finishm 0.0.1

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Files changed (554) hide show
  1. checksums.yaml +7 -0
  2. data/.document +5 -0
  3. data/.gitmodules +3 -0
  4. data/.rspec +1 -0
  5. data/Gemfile +31 -0
  6. data/LICENSE.txt +20 -0
  7. data/README.md +59 -0
  8. data/Rakefile +51 -0
  9. data/VERSION +1 -0
  10. data/bin/assembly_visualiser +106 -0
  11. data/bin/check_primer_combinations.rb +73 -0
  12. data/bin/contig_joiner.rb +244 -0
  13. data/bin/contigs_against_assembly.rb +153 -0
  14. data/bin/finishm +143 -0
  15. data/bin/finishm_assembler +55 -0
  16. data/bin/finishm_gap_closer.rb +241 -0
  17. data/bin/kmer_abundance_file_tool.rb +49 -0
  18. data/bin/kmer_pattern_to_assembly.rb +377 -0
  19. data/bin/kmer_profile_finder.rb +92 -0
  20. data/bin/kmers_count_parse.d +52 -0
  21. data/bin/kmers_count_tabulate.d +123 -0
  22. data/bin/kmers_count_tabulate.rb +84 -0
  23. data/bin/pcr_result_parser.rb +108 -0
  24. data/bin/primer_finder.rb +119 -0
  25. data/bin/read_selection_by_kmer.d +174 -0
  26. data/bin/scaffold_by_pattern.rb +119 -0
  27. data/bin/scaffold_connection_possibilities_to_knowns.rb +193 -0
  28. data/bin/scaffold_end_coverages.rb +69 -0
  29. data/bin/trail_validator.rb +84 -0
  30. data/ext/mkrf_conf.rb +56 -0
  31. data/ext/src/Makefile +140 -0
  32. data/ext/src/src/allocArray.c +305 -0
  33. data/ext/src/src/allocArray.h +86 -0
  34. data/ext/src/src/autoOpen.c +107 -0
  35. data/ext/src/src/autoOpen.h +18 -0
  36. data/ext/src/src/binarySequences.c +813 -0
  37. data/ext/src/src/binarySequences.h +125 -0
  38. data/ext/src/src/concatenatedGraph.c +233 -0
  39. data/ext/src/src/concatenatedGraph.h +30 -0
  40. data/ext/src/src/concatenatedPreGraph.c +262 -0
  41. data/ext/src/src/concatenatedPreGraph.h +29 -0
  42. data/ext/src/src/correctedGraph.c +2643 -0
  43. data/ext/src/src/correctedGraph.h +32 -0
  44. data/ext/src/src/dfib.c +509 -0
  45. data/ext/src/src/dfib.h +69 -0
  46. data/ext/src/src/dfibHeap.c +89 -0
  47. data/ext/src/src/dfibHeap.h +39 -0
  48. data/ext/src/src/dfibpriv.h +105 -0
  49. data/ext/src/src/fib.c +628 -0
  50. data/ext/src/src/fib.h +78 -0
  51. data/ext/src/src/fibHeap.c +79 -0
  52. data/ext/src/src/fibHeap.h +41 -0
  53. data/ext/src/src/fibpriv.h +110 -0
  54. data/ext/src/src/globals.h +154 -0
  55. data/ext/src/src/graph.c +3932 -0
  56. data/ext/src/src/graph.h +233 -0
  57. data/ext/src/src/graphReConstruction.c +1472 -0
  58. data/ext/src/src/graphReConstruction.h +30 -0
  59. data/ext/src/src/graphStats.c +2167 -0
  60. data/ext/src/src/graphStats.h +72 -0
  61. data/ext/src/src/graphStructures.h +52 -0
  62. data/ext/src/src/kmer.c +652 -0
  63. data/ext/src/src/kmer.h +73 -0
  64. data/ext/src/src/kmerOccurenceTable.c +236 -0
  65. data/ext/src/src/kmerOccurenceTable.h +44 -0
  66. data/ext/src/src/kseq.h +223 -0
  67. data/ext/src/src/locallyCorrectedGraph.c +557 -0
  68. data/ext/src/src/locallyCorrectedGraph.h +40 -0
  69. data/ext/src/src/passageMarker.c +677 -0
  70. data/ext/src/src/passageMarker.h +137 -0
  71. data/ext/src/src/preGraph.c +1717 -0
  72. data/ext/src/src/preGraph.h +106 -0
  73. data/ext/src/src/preGraphConstruction.c +990 -0
  74. data/ext/src/src/preGraphConstruction.h +26 -0
  75. data/ext/src/src/probe_node_finder.c +84 -0
  76. data/ext/src/src/probe_node_finder.h +6 -0
  77. data/ext/src/src/readCoherentGraph.c +557 -0
  78. data/ext/src/src/readCoherentGraph.h +30 -0
  79. data/ext/src/src/readSet.c +1734 -0
  80. data/ext/src/src/readSet.h +67 -0
  81. data/ext/src/src/readToNode.c +218 -0
  82. data/ext/src/src/readToNode.h +35 -0
  83. data/ext/src/src/recycleBin.c +199 -0
  84. data/ext/src/src/recycleBin.h +58 -0
  85. data/ext/src/src/roadMap.c +342 -0
  86. data/ext/src/src/roadMap.h +65 -0
  87. data/ext/src/src/run.c +318 -0
  88. data/ext/src/src/run.h +52 -0
  89. data/ext/src/src/run2.c +744 -0
  90. data/ext/src/src/runReadToNode.c +29 -0
  91. data/ext/src/src/scaffold.c +1876 -0
  92. data/ext/src/src/scaffold.h +64 -0
  93. data/ext/src/src/shortReadPairs.c +1243 -0
  94. data/ext/src/src/shortReadPairs.h +32 -0
  95. data/ext/src/src/splay.c +259 -0
  96. data/ext/src/src/splay.h +43 -0
  97. data/ext/src/src/splayTable.c +1315 -0
  98. data/ext/src/src/splayTable.h +31 -0
  99. data/ext/src/src/tightString.c +362 -0
  100. data/ext/src/src/tightString.h +82 -0
  101. data/ext/src/src/utility.c +199 -0
  102. data/ext/src/src/utility.h +98 -0
  103. data/ext/src/third-party/zlib-1.2.3/ChangeLog +855 -0
  104. data/ext/src/third-party/zlib-1.2.3/FAQ +339 -0
  105. data/ext/src/third-party/zlib-1.2.3/INDEX +51 -0
  106. data/ext/src/third-party/zlib-1.2.3/Makefile +154 -0
  107. data/ext/src/third-party/zlib-1.2.3/Makefile.in +154 -0
  108. data/ext/src/third-party/zlib-1.2.3/README +125 -0
  109. data/ext/src/third-party/zlib-1.2.3/adler32.c +149 -0
  110. data/ext/src/third-party/zlib-1.2.3/adler32.o +0 -0
  111. data/ext/src/third-party/zlib-1.2.3/algorithm.txt +209 -0
  112. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.pup +66 -0
  113. data/ext/src/third-party/zlib-1.2.3/amiga/Makefile.sas +65 -0
  114. data/ext/src/third-party/zlib-1.2.3/as400/bndsrc +132 -0
  115. data/ext/src/third-party/zlib-1.2.3/as400/compile.clp +123 -0
  116. data/ext/src/third-party/zlib-1.2.3/as400/readme.txt +111 -0
  117. data/ext/src/third-party/zlib-1.2.3/as400/zlib.inc +331 -0
  118. data/ext/src/third-party/zlib-1.2.3/compress.c +79 -0
