@gmod/cram 6.0.0 → 7.0.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (178) hide show
  1. package/dist/craiIndex.js +2 -2
  2. package/dist/craiIndex.js.map +1 -1
  3. package/dist/cram-bundle.js +1 -1
  4. package/dist/cramFile/file.d.ts +2 -2
  5. package/dist/cramFile/file.js +9 -13
  6. package/dist/cramFile/file.js.map +1 -1
  7. package/dist/htscodecs/index.d.ts +1 -5
  8. package/dist/htscodecs/index.js +11 -72
  9. package/dist/htscodecs/index.js.map +1 -1
  10. package/dist/htscodecs-wasm.d.ts +7 -0
  11. package/dist/htscodecs-wasm.js +183 -0
  12. package/dist/htscodecs-wasm.js.map +1 -0
  13. package/dist/unzip.d.ts +1 -1
  14. package/dist/unzip.js +3 -3
  15. package/dist/unzip.js.map +1 -1
  16. package/dist/wasm/htscodecs.d.ts +5 -0
  17. package/dist/wasm/htscodecs.js +0 -0
  18. package/dist/wasm/htscodecs.js.map +1 -0
  19. package/esm/craiIndex.js +2 -2
  20. package/esm/craiIndex.js.map +1 -1
  21. package/esm/cramFile/file.d.ts +2 -2
  22. package/esm/cramFile/file.js +7 -11
  23. package/esm/cramFile/file.js.map +1 -1
  24. package/esm/htscodecs/index.d.ts +1 -5
  25. package/esm/htscodecs/index.js +3 -31
  26. package/esm/htscodecs/index.js.map +1 -1
  27. package/esm/htscodecs-wasm.d.ts +7 -0
  28. package/esm/htscodecs-wasm.js +171 -0
  29. package/esm/htscodecs-wasm.js.map +1 -0
  30. package/esm/unzip.d.ts +1 -1
  31. package/esm/unzip.js +3 -3
  32. package/esm/unzip.js.map +1 -1
  33. package/esm/wasm/htscodecs.d.ts +5 -0
  34. package/esm/wasm/htscodecs.js +0 -0
  35. package/esm/wasm/htscodecs.js.map +1 -0
  36. package/package.json +9 -9
  37. package/src/craiIndex.ts +4 -2
  38. package/src/cramFile/file.ts +7 -11
  39. package/src/htscodecs/index.ts +12 -38
  40. package/src/htscodecs-wasm.ts +210 -0
  41. package/src/unzip.ts +3 -3
  42. package/src/wasm/htscodecs.d.ts +58 -0
  43. package/src/wasm/htscodecs.js +0 -0
  44. package/dist/htscodecs/arith_gen.d.ts +0 -16
  45. package/dist/htscodecs/arith_gen.js +0 -323
  46. package/dist/htscodecs/arith_gen.js.map +0 -1
  47. package/dist/htscodecs/arith_sh.d.ts +0 -9
  48. package/dist/htscodecs/arith_sh.js +0 -134
  49. package/dist/htscodecs/arith_sh.js.map +0 -1
  50. package/dist/htscodecs/byte_model.d.ts +0 -6
  51. package/dist/htscodecs/byte_model.js +0 -121
  52. package/dist/htscodecs/byte_model.js.map +0 -1
  53. package/dist/htscodecs/fqzcomp.d.ts +0 -1
  54. package/dist/htscodecs/fqzcomp.js +0 -346
  55. package/dist/htscodecs/fqzcomp.js.map +0 -1
  56. package/dist/htscodecs/iostream.d.ts +0 -16
  57. package/dist/htscodecs/iostream.js +0 -148
  58. package/dist/htscodecs/iostream.js.map +0 -1
  59. package/dist/htscodecs/rans.d.ts +0 -1
  60. package/dist/htscodecs/rans.js +0 -224
  61. package/dist/htscodecs/rans.js.map +0 -1
  62. package/dist/htscodecs/rans4x16.d.ts +0 -1
  63. package/dist/htscodecs/rans4x16.js +0 -445
  64. package/dist/htscodecs/rans4x16.js.map +0 -1
  65. package/dist/htscodecs/tok3.d.ts +0 -1
  66. package/dist/htscodecs/tok3.js +0 -206
  67. package/dist/htscodecs/tok3.js.map +0 -1
  68. package/dist/rans/constants.d.ts +0 -4
  69. package/dist/rans/constants.js +0 -10
  70. package/dist/rans/constants.js.map +0 -1
  71. package/dist/rans/d04.d.ts +0 -1
  72. package/dist/rans/d04.js +0 -100
  73. package/dist/rans/d04.js.map +0 -1
  74. package/dist/rans/d14.d.ts +0 -1
  75. package/dist/rans/d14.js +0 -96
  76. package/dist/rans/d14.js.map +0 -1
  77. package/dist/rans/decoding.d.ts +0 -27
  78. package/dist/rans/decoding.js +0 -119
  79. package/dist/rans/decoding.js.map +0 -1
  80. package/dist/rans/frequencies.d.ts +0 -2
  81. package/dist/rans/frequencies.js +0 -112
  82. package/dist/rans/frequencies.js.map +0 -1
  83. package/dist/rans/index.d.ts +0 -1
  84. package/dist/rans/index.js +0 -198
  85. package/dist/rans/index.js.map +0 -1
  86. package/dist/seek-bzip/bitreader.d.ts +0 -27
  87. package/dist/seek-bzip/bitreader.js +0 -101
  88. package/dist/seek-bzip/bitreader.js.map +0 -1
  89. package/dist/seek-bzip/crc32.d.ts +0 -26
  90. package/dist/seek-bzip/crc32.js +0 -115
  91. package/dist/seek-bzip/crc32.js.map +0 -1
  92. package/dist/seek-bzip/index.d.ts +0 -9
  93. package/dist/seek-bzip/index.js +0 -585
