ruby-minigraph 0.0.20.0

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  1. checksums.yaml +7 -0
  2. data/LICENSE.txt +21 -0
  3. data/README.md +62 -0
  4. data/ext/Rakefile +56 -0
  5. data/ext/cmappy/cmappy.c +7 -0
  6. data/ext/cmappy/cmappy.h +8 -0
  7. data/ext/minigraph/LICENSE.txt +23 -0
  8. data/ext/minigraph/Makefile +66 -0
  9. data/ext/minigraph/NEWS.md +317 -0
  10. data/ext/minigraph/README.md +207 -0
  11. data/ext/minigraph/algo.c +194 -0
  12. data/ext/minigraph/algo.h +33 -0
  13. data/ext/minigraph/asm-call.c +147 -0
  14. data/ext/minigraph/bseq.c +133 -0
  15. data/ext/minigraph/bseq.h +76 -0
  16. data/ext/minigraph/cal_cov.c +139 -0
  17. data/ext/minigraph/doc/example1.png +0 -0
  18. data/ext/minigraph/doc/example2.png +0 -0
  19. data/ext/minigraph/doc/examples.graffle +0 -0
  20. data/ext/minigraph/format.c +241 -0
  21. data/ext/minigraph/galign.c +140 -0
  22. data/ext/minigraph/gchain1.c +532 -0
  23. data/ext/minigraph/gcmisc.c +223 -0
  24. data/ext/minigraph/gfa-aug.c +260 -0
  25. data/ext/minigraph/gfa-base.c +526 -0
  26. data/ext/minigraph/gfa-bbl.c +372 -0
  27. data/ext/minigraph/gfa-ed.c +617 -0
  28. data/ext/minigraph/gfa-io.c +395 -0
  29. data/ext/minigraph/gfa-priv.h +154 -0
  30. data/ext/minigraph/gfa.h +166 -0
  31. data/ext/minigraph/ggen.c +182 -0
  32. data/ext/minigraph/ggen.h +21 -0
  33. data/ext/minigraph/ggsimple.c +570 -0
  34. data/ext/minigraph/gmap.c +211 -0
  35. data/ext/minigraph/index.c +230 -0
  36. data/ext/minigraph/kalloc.c +224 -0
  37. data/ext/minigraph/kalloc.h +82 -0
  38. data/ext/minigraph/kavl.h +414 -0
  39. data/ext/minigraph/kdq.h +134 -0
  40. data/ext/minigraph/ketopt.h +116 -0
  41. data/ext/minigraph/khashl.h +348 -0
  42. data/ext/minigraph/krmq.h +474 -0
  43. data/ext/minigraph/kseq.h +256 -0
  44. data/ext/minigraph/ksort.h +164 -0
  45. data/ext/minigraph/kstring.h +165 -0
  46. data/ext/minigraph/kthread.c +159 -0
  47. data/ext/minigraph/kthread.h +15 -0
  48. data/ext/minigraph/kvec-km.h +105 -0
  49. data/ext/minigraph/kvec.h +110 -0
  50. data/ext/minigraph/lchain.c +441 -0
  51. data/ext/minigraph/main.c +301 -0
  52. data/ext/minigraph/map-algo.c +500 -0
  53. data/ext/minigraph/mgpriv.h +128 -0
  54. data/ext/minigraph/minigraph.1 +359 -0
  55. data/ext/minigraph/minigraph.h +176 -0
  56. data/ext/minigraph/miniwfa.c +834 -0
  57. data/ext/minigraph/miniwfa.h +95 -0
  58. data/ext/minigraph/misc/mgutils.js +1451 -0
  59. data/ext/minigraph/misc.c +12 -0
  60. data/ext/minigraph/options.c +134 -0
  61. data/ext/minigraph/shortk.c +251 -0
  62. data/ext/minigraph/sketch.c +109 -0
  63. data/ext/minigraph/sys.c +147 -0
  64. data/ext/minigraph/sys.h +20 -0
  65. data/ext/minigraph/test/MT-chimp.fa +277 -0
  66. data/ext/minigraph/test/MT-human.fa +239 -0
  67. data/ext/minigraph/test/MT-orangA.fa +276 -0
  68. data/ext/minigraph/test/MT.gfa +19 -0
  69. data/ext/minigraph/tex/Makefile +13 -0
  70. data/ext/minigraph/tex/minigraph.bib +676 -0
  71. data/ext/minigraph/tex/minigraph.tex +986 -0
  72. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.gp +42 -0
  73. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.anno.tbl +13 -0
  74. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.gp +269 -0
  75. data/ext/minigraph/tex/plots/CHM13-f1-90.bb.mini-inter-none.win.sh +7 -0
  76. data/ext/minigraph/tex/plots/CHM13v1.cen.bed +23 -0
  77. data/ext/minigraph/tex/plots/CHM13v1.size +23 -0
  78. data/ext/minigraph/tex/plots/anno2tbl.js +40 -0
  79. data/ext/minigraph/tex/plots/bedutils.js +367 -0
  80. data/ext/minigraph/tex/plots/chr-plot.js +130 -0
  81. data/ext/minigraph/tex/plots/gen-anno.mak +24 -0
  82. data/ext/minigraph.patch +21 -0
  83. data/lib/minigraph/ffi/constants.rb +230 -0
  84. data/lib/minigraph/ffi/functions.rb +70 -0
  85. data/lib/minigraph/ffi/mappy.rb +8 -0
  86. data/lib/minigraph/ffi.rb +27 -0
  87. data/lib/minigraph/version.rb +5 -0
  88. data/lib/minigraph.rb +72 -0
  89. metadata +159 -0
@@ -0,0 +1,474 @@
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+ /* The MIT License
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+
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+ Copyright (c) 2019 by Attractive Chaos <attractor@live.co.uk>
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
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+ */
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+
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+ /* An example:
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+
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+ #include <stdio.h>
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+ #include <string.h>
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+ #include <stdlib.h>
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+ #include "krmq.h"
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+
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+ struct my_node {
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+ char key;
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+ KRMQ_HEAD(struct my_node) head;
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+ };
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+ #define my_cmp(p, q) (((q)->key < (p)->key) - ((p)->key < (q)->key))
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+ KRMQ_INIT(my, struct my_node, head, my_cmp)
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+
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+ int main(void) {
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+ const char *str = "MNOLKQOPHIA"; // from wiki, except a duplicate
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+ struct my_node *root = 0;
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+ int i, l = strlen(str);
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+ for (i = 0; i < l; ++i) { // insert in the input order
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+ struct my_node *q, *p = malloc(sizeof(*p));
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+ p->key = str[i];
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+ q = krmq_insert(my, &root, p, 0);
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+ if (p != q) free(p); // if already present, free
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+ }
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+ krmq_itr_t(my) itr;
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+ krmq_itr_first(my, root, &itr); // place at first
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+ do { // traverse