  119. data/ext/src/third-party/zlib-1.2.3/compress.o +0 -0
  120. data/ext/src/third-party/zlib-1.2.3/configure +459 -0
  121. data/ext/src/third-party/zlib-1.2.3/contrib/README.contrib +71 -0
  122. data/ext/src/third-party/zlib-1.2.3/contrib/ada/buffer_demo.adb +106 -0
  123. data/ext/src/third-party/zlib-1.2.3/contrib/ada/mtest.adb +156 -0
  124. data/ext/src/third-party/zlib-1.2.3/contrib/ada/read.adb +156 -0
  125. data/ext/src/third-party/zlib-1.2.3/contrib/ada/readme.txt +65 -0
  126. data/ext/src/third-party/zlib-1.2.3/contrib/ada/test.adb +463 -0
  127. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.adb +225 -0
  128. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-streams.ads +114 -0
  129. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.adb +141 -0
  130. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib-thin.ads +450 -0
  131. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.adb +701 -0
  132. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.ads +328 -0
  133. data/ext/src/third-party/zlib-1.2.3/contrib/ada/zlib.gpr +20 -0
  134. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/README.586 +43 -0
  135. data/ext/src/third-party/zlib-1.2.3/contrib/asm586/match.S +364 -0
  136. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/README.686 +34 -0
  137. data/ext/src/third-party/zlib-1.2.3/contrib/asm686/match.S +329 -0
  138. data/ext/src/third-party/zlib-1.2.3/contrib/blast/Makefile +8 -0
  139. data/ext/src/third-party/zlib-1.2.3/contrib/blast/README +4 -0
  140. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.c +444 -0
  141. data/ext/src/third-party/zlib-1.2.3/contrib/blast/blast.h +71 -0
  142. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.pk +0 -0
  143. data/ext/src/third-party/zlib-1.2.3/contrib/blast/test.txt +1 -0
  144. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLib.pas +557 -0
  145. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/ZLibConst.pas +11 -0
  146. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/readme.txt +76 -0
  147. data/ext/src/third-party/zlib-1.2.3/contrib/delphi/zlibd32.mak +93 -0
  148. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.build +33 -0
  149. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.chm +0 -0
  150. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib.sln +21 -0
  151. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/AssemblyInfo.cs +58 -0
  152. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/ChecksumImpl.cs +202 -0
  153. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CircularBuffer.cs +83 -0
  154. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/CodecBase.cs +198 -0
  155. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Deflater.cs +106 -0
  156. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.cs +288 -0
  157. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/DotZLib.csproj +141 -0
  158. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/GZipStream.cs +301 -0
  159. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/Inflater.cs +105 -0
  160. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/DotZLib/UnitTests.cs +274 -0
  161. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/LICENSE_1_0.txt +23 -0
  162. data/ext/src/third-party/zlib-1.2.3/contrib/dotzlib/readme.txt +58 -0
  163. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/README +1 -0
  164. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.c +608 -0
  165. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/infback9.h +37 -0
  166. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inffix9.h +107 -0
  167. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inflate9.h +47 -0
  168. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.c +323 -0
  169. data/ext/src/third-party/zlib-1.2.3/contrib/infback9/inftree9.h +55 -0
  170. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffas86.c +1157 -0
  171. data/ext/src/third-party/zlib-1.2.3/contrib/inflate86/inffast.S +1368 -0
  172. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/test.cpp +24 -0
  173. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.cpp +329 -0
  174. data/ext/src/third-party/zlib-1.2.3/contrib/iostream/zfstream.h +128 -0
  175. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream.h +307 -0
  176. data/ext/src/third-party/zlib-1.2.3/contrib/iostream2/zstream_test.cpp +25 -0
  177. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/README +35 -0
  178. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/TODO +17 -0
  179. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/test.cc +50 -0
  180. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.cc +479 -0
  181. data/ext/src/third-party/zlib-1.2.3/contrib/iostream3/zfstream.h +466 -0
  182. data/ext/src/third-party/zlib-1.2.3/contrib/masm686/match.asm +413 -0
  183. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/bld_ml64.bat +2 -0
  184. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.asm +513 -0
  185. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/gvmat64.obj +0 -0
  186. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffas8664.c +186 -0
  187. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.asm +392 -0
  188. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/inffasx64.obj +0 -0
  189. data/ext/src/third-party/zlib-1.2.3/contrib/masmx64/readme.txt +28 -0
  190. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/bld_ml32.bat +2 -0