  94. package/dist/seek-bzip/index.js.map +0 -1
  95. package/dist/seek-bzip/stream.d.ts +0 -8
  96. package/dist/seek-bzip/stream.js +0 -37
  97. package/dist/seek-bzip/stream.js.map +0 -1
  98. package/dist/seek-bzip/toHex.d.ts +0 -1
  99. package/dist/seek-bzip/toHex.js +0 -36
  100. package/dist/seek-bzip/toHex.js.map +0 -1
  101. package/esm/htscodecs/arith_gen.d.ts +0 -16
  102. package/esm/htscodecs/arith_gen.js +0 -317
  103. package/esm/htscodecs/arith_gen.js.map +0 -1
  104. package/esm/htscodecs/arith_sh.d.ts +0 -9
  105. package/esm/htscodecs/arith_sh.js +0 -131
  106. package/esm/htscodecs/arith_sh.js.map +0 -1
  107. package/esm/htscodecs/byte_model.d.ts +0 -6
  108. package/esm/htscodecs/byte_model.js +0 -118
  109. package/esm/htscodecs/byte_model.js.map +0 -1
  110. package/esm/htscodecs/fqzcomp.d.ts +0 -1
  111. package/esm/htscodecs/fqzcomp.js +0 -340
  112. package/esm/htscodecs/fqzcomp.js.map +0 -1
  113. package/esm/htscodecs/iostream.d.ts +0 -16
  114. package/esm/htscodecs/iostream.js +0 -145
  115. package/esm/htscodecs/iostream.js.map +0 -1
  116. package/esm/htscodecs/rans.d.ts +0 -1
  117. package/esm/htscodecs/rans.js +0 -218
  118. package/esm/htscodecs/rans.js.map +0 -1
  119. package/esm/htscodecs/rans4x16.d.ts +0 -1
  120. package/esm/htscodecs/rans4x16.js +0 -439
  121. package/esm/htscodecs/rans4x16.js.map +0 -1
  122. package/esm/htscodecs/tok3.d.ts +0 -1
  123. package/esm/htscodecs/tok3.js +0 -167
  124. package/esm/htscodecs/tok3.js.map +0 -1
  125. package/esm/rans/constants.d.ts +0 -4
  126. package/esm/rans/constants.js +0 -5
  127. package/esm/rans/constants.js.map +0 -1
  128. package/esm/rans/d04.d.ts +0 -1
  129. package/esm/rans/d04.js +0 -94
  130. package/esm/rans/d04.js.map +0 -1
  131. package/esm/rans/d14.d.ts +0 -1
  132. package/esm/rans/d14.js +0 -93
  133. package/esm/rans/d14.js.map +0 -1
  134. package/esm/rans/decoding.d.ts +0 -27
  135. package/esm/rans/decoding.js +0 -117
  136. package/esm/rans/decoding.js.map +0 -1
  137. package/esm/rans/frequencies.d.ts +0 -2
  138. package/esm/rans/frequencies.js +0 -105
  139. package/esm/rans/frequencies.js.map +0 -1
  140. package/esm/rans/index.d.ts +0 -1
  141. package/esm/rans/index.js +0 -192
  142. package/esm/rans/index.js.map +0 -1
  143. package/esm/seek-bzip/bitreader.d.ts +0 -27
  144. package/esm/seek-bzip/bitreader.js +0 -98
  145. package/esm/seek-bzip/bitreader.js.map +0 -1
  146. package/esm/seek-bzip/crc32.d.ts +0 -26
  147. package/esm/seek-bzip/crc32.js +0 -112
  148. package/esm/seek-bzip/crc32.js.map +0 -1
  149. package/esm/seek-bzip/index.d.ts +0 -9
  150. package/esm/seek-bzip/index.js +0 -579
  151. package/esm/seek-bzip/index.js.map +0 -1
  152. package/esm/seek-bzip/stream.d.ts +0 -8
  153. package/esm/seek-bzip/stream.js +0 -34
  154. package/esm/seek-bzip/stream.js.map +0 -1
  155. package/esm/seek-bzip/toHex.d.ts +0 -1
  156. package/esm/seek-bzip/toHex.js +0 -33
  157. package/esm/seek-bzip/toHex.js.map +0 -1
  158. package/src/htscodecs/arith_gen.ts +0 -371
  159. package/src/htscodecs/arith_sh.ts +0 -146
  160. package/src/htscodecs/byte_model.ts +0 -136
  161. package/src/htscodecs/fqzcomp.ts +0 -394
  162. package/src/htscodecs/iostream.ts +0 -159
  163. package/src/htscodecs/rans.ts +0 -250
  164. package/src/htscodecs/rans4x16.ts +0 -521
  165. package/src/htscodecs/tok3.ts +0 -197
  166. package/src/rans/README.md +0 -1
  167. package/src/rans/constants.ts +0 -5
  168. package/src/rans/d04.ts +0 -112
  169. package/src/rans/d14.ts +0 -106
  170. package/src/rans/decoding.ts +0 -138
  171. package/src/rans/frequencies.ts +0 -115
  172. package/src/rans/index.ts +0 -245
  173. package/src/seek-bzip/README.md +0 -6
  174. package/src/seek-bzip/bitreader.ts +0 -113
  175. package/src/seek-bzip/crc32.ts +0 -121
  176. package/src/seek-bzip/index.ts +0 -615
  177. package/src/seek-bzip/stream.ts +0 -33
  178. package/src/seek-bzip/toHex.ts +0 -33
@@ -1,445 +0,0 @@
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- "use strict";
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- /* eslint-disable no-var */
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- // @ts-nocheck
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- var __importDefault = (this && this.__importDefault) || function (mod) {