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+ const struct my_node *p = krmq_at(&itr);
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+ putchar(p->key);
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+ free((void*)p); // free node
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+ } while (krmq_itr_next(my, &itr));
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+ putchar('\n');
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+ return 0;
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+ }
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+ */
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+
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+ #ifndef KRMQ_H
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+ #define KRMQ_H
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+
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+ #ifdef __STRICT_ANSI__
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+ #define inline __inline__
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+ #endif
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+
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+ #define KRMQ_MAX_DEPTH 64
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+
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+ #define krmq_size(head, p) ((p)? (p)->head.size : 0)
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+ #define krmq_size_child(head, q, i) ((q)->head.p[(i)]? (q)->head.p[(i)]->head.size : 0)
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+
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+ #define KRMQ_HEAD(__type) \
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+ struct { \
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+ __type *p[2], *s; \
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+ signed char balance; /* balance factor */ \
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+ unsigned size; /* #elements in subtree */ \
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+ }
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+
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+ #define __KRMQ_FIND(suf, __scope, __type, __head, __cmp) \
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+ __scope __type *krmq_find_##suf(const __type *root, const __type *x, unsigned *cnt_) { \
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+ const __type *p = root; \
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+ unsigned cnt = 0; \
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+ while (p != 0) { \
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+ int cmp; \
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+ cmp = __cmp(x, p); \
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+ if (cmp >= 0) cnt += krmq_size_child(__head, p, 0) + 1; \
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+ if (cmp < 0) p = p->__head.p[0]; \
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+ else if (cmp > 0) p = p->__head.p[1]; \
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+ else break; \
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+ } \
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+ if (cnt_) *cnt_ = cnt; \
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+ return (__type*)p; \
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+ } \
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+ __scope __type *krmq_interval_##suf(const __type *root, const __type *x, __type **lower, __type **upper) { \
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+ const __type *p = root, *l = 0, *u = 0; \
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+ while (p != 0) { \
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+ int cmp; \
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+ cmp = __cmp(x, p); \
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+ if (cmp < 0) u = p, p = p->__head.p[0]; \
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+ else if (cmp > 0) l = p, p = p->__head.p[1]; \
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+ else { l = u = p; break; } \
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+ } \
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+ if (lower) *lower = (__type*)l; \
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+ if (upper) *upper = (__type*)u; \
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+ return (__type*)p; \
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+ }
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+
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+ #define __KRMQ_RMQ(suf, __scope, __type, __head, __cmp, __lt2) \
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+ __scope __type *krmq_rmq_##suf(const __type *root, const __type *lo, const __type *up) { /* CLOSED interval */ \
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+ const __type *p = root, *path[2][KRMQ_MAX_DEPTH], *min; \
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+ int plen[2] = {0, 0}, pcmp[2][KRMQ_MAX_DEPTH], i, cmp, lca; \
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+ if (root == 0) return 0; \
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+ while (p) { \
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+ cmp = __cmp(lo, p); \
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+ path[0][plen[0]] = p, pcmp[0][plen[0]++] = cmp; \
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+ if (cmp < 0) p = p->__head.p[0]; \
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+ else if (cmp > 0) p = p->__head.p[1]; \
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+ else break; \
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+ } \
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+ p = root; \
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+ while (p) { \
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+ cmp = __cmp(up, p); \
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+ path[1][plen[1]] = p, pcmp[1][plen[1]++] = cmp; \
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+ if (cmp < 0) p = p->__head.p[0]; \
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+ else if (cmp > 0) p = p->__head.p[1]; \
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+ else break; \
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+ } \
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+ for (i = 0; i < plen[0] && i < plen[1]; ++i) /* find the LCA */ \
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+ if (path[0][i] == path[1][i] && pcmp[0][i] <= 0 && pcmp[1][i] >= 0) \