  191. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.asm +972 -0
  192. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32.obj +0 -0
  193. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/gvmat32c.c +62 -0
  194. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.asm +1083 -0
  195. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/inffas32.obj +0 -0
  196. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/mkasm.bat +3 -0
  197. data/ext/src/third-party/zlib-1.2.3/contrib/masmx86/readme.txt +21 -0
  198. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ChangeLogUnzip +67 -0
  199. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/Makefile +25 -0
  200. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/crypt.h +132 -0
  201. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.c +177 -0
  202. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/ioapi.h +75 -0
  203. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.c +270 -0
  204. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/iowin32.h +21 -0
  205. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/miniunz.c +585 -0
  206. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/minizip.c +420 -0
  207. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.c +281 -0
  208. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/mztools.h +31 -0
  209. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.c +1598 -0
  210. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/unzip.h +354 -0
  211. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.c +1219 -0
  212. data/ext/src/third-party/zlib-1.2.3/contrib/minizip/zip.h +235 -0
  213. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/example.pas +599 -0
  214. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/readme.txt +76 -0
  215. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibd32.mak +93 -0
  216. data/ext/src/third-party/zlib-1.2.3/contrib/pascal/zlibpas.pas +236 -0
  217. data/ext/src/third-party/zlib-1.2.3/contrib/puff/Makefile +8 -0
  218. data/ext/src/third-party/zlib-1.2.3/contrib/puff/README +63 -0
  219. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.c +837 -0
  220. data/ext/src/third-party/zlib-1.2.3/contrib/puff/puff.h +31 -0
  221. data/ext/src/third-party/zlib-1.2.3/contrib/puff/zeros.raw +0 -0
  222. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.c +275 -0
  223. data/ext/src/third-party/zlib-1.2.3/contrib/testzlib/testzlib.txt +10 -0
  224. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile +14 -0
  225. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/Makefile.msc +17 -0
  226. data/ext/src/third-party/zlib-1.2.3/contrib/untgz/untgz.c +674 -0
  227. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/readme.txt +73 -0
  228. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/miniunz.vcproj +126 -0
  229. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/minizip.vcproj +126 -0
  230. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/testzlib.vcproj +126 -0
  231. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlib.rc +32 -0
  232. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibstat.vcproj +246 -0
  233. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc7/zlibvc.def +92 -0
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  236. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/miniunz.vcproj +566 -0
  237. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/minizip.vcproj +563 -0
  238. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlib.vcproj +948 -0
  239. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/testzlibdll.vcproj +567 -0
  240. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlib.rc +32 -0
  241. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibstat.vcproj +870 -0
  242. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.def +92 -0
  243. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.sln +144 -0
  244. data/ext/src/third-party/zlib-1.2.3/contrib/vstudio/vc8/zlibvc.vcproj +1219 -0
  245. data/ext/src/third-party/zlib-1.2.3/crc32.c +423 -0
  246. data/ext/src/third-party/zlib-1.2.3/crc32.h +441 -0
  247. data/ext/src/third-party/zlib-1.2.3/crc32.o +0 -0
  248. data/ext/src/third-party/zlib-1.2.3/deflate.c +1736 -0
  249. data/ext/src/third-party/zlib-1.2.3/deflate.h +331 -0
  250. data/ext/src/third-party/zlib-1.2.3/deflate.o +0 -0
  251. data/ext/src/third-party/zlib-1.2.3/example +0 -0
  252. data/ext/src/third-party/zlib-1.2.3/example.c +565 -0
  253. data/ext/src/third-party/zlib-1.2.3/examples/README.examples +42 -0
  254. data/ext/src/third-party/zlib-1.2.3/examples/fitblk.c +233 -0
  255. data/ext/src/third-party/zlib-1.2.3/examples/gun.c +693 -0
  256. data/ext/src/third-party/zlib-1.2.3/examples/gzappend.c +500 -0
  257. data/ext/src/third-party/zlib-1.2.3/examples/gzjoin.c +448 -0
  258. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.c +413 -0
  259. data/ext/src/third-party/zlib-1.2.3/examples/gzlog.h +58 -0
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@@ -0,0 +1,186 @@
1
+ /* inffas8664.c is a hand tuned assembler version of inffast.c - fast decoding
2
+ * version for AMD64 on Windows using Microsoft C compiler
3
+ *
4
+ * Copyright (C) 1995-2003 Mark Adler
5
+ * For conditions of distribution and use, see copyright notice in zlib.h
6
+ *
7
+ * Copyright (C) 2003 Chris Anderson <christop@charm.net>
8
+ * Please use the copyright conditions above.