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- return (mod && mod.__esModule) ? mod : { "default": mod };
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- };
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- Object.defineProperty(exports, "__esModule", { value: true });
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- exports.decode = decode;
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- /*
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- * Copyright (c) 2019,2020 Genome Research Ltd.
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- * Author(s): James Bonfield
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- *
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- * Redistribution and use in source and binary forms, with or without
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- * modification, are permitted provided that the following conditions are met:
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- *
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- * 1. Redistributions of source code must retain the above copyright notice,
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- * this list of conditions and the following disclaimer.
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- *
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- * 2. Redistributions in binary form must reproduce the above
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- * copyright notice, this list of conditions and the following
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- * disclaimer in the documentation and/or other materials provided
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- * with the distribution.
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- *
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- * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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- * Institute nor the names of its contributors may be used to endorse
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- * or promote products derived from this software without specific
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- * prior written permission.
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- *
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- * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
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- * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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- * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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- * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
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- * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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- * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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- * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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- */
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- const iostream_ts_1 = __importDefault(require("./iostream.js"));
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- // ----------------------------------------------------------------------
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- // rANS primitives itself
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- //
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- // RansGet* is decoder side
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- function RansGetCumulativeFreq(R, bits) {
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- return R & ((1 << bits) - 1);
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- }
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- function RansGetSymbolFromFreq(C, f) {
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- // NOTE: Inefficient.
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- // In practice we would implement this via a precomputed
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- // lookup table C2S[f]; see RansBuildC2S below.