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+ break; \
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+ if (i == plen[0] || i == plen[1]) return 0; /* no elements in the closed interval */ \
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+ lca = i, min = path[0][lca]; \
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+ for (i = lca + 1; i < plen[0]; ++i) { \
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+ if (pcmp[0][i] <= 0) { \
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+ if (__lt2(path[0][i], min)) min = path[0][i]; \
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+ if (path[0][i]->__head.p[1] && __lt2(path[0][i]->__head.p[1]->__head.s, min)) \
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+ min = path[0][i]->__head.p[1]->__head.s; \
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+ } \
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+ } \
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+ for (i = lca + 1; i < plen[1]; ++i) { \
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+ if (pcmp[1][i] >= 0) { \
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+ if (__lt2(path[1][i], min)) min = path[1][i]; \
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+ if (path[1][i]->__head.p[0] && __lt2(path[1][i]->__head.p[0]->__head.s, min)) \
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+ min = path[1][i]->__head.p[0]->__head.s; \
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+ } \
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+ } \
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+ return (__type*)min; \
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+ }
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+
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+ #define __KRMQ_ROTATE(suf, __type, __head, __lt2) \
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+ /* */ \
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+ static inline void krmq_update_min_##suf(__type *p, const __type *q, const __type *r) { \
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+ p->__head.s = !q || __lt2(p, q->__head.s)? p : q->__head.s; \
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+ p->__head.s = !r || __lt2(p->__head.s, r->__head.s)? p->__head.s : r->__head.s; \
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+ } \
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+ /* one rotation: (a,(b,c)q)p => ((a,b)p,c)q */ \
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+ static inline __type *krmq_rotate1_##suf(__type *p, int dir) { /* dir=0 to left; dir=1 to right */ \
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+ int opp = 1 - dir; /* opposite direction */ \
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+ __type *q = p->__head.p[opp], *s = p->__head.s; \
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+ unsigned size_p = p->__head.size; \
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+ p->__head.size -= q->__head.size - krmq_size_child(__head, q, dir); \
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+ q->__head.size = size_p; \
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+ krmq_update_min_##suf(p, p->__head.p[dir], q->__head.p[dir]); \
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+ q->__head.s = s; \
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+ p->__head.p[opp] = q->__head.p[dir]; \
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+ q->__head.p[dir] = p; \
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+ return q; \
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+ } \
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+ /* two consecutive rotations: (a,((b,c)r,d)q)p => ((a,b)p,(c,d)q)r */ \
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+ static inline __type *krmq_rotate2_##suf(__type *p, int dir) { \
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+ int b1, opp = 1 - dir; \
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+ __type *q = p->__head.p[opp], *r = q->__head.p[dir], *s = p->__head.s; \
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+ unsigned size_x_dir = krmq_size_child(__head, r, dir); \
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+ r->__head.size = p->__head.size; \
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+ p->__head.size -= q->__head.size - size_x_dir; \
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+ q->__head.size -= size_x_dir + 1; \
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+ krmq_update_min_##suf(p, p->__head.p[dir], r->__head.p[dir]); \
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+ krmq_update_min_##suf(q, q->__head.p[opp], r->__head.p[opp]); \
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+ r->__head.s = s; \
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+ p->__head.p[opp] = r->__head.p[dir]; \
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+ r->__head.p[dir] = p; \
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+ q->__head.p[dir] = r->__head.p[opp]; \
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+ r->__head.p[opp] = q; \
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+ b1 = dir == 0? +1 : -1; \
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+ if (r->__head.balance == b1) q->__head.balance = 0, p->__head.balance = -b1; \
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+ else if (r->__head.balance == 0) q->__head.balance = p->__head.balance = 0; \
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+ else q->__head.balance = b1, p->__head.balance = 0; \
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+ r->__head.balance = 0; \
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+ return r; \
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+ }
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+
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+ #define __KRMQ_INSERT(suf, __scope, __type, __head, __cmp, __lt2) \
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+ __scope __type *krmq_insert_##suf(__type **root_, __type *x, unsigned *cnt_) { \
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+ unsigned char stack[KRMQ_MAX_DEPTH]; \
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+ __type *path[KRMQ_MAX_DEPTH]; \
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+ __type *bp, *bq; \
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+ __type *p, *q, *r = 0; /* _r_ is potentially the new root */ \