9
+ *
10
+ * 2005 - Adaptation to Microsoft C Compiler for AMD64 by Gilles Vollant
11
+ *
12
+ * inffas8664.c call function inffas8664fnc in inffasx64.asm
13
+ * inffasx64.asm is automatically convert from AMD64 portion of inffas86.c
14
+ *
15
+ * Dec-29-2003 -- I added AMD64 inflate asm support. This version is also
16
+ * slightly quicker on x86 systems because, instead of using rep movsb to copy
17
+ * data, it uses rep movsw, which moves data in 2-byte chunks instead of single
18
+ * bytes. I've tested the AMD64 code on a Fedora Core 1 + the x86_64 updates
19
+ * from http://fedora.linux.duke.edu/fc1_x86_64
20
+ * which is running on an Athlon 64 3000+ / Gigabyte GA-K8VT800M system with
21
+ * 1GB ram. The 64-bit version is about 4% faster than the 32-bit version,
22
+ * when decompressing mozilla-source-1.3.tar.gz.
23
+ *
24
+ * Mar-13-2003 -- Most of this is derived from inffast.S which is derived from
25
+ * the gcc -S output of zlib-1.2.0/inffast.c. Zlib-1.2.0 is in beta release at
26
+ * the moment. I have successfully compiled and tested this code with gcc2.96,
27
+ * gcc3.2, icc5.0, msvc6.0. It is very close to the speed of inffast.S
28
+ * compiled with gcc -DNO_MMX, but inffast.S is still faster on the P3 with MMX
29
+ * enabled. I will attempt to merge the MMX code into this version. Newer
30
+ * versions of this and inffast.S can be found at
31
+ * http://www.eetbeetee.com/zlib/ and http://www.charm.net/~christop/zlib/
32
+ *
33
+ */
34
+
35
+ #include <stdio.h>
36
+ #include "zutil.h"
37
+ #include "inftrees.h"
38
+ #include "inflate.h"
39
+ #include "inffast.h"
40
+
41
+ /* Mark Adler's comments from inffast.c: */
42
+
43
+ /*
44
+ Decode literal, length, and distance codes and write out the resulting
45
+ literal and match bytes until either not enough input or output is
46
+ available, an end-of-block is encountered, or a data error is encountered.
47
+ When large enough input and output buffers are supplied to inflate(), for
48
+ example, a 16K input buffer and a 64K output buffer, more than 95% of the
49
+ inflate execution time is spent in this routine.
50
+
51
+ Entry assumptions:
52
+
53
+ state->mode == LEN
54
+ strm->avail_in >= 6
55
+ strm->avail_out >= 258
56
+ start >= strm->avail_out
57
+ state->bits < 8
58
+
59
+ On return, state->mode is one of:
60
+
61
+ LEN -- ran out of enough output space or enough available input
62
+ TYPE -- reached end of block code, inflate() to interpret next block
63
+ BAD -- error in block data
64
+
65
+ Notes:
66
+
67
+ - The maximum input bits used by a length/distance pair is 15 bits for the
68
+ length code, 5 bits for the length extra, 15 bits for the distance code,
69
+ and 13 bits for the distance extra. This totals 48 bits, or six bytes.
70
+ Therefore if strm->avail_in >= 6, then there is enough input to avoid
71
+ checking for available input while decoding.
72
+
73
+ - The maximum bytes that a single length/distance pair can output is 258
74
+ bytes, which is the maximum length that can be coded. inflate_fast()
75
+ requires strm->avail_out >= 258 for each loop to avoid checking for
76
+ output space.
