirs.push(0)
-      }
-    } else {
-      buf[j++] = buf[i] - 33 // ASCII phred to raw
-      len++
-    }
-  }
-  buf = buf.slice(0, j)
-  if (q_len > 0) q_lens = [q_lens[0]]
-
-  var buf2 = fqz.encode(buf, q_lens, q_dirs)
-  process.stderr.write('Compress ' + buf.length + ' => ' + buf2.length + '\n')
-  if (!raw) {
-    var hdr = new Buffer.allocUnsafe(8)
-    hdr.writeInt32LE(buf.length, 0)
-    hdr.writeInt32LE(buf2.length, 4)
-    process.stdout.write(hdr)
-  }
-  process.stdout.write(buf2)
-} else {
-  var q_lens = new Array()
-  // Consume ulen and clen from outer test harness (pointless as non-blocking atm)
-  var buf2
-  if (raw) buf2 = fqz.decode(buf, q_lens)
-  else buf2 = fqz.decode(buf.slice(8), q_lens)
-
-  // Split into newlines so we can do easy data comparison
-  var buf3 = new Buffer.allocUnsafe(buf2.length + q_lens.length)
-  var rec = 0
-  var len = q_lens[rec++]
-  var j = 0
-  for (var i = 0; i < buf2.length; i++) {
-    buf3[j++] = buf2[i] + 33
-    if (--len == 0) {
-      buf3[j++] = '\n'.charCodeAt(0)
-      len = q_lens[rec++]
-    }
-  }
-
-  process.stderr.write('Decompress ' + buf.length + ' => ' + buf3.length + '\n')
-  process.stdout.write(buf3)
-}

package/src/htscodecs/main_rans.js

@@ -1,88 +0,0 @@
-/*
- * Copyright (c) 2019-2020 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.
- */
-
-var fs = require('fs')
-var rans = require('./rans')
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] })
-
-if (argv._.length != 1) {
-  process.stderr.write(
-    'Usage: node main_rans.js [-d] [-o order] input-file > output-file\n',
-  )
-  process.exit(1)
-}
-
-var filein = argv._[0]
-
-var buf = fs.readFileSync(filein)
-var blk_size = 1024 * 1024
-var raw = argv.r
-
-if (!argv.d) {
-  var order = argv.o != undefined ? argv.o : 0
-  var pos = 0
-  var out_len = 0
-  if (raw) blk_size = buf.length
-  while (pos < buf.length) {
-    var buf2 = rans.encode(buf.slice(pos, pos + blk_size), order)
-    var header = new Buffer.allocUnsafe(5)
-    if (!raw) {
-      header[0] = order
-      header.writeInt32LE(buf2.length, 1)
-      process.stdout.write(header)
-    }
-    process.stdout.write(buf2)
-    pos += blk_size
-    out_len += buf2.length
-  }
-  process.stderr.write(
-    'Compress order ' + order + ', ' + buf.length + ' => ' + out_len + '\n',
-  )
-} else {
-  var pos = 0
-  var out_len = 0
-  var len = buf.length
-  while (pos < buf.length) {
-    if (!raw) {
-      var order = buf[0]
-      pos++
-      len = buf.readInt32LE(pos)
-      pos += 4
-    }
-    var buf2 = rans.decode(buf.slice(pos, pos + len))
-    process.stdout.write(buf2)
-    out_len += buf2.length
-    pos += len
-  }
-  process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n')
-}

package/src/htscodecs/main_rans4x16.js

@@ -1,87 +0,0 @@
-/*
- * Copyright (c) 2019-2020 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.
- */
-
-var fs = require('fs')
-var rans = require('./rans4x16')
-var argv = require('minimist')(process.argv.slice(2), { boolean: ['d', 'r'] })
-
-if (argv._.length != 1) {
-  processf.stderr.write(
-    'Usage: node main_rans4x16.js [-d] [-o order] input-file > output-file\n',
-  )
-  process.exit(1)
-}
-
-var filein = argv._[0]
-
-var buf = fs.readFileSync(filein)
-var blk_size = 1024 * 1024
-var raw = argv.r
-
-if (!argv.d) {
-  var order = argv.o != undefined ? argv.o : 0
-  // -o8.4 => 8+(256*4)
-  order += Math.round((order - (order >> 0)) * 10) * 256
-  var pos = 0
-  var out_len = 0
-  if (raw) blk_size = buf.length
-  while (pos < buf.length) {
-    var buf2 = rans.encode(buf.slice(pos, pos + blk_size), order)
-    var header = new Buffer.allocUnsafe(4)
-    if (!raw) {
-      header.writeInt32LE(buf2.length, 0)
-      process.stdout.write(header)
-    }
-    process.stdout.write(buf2)
-    pos += blk_size
-    out_len += buf2.length + 4
-  }
-  process.stderr.write(
-    'Compress order ' + order + ', ' + buf.length + ' => ' + out_len + '\n',
-  )
-} else {
-  var pos = 0
-  var out_len = 0
-  var len = buf.length
-  while (pos < buf.length) {
-    if (!raw) {
-      len = buf.readInt32LE(pos)
-      pos += 4
-    }
-    var buf2 = rans.decode(buf.slice(pos, pos + len))
-    process.stdout.write(buf2)
-    out_len += buf2.length
-    pos += len
-  }
-  process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n')
-}

package/src/htscodecs/main_tok3.js

@@ -1,86 +0,0 @@
-/*
- * Copyright (c) 2019,2020 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.
- */
-
-var fs = require('fs')
-var tok3 = require('./tok3')
-var argv = require('minimist')(process.argv.slice(2), {
-  boolean: ['d', 'a', 'r'],
-})
-
-if (argv._.length != 1) {
-  process.stderr.write(
-    'Usage: node main_tok3.js [-a] [-d] input-file > output-file\n',
-  )
-  process.exit(1)
-}
-
-var filein = argv._[0]
-
-var buf = fs.readFileSync(filein)
-var blk_size = 1024 * 1024
-var raw = argv.r
-
-if (!argv.d) {
-  var pos = 0
-  var out_len = 0
-  if (raw) blk_size = buf.length
-  while (pos < buf.length) {
-    var blk_end = blk_size
-    while (pos + blk_end < buf.length && buf[pos + blk_end - 1] != 10) blk_end--
-    var buf2 = tok3.encode(buf.slice(pos, pos + blk_end), argv.a)
-    var header = new Buffer.allocUnsafe(4)
-    if (!raw) {
-      header.writeInt32LE(buf2.length, 0)
-      process.stdout.write(header)
-    }
-    process.stdout.write(buf2)
-    pos += blk_end
-    out_len += buf2.length + 4
-  }
-  process.stderr.write('Compress ' + buf.length + ' => ' + out_len + '\n')
-} else {
-  var pos = 0
-  var out_len = 0
-  var len = buf.length
-  while (pos < buf.length) {
-    if (!raw) {
-      len = buf.readInt32LE(pos)
-      pos += 4
-    }
-    var buf2 = tok3.decode(buf.slice(pos, pos + len), len)
-    process.stdout.write(buf2)
-    out_len += buf2.length
-    pos += len
-  }
-  process.stderr.write('Decompress ' + buf.length + ' => ' + out_len + '\n')
-}

package/src/unzip-pako.ts

@@ -1,6 +0,0 @@
-import { inflate } from 'pako'
-import { Buffer } from 'buffer'
-
-export function unzip(input: Buffer) {
-  return Buffer.from(inflate(input))
-}