@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 +0,0 @@
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@@ -1 +0,0 @@
1
- export declare function decode(src: Uint8Array, q_lens: any): Uint8Array<ArrayBuffer> | undefined;
@@ -1,340 +0,0 @@
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- /* eslint-disable no-var */
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- // @ts-nocheck
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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
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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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- import RangeCoder from "./arith_sh.js";
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- import ByteModel from "./byte_model.js";
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- import IOStream from "./iostream.js";
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- // ----------------------------------------------------------------------
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- // Main arithmetic entry function: decodes a compressed src and
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- // returns the uncompressed buffer.
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- function read_array(src, tab, size) {
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- let j = 0; // array value
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- let z = 0; // array index: tab[j]
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- let last = -1;
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- // Remove first level of run-length encoding
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- const R = new Array(1024); // runs
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- while (z < size) {
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- const run = src.ReadByte();
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- R[j++] = run;
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- z += run;
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- if (run == last) {
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- let copy = src.ReadByte();
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- z += run * copy;
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- while (copy--) {
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- R[j++] = run;
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- }
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- }
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- last = run;
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- }
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- // Now expand runs in R to tab, noting 255 is max run
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- let i = 0;
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- j = 0;
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- z = 0;
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- while (z < size) {
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- let run_len = 0;
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- do {
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- var part = R[j++];
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- run_len += part;
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- } while (part == 255);
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- while (run_len--) {
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- tab[z++] = i;
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- }
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- i++;
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- }
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- }
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- const QMAX = 256;
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- const FLAG_DEDUP = 2;
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- const FLAG_FLEN = 4;
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- const FLAG_SEL = 8; // whether selector is used in context
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- const FLAG_QMAP = 16;
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- const FLAG_PTAB = 32;
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- const FLAG_DTAB = 64;
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- const FLAG_QTAB = 128;
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- const GFLAG_MULTI_PARAM = 1;
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- const GFLAG_HAVE_STAB = 2;
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- const GFLAG_DO_REV = 4;
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- // Compute a new context from our current state and qual q
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- function fqz_update_ctx(params, state, q) {
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- let last = params.context;
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- state.qctx = (state.qctx << params.qshift) + params.qtab[q]; // >>> 0