77
+ */
78
+
79
+
80
+
81
+ typedef struct inffast_ar {
82
+ /* 64 32 x86 x86_64 */
83
+ /* ar offset register */
84
+ /* 0 0 */ void *esp; /* esp save */
85
+ /* 8 4 */ void *ebp; /* ebp save */
86
+ /* 16 8 */ unsigned char FAR *in; /* esi rsi local strm->next_in */
87
+ /* 24 12 */ unsigned char FAR *last; /* r9 while in < last */
88
+ /* 32 16 */ unsigned char FAR *out; /* edi rdi local strm->next_out */
89
+ /* 40 20 */ unsigned char FAR *beg; /* inflate()'s init next_out */
90
+ /* 48 24 */ unsigned char FAR *end; /* r10 while out < end */
91
+ /* 56 28 */ unsigned char FAR *window;/* size of window, wsize!=0 */
92
+ /* 64 32 */ code const FAR *lcode; /* ebp rbp local strm->lencode */
93
+ /* 72 36 */ code const FAR *dcode; /* r11 local strm->distcode */
94
+ /* 80 40 */ size_t /*unsigned long */hold; /* edx rdx local strm->hold */
95
+ /* 88 44 */ unsigned bits; /* ebx rbx local strm->bits */
96
+ /* 92 48 */ unsigned wsize; /* window size */
97
+ /* 96 52 */ unsigned write; /* window write index */
98
+ /*100 56 */ unsigned lmask; /* r12 mask for lcode */
99
+ /*104 60 */ unsigned dmask; /* r13 mask for dcode */
100
+ /*108 64 */ unsigned len; /* r14 match length */
101
+ /*112 68 */ unsigned dist; /* r15 match distance */
102
+ /*116 72 */ unsigned status; /* set when state chng*/
103
+ } type_ar;
104
+ #ifdef ASMINF
105
+
106
+ void inflate_fast(strm, start)
107
+ z_streamp strm;
108
+ unsigned start; /* inflate()'s starting value for strm->avail_out */
109
+ {
110
+ struct inflate_state FAR *state;
111
+ type_ar ar;
112
+ void inffas8664fnc(struct inffast_ar * par);
113
+
114
+
115
+
116
+ #if (defined( __GNUC__ ) && defined( __amd64__ ) && ! defined( __i386 )) || (defined(_MSC_VER) && defined(_M_AMD64))
117
+ #define PAD_AVAIL_IN 6
118
+ #define PAD_AVAIL_OUT 258
119
+ #else
120
+ #define PAD_AVAIL_IN 5
121
+ #define PAD_AVAIL_OUT 257
122
+ #endif
123
+
124
+ /* copy state to local variables */
125
+ state = (struct inflate_state FAR *)strm->state;
126
+
127
+ ar.in = strm->next_in;
128
+ ar.last = ar.in + (strm->avail_in - PAD_AVAIL_IN);
129
+ ar.out = strm->next_out;
130
+ ar.beg = ar.out - (start - strm->avail_out);
131
+ ar.end = ar.out + (strm->avail_out - PAD_AVAIL_OUT);
132
+ ar.wsize = state->wsize;
133
+ ar.write = state->write;
134
+ ar.window = state->window;
135
+ ar.hold = state->hold;
136
+ ar.bits = state->bits;
137
+ ar.lcode = state->lencode;
138
+ ar.dcode = state->distcode;
139
+ ar.lmask = (1U << state->lenbits) - 1;
140
+ ar.dmask = (1U << state->distbits) - 1;
141
+
142
+ /* decode literals and length/distances until end-of-block or not enough
143
+ input data or output space */
144
+
145
+ /* align in on 1/2 hold size boundary */
146
+ while (((size_t)(void *)ar.in & (sizeof(ar.hold) / 2 - 1)) != 0) {
147
+ ar.hold += (unsigned long)*ar.in++ << ar.bits;
148
+ ar.bits += 8;
149
+ }
150
+
151
+ inffas8664fnc(&ar);
152
+
153
+ if (ar.status > 1) {
154
+ if (ar.status == 2)
155
+ strm->msg = "invalid literal/length code";
156
+ else if (ar.status == 3)
157
+ strm->msg = "invalid distance code";
158
+ else
159
+ strm->msg = "invalid distance too far back";
160
+ state->mode = BAD;
161
+ }
162
+ else if ( ar.status == 1 ) {
163
+ state->mode = TYPE;
164
+ }
165
+
166
+ /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
167
+ ar.len = ar.bits >> 3;
168
+ ar.in -= ar.len;
169
+ ar.bits -= ar.len << 3;
170
+ ar.hold &= (1U << ar.bits) - 1;
171
+
172
+ /* update state and return */
173
+ strm->next_in = ar.in;
174
+ strm->next_out = ar.out;
175
+ strm->avail_in = (unsigned)(ar.in < ar.last ?
176
+ PAD_AVAIL_IN + (ar.last - ar.in) :
177
+ PAD_AVAIL_IN - (ar.in - ar.last));
178
+ strm->avail_out = (unsigned)(ar.out < ar.end ?
179
+ PAD_AVAIL_OUT + (ar.end - ar.out) :
180
+ PAD_AVAIL_OUT - (ar.out - ar.end));
181
+ state->hold = (unsigned long)ar.hold;
182
+ state->bits = ar.bits;
183
+ return;
184
+ }
185
+
186
+ #endif
@@ -0,0 +1,392 @@
1
+ ; inffasx64.asm is a hand tuned assembler version of inffast.c - fast decoding
2
+ ; version for AMD64 on Windows using Microsoft C compiler
3
+ ;
4
+ ; inffasx64.asm is automatically convert from AMD64 portion of inffas86.c
5
+ ; inffasx64.asm is called by inffas8664.c, which contain more info.