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- let s = 0;
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- while (f >= C[s + 1]) {
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- s++;
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- }
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- // console.error(f, C, s)
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- return s;
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- }
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- function RansBuildC2S(C, bits) {
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- const max = 1 << bits;
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- const C2S = new Array(max);
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- let s = 0;
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- for (let f = 0; f < max; f++) {
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- while (f >= C[s + 1]) {
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- s++;
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- }
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- C2S[f] = s;
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- }
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- return C2S;
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- }
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- function RansAdvanceStep(R, c, f, bits) {
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- return f * (R >> bits) + (R & ((1 << bits) - 1)) - c;
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- }
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- function RansRenorm(src, R) {
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- if (R < 1 << 15) {
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- R = (R << 16) + src.ReadUint16();
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- }
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- return R;
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- }
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- function DecodeRLEMeta(src, N) {
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- const u_meta_len = src.ReadUint7();
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- const rle_len = src.ReadUint7();
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- // Decode RLE lengths
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- if (u_meta_len & 1) {
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- var rle_meta = src.ReadData((u_meta_len - 1) / 2);
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- }
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- else {
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- const comp_meta_len = src.ReadUint7();
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- var rle_meta = src.ReadData(comp_meta_len);
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- rle_meta = RansDecode0(new iostream_ts_1.default(rle_meta), u_meta_len / 2, N);
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- }
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- // Decode list of symbols for which RLE lengths are applied
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- var rle_meta = new iostream_ts_1.default(rle_meta);
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- const L = new Array(256);
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- let n = rle_meta.ReadByte();
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- if (n == 0) {
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- n = 256;
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- }
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- for (let i = 0; i < n; i++) {
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- L[rle_meta.ReadByte()] = 1;
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- }
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- return [L, rle_meta, rle_len];
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- }
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- function DecodeRLE(buf, L, rle_meta, len) {
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- const src = new iostream_ts_1.default(buf);
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- const out = new Uint8Array(len);
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- // Expand up buf+meta to out; i = buf index, j = out index
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- let j = 0;
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- for (let i = 0; j < len; i++) {
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- const sym = buf[i];
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- if (L[sym]) {
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- const run = rle_meta.ReadUint7();
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- for (let r = 0; r <= run; r++) {
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- out[j++] = sym;
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- }
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- }
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- else {
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- out[j++] = sym;
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- }
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- }
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- return out;
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- }
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- // Pack meta data is the number and value of distinct symbols plus
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- // the length of the packed byte stream.
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- function DecodePackMeta(src) {
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- const nsym = src.ReadByte();
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- const P = new Array(nsym);
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- for (let i = 0; i < nsym; i++) {
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- P[i] = src.ReadByte();
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- }
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- const len = src.ReadUint7();
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- return [P, nsym, len];
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- }
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- // Extract bits from src producing output of length len.
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- // Nsym is number of distinct symbols used.
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- function DecodePack(data, P, nsym, len) {
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- const out = new Uint8Array(len);
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- let j = 0;
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- // Constant value
141
- if (nsym <= 1) {
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- for (var i = 0; i < len; i++) {
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- out[i] = P[0];
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- }
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- }
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- // 1 bit per value
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- else if (nsym <= 2) {
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- for (i = 0; i < len; i++) {
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- if (i % 8 == 0) {
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- var v = data[j++];
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- }
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- out[i] = P[v & 1];
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- v >>= 1;
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- }
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- }
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- // 2 bits per value
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- else if (nsym <= 4) {
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- for (i = 0; i < len; i++) {
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- if (i % 4 == 0) {
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- var v = data[j++];
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- }
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- out[i] = P[v & 3];
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- v >>= 2;
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- }
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- }
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- // 4 bits per value
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- else if (nsym <= 16) {
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- for (i = 0; i < len; i++) {
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- if (i % 2 == 0) {
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- var v = data[j++];
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- }
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- out[i] = P[v & 15];
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- v >>= 4;
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- }
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- }
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- return out;
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- }
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- function RansDecodeStripe(src, len) {
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- const N = src.ReadByte();
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- // Retrieve lengths
181
- const clen = new Array(N);
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- const ulen = new Array(N);
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- for (var j = 0; j < N; j++) {
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- clen[j] = src.ReadUint7();
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- }
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- // Decode streams
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- const T = new Array(N);
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- for (var j = 0; j < N; j++) {
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- ulen[j] = Math.floor(len / N) + (len % N > j);
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- T[j] = RansDecodeStream(src, ulen[j]);
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- }
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- // Transpose
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- const out = new Uint8Array(len);
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- for (var j = 0; j < N; j++) {
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- for (let i = 0; i < ulen[j]; i++) {
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- out[i * N + j] = T[j][i];
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- }
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- }
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- return out;
200
- }
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- // ----------------------------------------------------------------------
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- // Main rANS entry function: decodes a compressed src and
203
- // returns the uncompressed buffer.