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- last += (state.qctx & ((1 << params.qbits) - 1)) << params.qloc; // >>> 0
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- if (params.do_pos) {
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- last += params.ptab[Math.min(state.p, 1023)] << params.ploc;
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- }
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- if (params.do_delta) {
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- last += params.dtab[Math.min(state.delta, 255)] << params.dloc;
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- // Is it better to use q here or qtab[q]?
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- // If qtab[q] we can map eg [a-z0-9A-Z]->0 ,->1 and have
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- // delta being a token number count into comma separated lists?
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- state.delta += state.prevq != q ? 1 : 0;
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- state.prevq = q;
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- }
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- if (params.do_sel) {
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- last += state.s << params.sloc;
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- }
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- state.p--;
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- return last & 0xffff;
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- }
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- function decode_fqz_single_param(src) {
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- const p = {}; // params
111
- // Load FQZ parameters
112
- p.context = src.ReadUint16();
113
- p.pflags = src.ReadByte();
114
- p.do_dedup = p.pflags & FLAG_DEDUP;
115
- p.fixed_len = p.pflags & FLAG_FLEN;
116
- p.do_sel = p.pflags & FLAG_SEL;
117
- p.do_qmap = p.pflags & FLAG_QMAP;
118
- p.do_pos = p.pflags & FLAG_PTAB;
119
- p.do_delta = p.pflags & FLAG_DTAB;
120
- p.do_qtab = p.pflags & FLAG_QTAB;
121
- p.max_sym = src.ReadByte();
122
- let x = src.ReadByte();
123
- p.qbits = x >> 4;
124
- p.qshift = x & 15;
125
- x = src.ReadByte();
126
- p.qloc = x >> 4;
127
- p.sloc = x & 15;
128
- x = src.ReadByte();
129
- p.ploc = x >> 4;
130
- p.dloc = x & 15;
131
- // Qual map, eg to "unbin" Illumina qualities
132
- p.qmap = new Array(256);
133
- if (p.pflags & FLAG_QMAP) {
134
- for (var i = 0; i < p.max_sym; i++) {
135
- p.qmap[i] = src.ReadByte();
136
- }
137
- }
138
- else {
139
- // Useful optimisation to speed up main loop
140
- for (var i = 0; i < 256; i++) {
141
- p.qmap[i] = i;
142
- } // NOP
143
- }
144
- // Read tables
145
- p.qtab = new Array(1024);
146
- if (p.qbits > 0 && p.pflags & FLAG_QTAB) {
147
- read_array(src, p.qtab, 256);
148
- }
149
- else {
150
- // Useful optimisation to speed up main loop
151
- for (var i = 0; i < 256; i++) {
152
- p.qtab[i] = i;
153
- } // NOP
154
- }
155
- p.ptab = new Array(1024);
156
- if (p.pflags & FLAG_PTAB) {
157
- read_array(src, p.ptab, 1024);
158
- }
159
- p.dtab = new Array(256);
160
- if (p.pflags & FLAG_DTAB) {
161
- read_array(src, p.dtab, 256);
162
- }
163
- return p;
164
- }
165
- function decode_fqz_params(src) {
166
- const gparams = {
167
- max_sym: 0,
168
- };
169
- // Check fqz format version
170
- const vers = src.ReadByte();
171
- if (vers != 5) {
172
- console.error('Invalid FQZComp version number');
173
- return;
174
- }
175
- const gflags = src.ReadByte();
176
- const nparam = gflags & GFLAG_MULTI_PARAM ? src.ReadByte() : 1;
177
- let max_sel = gflags.nparam > 1 ? gflags.nparam - 1 : 0; // Note max_sel, not num_sel
178
- const stab = new Array(256);
179
- if (gflags & GFLAG_HAVE_STAB) {
180
- max_sel = src.ReadByte();
181
- read_array(src, stab, 256);
182
- }
183
- else {
184
- for (var i = 0; i < nparam; i++) {
185
- stab[i] = i;
186
- }
187
- for (; i < 256; i++) {
188
- stab[i] = nparam - 1;
189
- }
190
- }
191
- gparams.do_rev = gflags & GFLAG_DO_REV;
192
- gparams.stab = stab;
193
- gparams.max_sel = max_sel;
194
- gparams.params = new Array(gparams.nparam);
195
- for (let p = 0; p < nparam; p++) {
196
- gparams.params[p] = decode_fqz_single_param(src);
197
- if (gparams.max_sym < gparams.params[p].max_sym) {
198
- gparams.max_sym = gparams.params[p].max_sym;
199
- }
200
- }
201
- return gparams;
202
- }
203
- function fqz_create_models(gparams) {
204
- const model = {};
205
- model.qual = new Array(1 << 16);
206
- for (var i = 0; i < 1 << 16; i++) {
207
- model.qual[i] = new ByteModel(gparams.max_sym + 1);
208
- } // +1 as max value not num. values
209
- model.len = new Array(4);
210
- for (var i = 0; i < 4; i++) {
211
- model.len[i] = new ByteModel(256);
212
- }
213
- model.rev = new ByteModel(2);
214
- model.dup = new ByteModel(2);
215
- if (gparams.max_sel > 0) {
216
- model.sel = new ByteModel(gparams.max_sel + 1);
217
- } // +1 as max value not num. values
218
- return model;
219
- }
220
- // Initialise a new record, updating state.