6
+
7
+
8
+ ; to compile this file, I use option
9
+ ; ml64.exe /Flinffasx64 /c /Zi inffasx64.asm
10
+ ; with Microsoft Macro Assembler (x64) for AMD64
11
+ ;
12
+ ; ml64.exe is given with Visual Studio 2005, Windows 2003 server DDK
13
+ ;
14
+ ; (you can get Windows 2003 server DDK with ml64 and cl.exe for AMD64 from
15
+ ; http://www.microsoft.com/whdc/devtools/ddk/default.mspx for low price)
16
+ ;
17
+
18
+ .code
19
+ inffas8664fnc PROC
20
+
21
+ ; see http://weblogs.asp.net/oldnewthing/archive/2004/01/14/58579.aspx and
22
+ ; http://msdn.microsoft.com/library/en-us/kmarch/hh/kmarch/64bitAMD_8e951dd2-ee77-4728-8702-55ce4b5dd24a.xml.asp
23
+ ;
24
+ ; All registers must be preserved across the call, except for
25
+ ; rax, rcx, rdx, r8, r-9, r10, and r11, which are scratch.
26
+
27
+
28
+ mov [rsp-8],rsi
29
+ mov [rsp-16],rdi
30
+ mov [rsp-24],r12
31
+ mov [rsp-32],r13
32
+ mov [rsp-40],r14
33
+ mov [rsp-48],r15
34
+ mov [rsp-56],rbx
35
+
36
+ mov rax,rcx
37
+
38
+ mov [rax+8], rbp ; /* save regs rbp and rsp */
39
+ mov [rax], rsp
40
+
41
+ mov rsp, rax ; /* make rsp point to &ar */
42
+
43
+ mov rsi, [rsp+16] ; /* rsi = in */
44
+ mov rdi, [rsp+32] ; /* rdi = out */
45
+ mov r9, [rsp+24] ; /* r9 = last */
46
+ mov r10, [rsp+48] ; /* r10 = end */
47
+ mov rbp, [rsp+64] ; /* rbp = lcode */
48
+ mov r11, [rsp+72] ; /* r11 = dcode */
49
+ mov rdx, [rsp+80] ; /* rdx = hold */
50
+ mov ebx, [rsp+88] ; /* ebx = bits */
51
+ mov r12d, [rsp+100] ; /* r12d = lmask */
52
+ mov r13d, [rsp+104] ; /* r13d = dmask */
53
+ ; /* r14d = len */
54
+ ; /* r15d = dist */
55
+
56
+
57
+ cld
58
+ cmp r10, rdi
59
+ je L_one_time ; /* if only one decode left */
60
+ cmp r9, rsi
61
+
62
+ jne L_do_loop
63
+
64
+
65
+ L_one_time:
66
+ mov r8, r12 ; /* r8 = lmask */
67
+ cmp bl, 32
68
+ ja L_get_length_code_one_time
69
+
70
+ lodsd ; /* eax = *(uint *)in++ */
71
+ mov cl, bl ; /* cl = bits, needs it for shifting */
72
+ add bl, 32 ; /* bits += 32 */
73
+ shl rax, cl
74
+ or rdx, rax ; /* hold |= *((uint *)in)++ << bits */
75
+ jmp L_get_length_code_one_time
76
+
77
+ ALIGN 4
78
+ L_while_test:
79
+ cmp r10, rdi
80
+ jbe L_break_loop
81
+ cmp r9, rsi
82
+ jbe L_break_loop
83
+
84
+ L_do_loop:
85
+ mov r8, r12 ; /* r8 = lmask */
86
+ cmp bl, 32
87
+ ja L_get_length_code ; /* if (32 < bits) */
88
+
89
+ lodsd ; /* eax = *(uint *)in++ */
90
+ mov cl, bl ; /* cl = bits, needs it for shifting */
91
+ add bl, 32 ; /* bits += 32 */
92
+ shl rax, cl
93
+ or rdx, rax ; /* hold |= *((uint *)in)++ << bits */
94
+
95
+ L_get_length_code:
96
+ and r8, rdx ; /* r8 &= hold */
97
+ mov eax, [rbp+r8*4] ; /* eax = lcode[hold & lmask] */
98
+
99
+ mov cl, ah ; /* cl = this.bits */
100
+ sub bl, ah ; /* bits -= this.bits */
101
+ shr rdx, cl ; /* hold >>= this.bits */
102
+
103
+ test al, al
104
+ jnz L_test_for_length_base ; /* if (op != 0) 45.7% */
105
+
106
+ mov r8, r12 ; /* r8 = lmask */
107
+ shr eax, 16 ; /* output this.val char */
108
+ stosb
109
+
110
+ L_get_length_code_one_time:
111
+ and r8, rdx ; /* r8 &= hold */
112
+ mov eax, [rbp+r8*4] ; /* eax = lcode[hold & lmask] */
113
+
114
+ L_dolen:
115
+ mov cl, ah ; /* cl = this.bits */
116
+ sub bl, ah ; /* bits -= this.bits */
117
+ shr rdx, cl ; /* hold >>= this.bits */
118
+
119
+ test al, al
120
+ jnz L_test_for_length_base ; /* if (op != 0) 45.7% */
121
+
122
+ shr eax, 16 ; /* output this.val char */
123
+ stosb
124
+ jmp L_while_test
125
+
126
+ ALIGN 4
127
+ L_test_for_length_base:
128
+ mov r14d, eax ; /* len = this */
129
+ shr r14d, 16 ; /* len = this.val */