204
- function decode(src) {
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- const stream = new iostream_ts_1.default(src);
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- return RansDecodeStream(stream, 0);
207
- }
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- function RansDecodeStream(stream, n_out) {
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- const format = stream.ReadByte();
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- const order = format & 1;
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- const x32 = format & 4;
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- const stripe = format & 8;
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- const nosz = format & 16;
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- const cat = format & 32;
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- const rle = format & 64;
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- const pack = format & 128;
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- const Nway = x32 ? 32 : 4;
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- if (!nosz) {
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- n_out = stream.ReadUint7();
220
- }
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- // N-way interleaving
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- if (stripe) {
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- return RansDecodeStripe(stream, n_out);
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- }
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- // Bit packing
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- if (pack) {
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- var pack_len = n_out;
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- var [P, nsym, n_out] = DecodePackMeta(stream);
229
- }
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- // Run length encoding
231
- if (rle) {
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- var rle_len = n_out;
233
- var [L, rle_meta, n_out] = DecodeRLEMeta(stream, Nway);
234
- }
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- // Uncompress data (all, packed or run literals)
236
- if (cat) {
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- var buf = stream.ReadData(n_out);
238
- }
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- else if (order == 0) {
240
- var buf = RansDecode0(stream, n_out, Nway);
241
- }
242
- else {
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- var buf = RansDecode1(stream, n_out, Nway);
244
- }
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- // Apply expansion transforms
246
- if (rle) {
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- buf = DecodeRLE(buf, L, rle_meta, rle_len);
248
- }
249
- if (pack) {
250
- buf = DecodePack(buf, P, nsym, pack_len);
251
- }
252
- return buf;
253
- }
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- // ----------------------------------------------------------------------
255
- // Order-0 decoder
256
- function ReadAlphabet(src) {
257
- const A = new Array(256);
258
- for (let i = 0; i < 256; i++) {
259
- A[i] = 0;
260
- }
261
- let rle = 0;
262
- let sym = src.ReadByte();
263
- let last_sym = sym;
264
- do {
265
- A[sym] = 1;
266
- if (rle > 0) {
267
- rle--;
268
- sym++;
269
- }
270
- else {
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- sym = src.ReadByte();
272
- if (sym == last_sym + 1) {
273
- rle = src.ReadByte();
274
- }
275
- }
276
- last_sym = sym;
277
- } while (sym != 0);
278
- return A;
279
- }
280
- // Decode a single table of order-0 frequencies,
281
- // filling out the F and C arrays.
282
- function ReadFrequencies0(src, F, C) {
283
- // Initialise; not in the specification - implicit?