221
- // Returns 1 if dup, otherwise 0
222
- function decode_fqz_new_record(src, rc, gparams, model, state, rev) {
223
- // Parameter selector
224
- state.s = gparams.max_sel > 0 ? model.sel.ModelDecode(src, rc) : 0;
225
- state.x = gparams.stab[state.s];
226
- const params = gparams.params[state.x];
227
- // Reset contexts at the start of each new record
228
- if (params.fixed_len >= 0) {
229
- // Not fixed or fixed but first record
230
- var len = model.len[0].ModelDecode(src, rc);
231
- len |= model.len[1].ModelDecode(src, rc) << 8;
232
- len |= model.len[2].ModelDecode(src, rc) << 16;
233
- len |= model.len[3].ModelDecode(src, rc) << 24;
234
- if (params.fixed_len > 0) {
235
- params.fixed_len = -len;
236
- }
237
- }
238
- else {
239
- len = -params.fixed_len;
240
- }
241
- state.len = len;
242
- if (gparams.do_rev) {
243
- rev[state.rec] = model.rev.ModelDecode(src, rc);
244
- }
245
- state.is_dup = 0;
246
- if (params.pflags & FLAG_DEDUP) {
247
- if (model.dup.ModelDecode(src, rc)) {
248
- state.is_dup = 1;
249
- }
250
- }
251
- state.p = len; // number of remaining bytes in this record
252
- state.delta = 0;
253
- state.qctx = 0;
254
- state.prevq = 0;
255
- state.rec++;
256
- }
257
- function decode_fqz(src, q_lens) {
258
- // Decode parameter block
259
- const n_out = src.ReadUint7();
260
- const gparams = decode_fqz_params(src);
261
- if (!gparams) {
262
- return;
263
- }
264
- var params = gparams.params;
265
- const rev = new Array(q_lens.length);
266
- // Create initial models
267
- const model = fqz_create_models(gparams);
268
- // Create our entropy encoder and output buffers
269
- const rc = new RangeCoder(src);
270
- rc.RangeStartDecode(src);
271
- const output = new Uint8Array(n_out);
272
- // Internal FQZ state
273
- const state = {
274
- qctx: 0, // Qual-only sub-context
275
- prevq: 0, // Previous quality value
276
- delta: 0, // Running delta (q vs prevq)
277
- p: 0, // Number of bases left in current record
278
- s: 0, // Current parameter selector value (0 if unused)
279
- x: 0, // "stab" tabulated copy of s
280
- len: 0, // Length of current string
281
- is_dup: 0, // This string is a duplicate of last
282
- rec: 0, // Record number
283
- };
284
- // The main decode loop itself
285
- let i = 0; // position in output buffer
286
- while (i < n_out) {
287
- if (state.p == 0) {
288
- decode_fqz_new_record(src, rc, gparams, model, state, rev);
289
- if (state.is_dup > 0) {
290
- if (model.dup.ModelDecode(src, rc)) {
291
- // Duplicate of last line
292
- for (let x = 0; x < len; x++) {
293
- output[i + x] = output[i + x - state.len];
294
- }
295
- i += state.len;
296
- state.p = 0;
297
- continue;
298
- }
299
- }
300
- q_lens.push(state.len);
301
- var params = gparams.params[state.x];
302
- var last = params.context;
303
- }
304
- // Decode the current quality (possibly mapped via qmap)
305
- const Q = model.qual[last].ModelDecode(src, rc);
306
- // if (params.do_qmap)
307
- // output[i++] = params.qmap[Q];
308
- // else
309
- // output[i++] = Q
310
- output[i++] = params.qmap[Q]; // optimised version of above
311
- last = fqz_update_ctx(params, state, Q);
312
- }
313
- if (gparams.do_rev) {
314
- reverse_qualities(output, n_out, rev, q_lens);
315
- }
316
- return output;
317
- }
318
- function reverse_qualities(qual, qual_len, rev, len) {
319
- let rec = 0;
320
- let i = 0;
321
- while (i < qual_len) {
322
- if (rev[rec]) {
323
- let j = 0;
324
- let k = len[rec] - 1;
325
- while (j < k) {
326
- const tmp = qual[i + j];
327
- qual[i + j] = qual[i + k];
328
- qual[i + k] = tmp;
329
- j++;
330
- k--;
331
- }
332
- }
333
- i += len[rec++];
334
- }
335
- }
336
- export function decode(src, q_lens) {
337
- const stream = new IOStream(src);
338
- return decode_fqz(stream, q_lens);
339
- }
340
- //# sourceMappingURL=fqzcomp.js.map
@@ -1 +0,0 @@
1
- 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@@ -1,16 +0,0 @@
1
- export default class IOStream {
2
- buf: Uint8Array;
3
- length: number;
4
- pos: number;
5
- dataView: DataView;
6
- constructor(buf: Uint8Array, start_pos?: number, size?: number);
7
- EOF(): boolean;
8
- ReadData(len: number): Uint8Array<ArrayBuffer>;
9
- ReadByte(): number;
10
- ReadChar(): string;
11
- ReadUint16(): number;
12
- ReadUint32(): number;
13
- ReadString(): string;
14
- ReadUint7(): number;
15
- ReadITF8(): number;
16
- }
@@ -1,145 +0,0 @@
1
- // @ts-nocheck
2
- /*
3
- * Copyright (c) 2019 Genome Research Ltd.
4
- * Author(s): James Bonfield
5
- *
6
- * Redistribution and use in source and binary forms, with or without
7
- * modification, are permitted provided that the following conditions are met:
8
- *
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- * 1. Redistributions of source code must retain the above copyright notice,
10
- * this list of conditions and the following disclaimer.