130
+ mov cl, al
131
+
132
+ test al, 16
133
+ jz L_test_for_second_level_length ; /* if ((op & 16) == 0) 8% */
134
+ and cl, 15 ; /* op &= 15 */
135
+ jz L_decode_distance ; /* if (!op) */
136
+
137
+ L_add_bits_to_len:
138
+ sub bl, cl
139
+ xor eax, eax
140
+ inc eax
141
+ shl eax, cl
142
+ dec eax
143
+ and eax, edx ; /* eax &= hold */
144
+ shr rdx, cl
145
+ add r14d, eax ; /* len += hold & mask[op] */
146
+
147
+ L_decode_distance:
148
+ mov r8, r13 ; /* r8 = dmask */
149
+ cmp bl, 32
150
+ ja L_get_distance_code ; /* if (32 < bits) */
151
+
152
+ lodsd ; /* eax = *(uint *)in++ */
153
+ mov cl, bl ; /* cl = bits, needs it for shifting */
154
+ add bl, 32 ; /* bits += 32 */
155
+ shl rax, cl
156
+ or rdx, rax ; /* hold |= *((uint *)in)++ << bits */
157
+
158
+ L_get_distance_code:
159
+ and r8, rdx ; /* r8 &= hold */
160
+ mov eax, [r11+r8*4] ; /* eax = dcode[hold & dmask] */
161
+
162
+ L_dodist:
163
+ mov r15d, eax ; /* dist = this */
164
+ shr r15d, 16 ; /* dist = this.val */
165
+ mov cl, ah
166
+ sub bl, ah ; /* bits -= this.bits */
167
+ shr rdx, cl ; /* hold >>= this.bits */
168
+ mov cl, al ; /* cl = this.op */
169
+
170
+ test al, 16 ; /* if ((op & 16) == 0) */
171
+ jz L_test_for_second_level_dist
172
+ and cl, 15 ; /* op &= 15 */
173
+ jz L_check_dist_one
174
+
175
+ L_add_bits_to_dist:
176
+ sub bl, cl
177
+ xor eax, eax
178
+ inc eax
179
+ shl eax, cl
180
+ dec eax ; /* (1 << op) - 1 */
181
+ and eax, edx ; /* eax &= hold */
182
+ shr rdx, cl
183
+ add r15d, eax ; /* dist += hold & ((1 << op) - 1) */
184
+
185
+ L_check_window:
186
+ mov r8, rsi ; /* save in so from can use it's reg */
187
+ mov rax, rdi
188
+ sub rax, [rsp+40] ; /* nbytes = out - beg */
189
+
190
+ cmp eax, r15d
191
+ jb L_clip_window ; /* if (dist > nbytes) 4.2% */
192
+
193
+ mov ecx, r14d ; /* ecx = len */
194
+ mov rsi, rdi
195
+ sub rsi, r15 ; /* from = out - dist */
196
+
197
+ sar ecx, 1
198
+ jnc L_copy_two ; /* if len % 2 == 0 */
199
+
200
+ rep movsw
201
+ mov al, [rsi]
202
+ mov [rdi], al
203
+ inc rdi
204
+
205
+ mov rsi, r8 ; /* move in back to %rsi, toss from */
206
+ jmp L_while_test
207
+
208
+ L_copy_two:
209
+ rep movsw
210
+ mov rsi, r8 ; /* move in back to %rsi, toss from */
211
+ jmp L_while_test
212
+
213
+ ALIGN 4
214
+ L_check_dist_one:
215
+ cmp r15d, 1 ; /* if dist 1, is a memset */
216
+ jne L_check_window
217
+ cmp [rsp+40], rdi ; /* if out == beg, outside window */
218
+ je L_check_window
219
+
220
+ mov ecx, r14d ; /* ecx = len */
221
+ mov al, [rdi-1]
222
+ mov ah, al
223
+
224
+ sar ecx, 1
225
+ jnc L_set_two
226
+ mov [rdi], al
227
+ inc rdi
228
+
229
+ L_set_two:
230
+ rep stosw
231
+ jmp L_while_test
232
+
233
+ ALIGN 4
234
+ L_test_for_second_level_length:
235
+ test al, 64
236
+ jnz L_test_for_end_of_block ; /* if ((op & 64) != 0) */
237
+
238
+ xor eax, eax
239
+ inc eax
240
+ shl eax, cl
241
+ dec eax
242
+ and eax, edx ; /* eax &= hold */
243
+ add eax, r14d ; /* eax += len */
244
+ mov eax, [rbp+rax*4] ; /* eax = lcode[val+(hold&mask[op])]*/
245
+ jmp L_dolen
246
+
247
+ ALIGN 4
248
+ L_test_for_second_level_dist:
249
+ test al, 64
250
+ jnz L_invalid_distance_code ; /* if ((op & 64) != 0) */
251
+
252
+ xor eax, eax
253
+ inc eax
254
+ shl eax, cl
255
+ dec eax
256
+ and eax, edx ; /* eax &= hold */
257
+ add eax, r15d ; /* eax += dist */
258
+ mov eax, [r11+rax*4] ; /* eax = dcode[val+(hold&mask[op])]*/
259
+ jmp L_dodist
260
+
261
+ ALIGN 4
262
+ L_clip_window:
263
+ mov ecx, eax ; /* ecx = nbytes */
264