284
- for (var i = 0; i < 256; i++) {
285
- F[i] = 0;
286
- }
287
- // Fetch alphabet
288
- const A = ReadAlphabet(src);
289
- // Fetch frequencies for the symbols listed in our alphabet
290
- for (var i = 0; i < 256; i++) {
291
- if (A[i] > 0) {
292
- F[i] = src.ReadUint7();
293
- }
294
- }
295
- NormaliseFrequencies0_Shift(F, 12);
296
- // Compute C[] from F[]
297
- C[0] = 0;
298
- for (var i = 0; i <= 255; i++) {
299
- C[i + 1] = C[i] + F[i];
300
- }
301
- }
302
- function RansDecode0(src, nbytes, N) {
303
- // Decode frequencies
304
- const F = new Array(256);
305
- const C = new Array(256);
306
- ReadFrequencies0(src, F, C);
307
- // Fast lookup to avoid slow RansGetSymbolFromFreq
308
- const C2S = RansBuildC2S(C, 12);
309
- // Initialise rANS state
310
- const R = new Array(N);
311
- for (var i = 0; i < N; i++) {
312
- R[i] = src.ReadUint32();
313
- }
314
- // Main decode loop
315
- const output = new Uint8Array(nbytes);
316
- for (var i = 0; i < nbytes; i++) {
317
- const ix = i & (N - 1); // equiv to i%N as N is power of 2
318
- const f = RansGetCumulativeFreq(R[ix], 12);
319
- const s = C2S[f]; // Equiv to RansGetSymbolFromFreq(C, f);
320
- output[i] = s;
321
- R[ix] = RansAdvanceStep(R[ix], C[s], F[s], 12);
322
- R[ix] = RansRenorm(src, R[ix]);
323
- }
324
- // Main decode loop
325
- return output;
326
- }
327
- function NormaliseFrequencies0_Shift(F, bits) {
328
- // Compute total and number of bits to shift by
329
- let tot = 0;
330
- for (var i = 0; i < 256; i++) {
331
- tot += F[i];
332
- }
333
- if (tot == 0 || tot == 1 << bits) {
334
- return;
335
- }
336
- let shift = 0;
337
- while (tot < 1 << bits) {
338
- tot *= 2;
339
- shift++;
340
- }
341
- // Scale total of frequencies to (1<<bits)
342
- for (var i = 0; i < 256; i++) {
343
- F[i] <<= shift;
344
- }
345
- }
346
- // ----------------------------------------------------------------------
347
- // Order-1 decoder
348
- // Decode a table of order-1 frequencies,
349
- // filling out the F and C arrays.
350
- function ReadFrequencies1(src, F, C, shift) {
351
- // Initialise; not in the specification - implicit?
352
- for (var i = 0; i < 256; i++) {
353
- F[i] = new Array(256);
354
- C[i] = new Array(256);
355
- for (var j = 0; j < 256; j++) {
356
- F[i][j] = 0;
357
- }
358
- }
359
- // Fetch alphabet
360
- const A = ReadAlphabet(src);
361
- // Read F[]
362
- for (var i = 0; i < 256; i++) {
363
- if (!A[i]) {
364
- continue;
365
- }
366
- let run = 0;
367
- for (var j = 0; j < 256; j++) {
368
- if (!A[j]) {
369
- continue;
370
- }
371
- if (run > 0) {
372
- run--;
373
- }
374
- else {
375
- F[i][j] = src.ReadUint7();
376
- if (F[i][j] == 0) {
377
- run = src.ReadByte();
378
- }
379
- }
380
- }
381
- NormaliseFrequencies0_Shift(F[i], shift);
382
- // Compute C[] from F[]
383
- C[i][0] = 0;
384
- for (var j = 0; j < 256; j++) {
385
- C[i][j + 1] = C[i][j] + F[i][j];
386
- }
387
- }
388
- }
389
- function RansDecode1(src, nbytes, N) {
390
- // FIXME: this bit is missing from the RansDecode0 pseudocode.
391
- var comp = src.ReadByte();
392
- const shift = comp >> 4;
393
- var freq_src = src;
394
- if (comp & 1) {
395
- const ulen = src.ReadUint7();
396
- const clen = src.ReadUint7();
397
- var comp = new iostream_ts_1.default(src.ReadData(clen));
398
- var freq_src = new iostream_ts_1.default(RansDecode0(comp, ulen, 4));
399
- }
400
- // Decode frequencies
401
- const F = new Array(256);
402
- const C = new Array(256);
403
- ReadFrequencies1(freq_src, F, C, shift);
404
- // Fast lookup to avoid slow RansGetSymbolFromFreq
405
- const C2S = new Array(256);
406
- for (var i = 0; i < 256; i++ // Could do only for symbols in alphabet?
407
- ) {
408
- C2S[i] = RansBuildC2S(C[i], shift);
409
- }
410
- // Initialise rANS state
411
- const R = new Array(N);
412
- const L = new Array(N);
413
- for (var j = 0; j < N; j++) {
414
- R[j] = src.ReadUint32();
415
- L[j] = 0;
416
- }
417
- // Main decode loop
418
- const output = new Uint8Array(nbytes);
419
- const nbytesx = Math.floor(nbytes / N);
420
- for (var i = 0; i < nbytesx; i++) {
421
- for (var j = 0; j < N; j++) {
422
- var f = RansGetCumulativeFreq(R[j], shift);
423
- // var s = RansGetSymbolFromFreq(C[L[j]], f);
424
- var s = C2S[L[j]][f]; // Precomputed version of above
425
- output[i + j * nbytesx] = s;
426
- R[j] = RansAdvanceStep(R[j], C[L[j]][s], F[L[j]][s], shift);
427
- R[j] = RansRenorm(src, R[j]);
428
- L[j] = s;
429
- }
430
- }
431
- // Now deal with the remainder if buffer size is not a multiple of N,
432
- // using the last rANS state exclusively. (It'd have been nice to have
433
- // designed this to just act as if we kept going with a bail out.)