11
- *
12
- * 2. Redistributions in binary form must reproduce the above
13
- * copyright notice, this list of conditions and the following
14
- * disclaimer in the documentation and/or other materials provided
15
- * with the distribution.
16
- *
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- * 3. Neither the names Genome Research Ltd and Wellcome Trust Sanger
18
- * Institute nor the names of its contributors may be used to endorse
19
- * or promote products derived from this software without specific
20
- * prior written permission.
21
- *
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- * THIS SOFTWARE IS PROVIDED BY GENOME RESEARCH LTD AND CONTRIBUTORS "AS
23
- * IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
24
- * TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
25
- * PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL GENOME RESEARCH
26
- * LTD OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
27
- * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
28
- * 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
30
- * 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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- // Turn a buffer into a fake stream with get / put commands.
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- // This enables up to closely match the published pseudocode.
36
- export default class IOStream {
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- constructor(buf, start_pos = 0, size = 0) {
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- if (size !== 0) {
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- this.buf = new Uint8Array(size);
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- this.length = size;
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- }
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- else {
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- this.buf = buf;
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- this.length = buf.length;
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- }
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- this.dataView = new DataView(this.buf.buffer);
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- this.pos = start_pos;
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- }
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- // ----------
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- // Reading
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- EOF() {
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- return this.pos >= this.length;
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- }
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- ReadData(len) {
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- const A = this.buf.slice(this.pos, this.pos + len);
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- this.pos += len;
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- return A;
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- }
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- ReadByte() {
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- const b = this.buf[this.pos];
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- this.pos++;
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- return b;
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- }
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- ReadChar() {
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- const b = this.buf[this.pos];
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- this.pos++;
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- return String.fromCharCode(b);
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- }
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- ReadUint16() {
70
- let i = this.ReadByte();
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- i |= this.ReadByte() << 8;
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- return i;
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- }
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- ReadUint32() {
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- const i = this.dataView.getInt32(this.pos, true);
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- this.pos += 4;
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- return i;
78
- }
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- // nul terminated string
80
- ReadString() {
81
- let s = '';
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- let b;
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- do {
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- b = this.buf[this.pos++];
85
- if (b) {
86
- s += String.fromCharCode(b);
87
- }
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- } while (b);
89
- return s;
90
- }
91
- ReadUint7() {
92
- // Variable sized unsigned integers
93
- let i = 0;
94
- let c;
95
- do {
96
- c = this.ReadByte();
97
- i = (i << 7) | (c & 0x7f);
98
- } while (c & 0x80);
99
- return i;
100
- }
101
- ReadITF8() {
102
- let i = this.buf[this.pos];
103
- this.pos++;
104
- // process.stderr.write("i="+i+"\n");
105
- if (i >= 0xf0) {
106
- // 1111xxxx => +4 bytes
107
- i = (i & 0x0f) << 28;
108
- i +=
109
- (this.buf[this.pos + 0] << 20) +
110
- (this.buf[this.pos + 1] << 12) +
111
- (this.buf[this.pos + 2] << 4) +
112
- (this.buf[this.pos + 3] >> 4);
113
- this.pos += 4;
114
- // process.stderr.write(" 4i="+i+"\n");
115
- }
116
- else if (i >= 0xe0) {
117
- // 1110xxxx => +3 bytes
118
- i = (i & 0x0f) << 24;
119
- i +=
120
- (this.buf[this.pos + 0] << 16) +
121
- (this.buf[this.pos + 1] << 8) +
122
- (this.buf[this.pos + 2] << 0);
123
- this.pos += 3;
124
- // process.stderr.write(" 3i="+i+"\n");
125
- }
126
- else if (i >= 0xc0) {
127
- // 110xxxxx => +2 bytes
128
- i = (i & 0x1f) << 16;
129
- i += (this.buf[this.pos + 0] << 8) + (this.buf[this.pos + 1] << 0);
130
- this.pos += 2;
131
- // process.stderr.write(" 2i="+i+"\n");
132
- }
133
- else if (i >= 0x80) {
134
- // 10xxxxxx => +1 bytes
135
- i = (i & 0x3f) << 8;
136
- i += this.buf[this.pos];
137
- this.pos++;
138
- }
139
- else {
140
- // 0xxxxxxx => +0 bytes
141
- }
142
- return i;
143
- }
144
- }
145
- //# sourceMappingURL=iostream.js.map
@@ -1 +0,0 @@
1
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@@ -1 +0,0 @@
1
- export declare function decode(src: any): Uint8Array<any>;