+ mov eax, [rsp+92] ; /* eax = wsize, prepare for dist cmp */
265
+ neg ecx ; /* nbytes = -nbytes */
266
+
267
+ cmp eax, r15d
268
+ jb L_invalid_distance_too_far ; /* if (dist > wsize) */
269
+
270
+ add ecx, r15d ; /* nbytes = dist - nbytes */
271
+ cmp dword ptr [rsp+96], 0
272
+ jne L_wrap_around_window ; /* if (write != 0) */
273
+
274
+ mov rsi, [rsp+56] ; /* from = window */
275
+ sub eax, ecx ; /* eax -= nbytes */
276
+ add rsi, rax ; /* from += wsize - nbytes */
277
+
278
+ mov eax, r14d ; /* eax = len */
279
+ cmp r14d, ecx
280
+ jbe L_do_copy ; /* if (nbytes >= len) */
281
+
282
+ sub eax, ecx ; /* eax -= nbytes */
283
+ rep movsb
284
+ mov rsi, rdi
285
+ sub rsi, r15 ; /* from = &out[ -dist ] */
286
+ jmp L_do_copy
287
+
288
+ ALIGN 4
289
+ L_wrap_around_window:
290
+ mov eax, [rsp+96] ; /* eax = write */
291
+ cmp ecx, eax
292
+ jbe L_contiguous_in_window ; /* if (write >= nbytes) */
293
+
294
+ mov esi, [rsp+92] ; /* from = wsize */
295
+ add rsi, [rsp+56] ; /* from += window */
296
+ add rsi, rax ; /* from += write */
297
+ sub rsi, rcx ; /* from -= nbytes */
298
+ sub ecx, eax ; /* nbytes -= write */
299
+
300
+ mov eax, r14d ; /* eax = len */
301
+ cmp eax, ecx
302
+ jbe L_do_copy ; /* if (nbytes >= len) */
303
+
304
+ sub eax, ecx ; /* len -= nbytes */
305
+ rep movsb
306
+ mov rsi, [rsp+56] ; /* from = window */
307
+ mov ecx, [rsp+96] ; /* nbytes = write */
308
+ cmp eax, ecx
309
+ jbe L_do_copy ; /* if (nbytes >= len) */
310
+
311
+ sub eax, ecx ; /* len -= nbytes */
312
+ rep movsb
313
+ mov rsi, rdi
314
+ sub rsi, r15 ; /* from = out - dist */
315
+ jmp L_do_copy
316
+
317
+ ALIGN 4
318
+ L_contiguous_in_window:
319
+ mov rsi, [rsp+56] ; /* rsi = window */
320
+ add rsi, rax
321
+ sub rsi, rcx ; /* from += write - nbytes */
322
+
323
+ mov eax, r14d ; /* eax = len */
324
+ cmp eax, ecx
325
+ jbe L_do_copy ; /* if (nbytes >= len) */
326
+
327
+ sub eax, ecx ; /* len -= nbytes */
328
+ rep movsb
329
+ mov rsi, rdi
330
+ sub rsi, r15 ; /* from = out - dist */
331
+ jmp L_do_copy ; /* if (nbytes >= len) */
332
+
333
+ ALIGN 4
334
+ L_do_copy:
335
+ mov ecx, eax ; /* ecx = len */
336
+ rep movsb
337
+
338
+ mov rsi, r8 ; /* move in back to %esi, toss from */
339
+ jmp L_while_test
340
+
341
+ L_test_for_end_of_block:
342
+ test al, 32
343
+ jz L_invalid_literal_length_code
344
+ mov dword ptr [rsp+116], 1
345
+ jmp L_break_loop_with_status
346
+
347
+ L_invalid_literal_length_code:
348
+ mov dword ptr [rsp+116], 2
349
+ jmp L_break_loop_with_status
350
+
351
+ L_invalid_distance_code:
352
+ mov dword ptr [rsp+116], 3
353
+ jmp L_break_loop_with_status
354
+
355
+ L_invalid_distance_too_far:
356
+ mov dword ptr [rsp+116], 4
357
+ jmp L_break_loop_with_status
358
+
359
+ L_break_loop:
360
+ mov dword ptr [rsp+116], 0
361
+
362
+ L_break_loop_with_status:
363
+ ; /* put in, out, bits, and hold back into ar and pop esp */
364
+ mov [rsp+16], rsi ; /* in */
365
+ mov [rsp+32], rdi ; /* out */
366
+ mov [rsp+88], ebx ; /* bits */
367
+ mov [rsp+80], rdx ; /* hold */
368
+
369
+ mov rax, [rsp] ; /* restore rbp and rsp */
370
+ mov rbp, [rsp+8]
371
+ mov rsp, rax
372
+
373
+
374
+
375
+ mov rsi,[rsp-8]
376
+ mov rdi,[rsp-16]
377
+ mov r12,[rsp-24]
378
+ mov r13,[rsp-32]
379
+ mov r14,[rsp-40]
380
+ mov r15,[rsp-48]
381
+ mov rbx,[rsp-56]
382
+
383
+ ret 0
384
+ ; :
385
+ ; : "m" (ar)
386
+ ; : "memory", "%rax", "%rbx", "%rcx", "%rdx", "%rsi", "%rdi",
387
+ ; "%r8", "%r9", "%r10", "%r11", "%r12", "%r13", "%r14", "%r15"
388
+ ; );
389
+
390
+ inffas8664fnc ENDP
391
+ ;_TEXT ENDS
392
+ END