434
- i = N * i;
435
- while (i < nbytes) {
436
- var f = RansGetCumulativeFreq(R[N - 1], shift);
437
- var s = RansGetSymbolFromFreq(C[L[N - 1]], f);
438
- output[i++] = s;
439
- R[N - 1] = RansAdvanceStep(R[N - 1], C[L[N - 1]][s], F[L[N - 1]][s], shift);
440
- R[N - 1] = RansRenorm(src, R[N - 1]);
441
- L[N - 1] = s;
442
- }
443
- return output;
444
- }
445
- //# sourceMappingURL=rans4x16.js.map
@@ -1 +0,0 @@
1
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@@ -1 +0,0 @@
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- export declare function decode(src: any, len: any, separator: any): string;
@@ -1,206 +0,0 @@
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- "use strict";
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- /* eslint-disable no-var */
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- // @ts-nocheck
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- var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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- if (k2 === undefined) k2 = k;
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- var desc = Object.getOwnPropertyDescriptor(m, k);
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- if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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- desc = { enumerable: true, get: function() { return m[k]; } };
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- }
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- Object.defineProperty(o, k2, desc);
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- }) : (function(o, m, k, k2) {
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- if (k2 === undefined) k2 = k;
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- o[k2] = m[k];
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- }));
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- var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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- Object.defineProperty(o, "default", { enumerable: true, value: v });
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- }) : function(o, v) {
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- o["default"] = v;
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- });
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- var __importStar = (this && this.__importStar) || (function () {
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- var ownKeys = function(o) {
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- ownKeys = Object.getOwnPropertyNames || function (o) {
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- var ar = [];
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- for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
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- return ar;
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- };
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- return ownKeys(o);
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- };
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- return function (mod) {
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- if (mod && mod.__esModule) return mod;
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- var result = {};
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- if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
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- __setModuleDefault(result, mod);
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- return result;
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- };
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- })();
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- var __importDefault = (this && this.__importDefault) || function (mod) {
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- return (mod && mod.__esModule) ? mod : { "default": mod };
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- };
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- Object.defineProperty(exports, "__esModule", { value: true });
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- exports.decode = decode;
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- /*
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- * Copyright (c) 2019 Genome Research Ltd.
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- * Author(s): James Bonfield
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- *
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- * Redistribution and use in source and binary forms, with or without
47
- * modification, are permitted provided that the following conditions are met:
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- *
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- * 1. Redistributions of source code must retain the above copyright notice,
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- * this list of conditions and the following disclaimer.
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- *
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- * 2. Redistributions in binary form must reproduce the above
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- * copyright notice, this list of conditions and the following
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- * disclaimer in the documentation and/or other materials provided
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- * with the distribution.
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- *
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- * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
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- * Institute nor the names of its contributors may be used to endorse
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- * or promote products derived from this software without specific
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- * prior written permission.
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- *
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- * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
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- * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
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- * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
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- * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
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- * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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- * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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- * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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- * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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- * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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- */
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- // Name tokeniser
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- //
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- // This is a reference implementation designed to match the
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- // written specification as closely as possible. It is *NOT*
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- // an efficient implementation, but see comments below.
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- const util_ts_1 = require("../util.js");
80
- const arith_gen_ts_1 = __importDefault(require("./arith_gen.js"));
81
- const iostream_ts_1 = __importDefault(require("./iostream.js"));
82
- const rans = __importStar(require("./rans4x16.js"));
83
- const arith = new arith_gen_ts_1.default();
84
- const TOK_TYPE = 0;
85
- const TOK_STRING = 1;
86
- const TOK_CHAR = 2;
87
- const TOK_DIGITS0 = 3;
88
- const TOK_DZLEN = 4;
89
- const TOK_DUP = 5;
90
- const TOK_DIFF = 6;
91
- const TOK_DIGITS = 7;
92
- const TOK_DELTA = 8;
93
- const TOK_DELTA0 = 9;
94
- const TOK_MATCH = 10;
95
- const TOK_NOP = 11;
96
- const TOK_END = 12;
97
- // ----------------------------------------------------------------------
98
- // Token byte streams
99
- function DecodeTokenByteStreams(src, in_size, use_arith, nnames) {
100
- let t = -1;
101
- const B = new Array(256);
102
- while (!src.EOF()) {
103
- const ttype = src.ReadByte();
104
- const tok_new = ttype & 128;
105
- const tok_dup = ttype & 64;
106
- const type = ttype & 63;
107
- if (tok_new) {
108
- t++;
109
- B[t] = new Array(13);
110
- }
111
- if (type != TOK_TYPE && tok_new) {
112
- const M = new Array(nnames - 1).fill(TOK_MATCH);
113
- B[t][TOK_TYPE] = new iostream_ts_1.default((0, util_ts_1.concatUint8Array)([new Uint8Array(type), M]));
114
- }
115
- if (tok_dup) {
116
- const dup_pos = src.ReadByte();
117
- const dup_type = src.ReadByte();
118
- B[t][type] = new iostream_ts_1.default(B[dup_pos][dup_type].buf);
119
- }
120
- else {
121
- const clen = src.ReadUint7();
122
- const data = src.ReadData(clen);
123
- B[t][type] = use_arith ? arith.decode(data) : rans.decode(data);
124
- B[t][type] = new iostream_ts_1.default(B[t][type]);
125
- }
126
- }
127
- return B;
128
- }
129
- // ----------------------------------------------------------------------
130
- // Token decode
131
- function LeftPadNumber(val, len) {
132
- let str = val + '';
133
- while (str.length < len) {
134
- str = '0' + str;
135
- }
136
- return str;
137
- }
138
- function DecodeSingleName(B, N, T, n) {
139
- let type = B[0][TOK_TYPE].ReadByte();
140
- const dist = B[0][type].ReadUint32();
141
- const m = n - dist;
142
- if (type == TOK_DUP) {
143
- N[n] = N[m];
144
- T[n] = T[m];
145
- return N[n];
146
- }
147
- let t = 1;
148
- N[n] = '';
149
- T[n] = new Array(256);
150
- do {
151
- type = B[t][TOK_TYPE].ReadByte();
152
- switch (type) {
153
- case TOK_CHAR:
154
- T[n][t] = B[t][TOK_CHAR].ReadChar();
155
- break;
156
- case TOK_STRING:
157
- T[n][t] = B[t][TOK_STRING].ReadString();
158
- break;
159
- case TOK_DIGITS:
160
- T[n][t] = B[t][TOK_DIGITS].ReadUint32();
161
- break;
162
- case TOK_DIGITS0:
163
- var d = B[t][TOK_DIGITS0].ReadUint32();
164
- var l = B[t][TOK_DZLEN].ReadByte();
165
- T[n][t] = LeftPadNumber(d, l);
166
- break;
167
- case TOK_DELTA:
168
- T[n][t] = (T[m][t] >> 0) + B[t][TOK_DELTA].ReadByte();
169
- break;
170
- case TOK_DELTA0:
171
- var d = (T[m][t] >> 0) + B[t][TOK_DELTA0].ReadByte();
172
- var l = T[m][t].length;
173
- T[n][t] = LeftPadNumber(d, l);
174
- break;
175
- case TOK_MATCH:
176
- T[n][t] = T[m][t];
177
- break;
178
- default:
179
- T[n][t] = '';
180
- break;
181
- }
182
- N[n] += T[n][t++];
183
- } while (type != TOK_END);
184
- return N[n];
185
- }
186
- // ----------------------------------------------------------------------
187
- // Main tokeniser decode entry function: decodes a compressed src and
188
- // returns the uncompressed buffer.
189
- function decode(src, len, separator) {
190
- var src = new iostream_ts_1.default(src);
191
- const ulen = src.ReadUint32();
192
- const nnames = src.ReadUint32();
193
- const use_arith = src.ReadByte();
194
- const B = DecodeTokenByteStreams(src, len, use_arith, nnames);
195
- const N = new Array(nnames);
196
- const T = new Array(nnames);
197
- let str = '';
198
- if (separator === undefined) {
199
- separator = '\n';
200
- }
201
- for (let i = 0; i < nnames; i++) {
202
- str += DecodeSingleName(B, N, T, i) + separator;
203
- }
204
- return str;
205
- }
206
- //# sourceMappingURL=tok3.js.map