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+ int i, which = 0, top, b1, path_len; \
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+ unsigned cnt = 0; \
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+ bp = *root_, bq = 0; \
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+ /* find the insertion location */ \
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+ for (p = bp, q = bq, top = path_len = 0; p; q = p, p = p->__head.p[which]) { \
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+ int cmp; \
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+ cmp = __cmp(x, p); \
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+ if (cmp >= 0) cnt += krmq_size_child(__head, p, 0) + 1; \
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+ if (cmp == 0) { \
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+ if (cnt_) *cnt_ = cnt; \
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+ return p; \
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+ } \
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+ if (p->__head.balance != 0) \
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+ bq = q, bp = p, top = 0; \
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+ stack[top++] = which = (cmp > 0); \
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+ path[path_len++] = p; \
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+ } \
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+ if (cnt_) *cnt_ = cnt; \
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+ x->__head.balance = 0, x->__head.size = 1, x->__head.p[0] = x->__head.p[1] = 0, x->__head.s = x; \
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+ if (q == 0) *root_ = x; \
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+ else q->__head.p[which] = x; \
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+ if (bp == 0) return x; \
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+ for (i = 0; i < path_len; ++i) ++path[i]->__head.size; \
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+ for (i = path_len - 1; i >= 0; --i) { \
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+ krmq_update_min_##suf(path[i], path[i]->__head.p[0], path[i]->__head.p[1]); \
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+ if (path[i]->__head.s != x) break; \
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+ } \
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+ for (p = bp, top = 0; p != x; p = p->__head.p[stack[top]], ++top) /* update balance factors */ \
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+ if (stack[top] == 0) --p->__head.balance; \
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+ else ++p->__head.balance; \
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+ if (bp->__head.balance > -2 && bp->__head.balance < 2) return x; /* no re-balance needed */ \
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+ /* re-balance */ \
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+ which = (bp->__head.balance < 0); \
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+ b1 = which == 0? +1 : -1; \
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+ q = bp->__head.p[1 - which]; \
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+ if (q->__head.balance == b1) { \
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+ r = krmq_rotate1_##suf(bp, which); \
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+ q->__head.balance = bp->__head.balance = 0; \
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+ } else r = krmq_rotate2_##suf(bp, which); \
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+ if (bq == 0) *root_ = r; \
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+ else bq->__head.p[bp != bq->__head.p[0]] = r; \
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+ return x; \
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+ }
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+
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+ #define __KRMQ_ERASE(suf, __scope, __type, __head, __cmp, __lt2) \
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+ __scope __type *krmq_erase_##suf(__type **root_, const __type *x, unsigned *cnt_) { \
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+ __type *p, *path[KRMQ_MAX_DEPTH], fake; \
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+ unsigned char dir[KRMQ_MAX_DEPTH]; \
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+ int i, d = 0, cmp; \
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+ unsigned cnt = 0; \
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+ fake = **root_, fake.__head.p[0] = *root_, fake.__head.p[1] = 0; \
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+ if (cnt_) *cnt_ = 0; \
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+ if (x) { \
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+ for (cmp = -1, p = &fake; cmp; cmp = __cmp(x, p)) { \
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+ int which = (cmp > 0); \
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+ if (cmp > 0) cnt += krmq_size_child(__head, p, 0) + 1; \
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+ dir[d] = which; \
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+ path[d++] = p; \
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+ p = p->__head.p[which]; \
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+ if (p == 0) { \
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+ if (cnt_) *cnt_ = 0; \
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+ return 0; \
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+ } \
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+ } \
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+ cnt += krmq_size_child(__head, p, 0) + 1; /* because p==x is not counted */ \
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+ } else { \
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+ for (p = &fake, cnt = 1; p; p = p->__head.p[0]) \
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+ dir[d] = 0, path[d++] = p; \
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+ p = path[--d]; \
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+ } \
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+ if (cnt_) *cnt_ = cnt; \
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+ for (i = 1; i < d; ++i) --path[i]->__head.size; \
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+ if (p->__head.p[1] == 0) { /* ((1,.)2,3)4 => (1,3)4; p=2 */ \
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+ path[d-1]->__head.p[dir[d-1]] = p->__head.p[0]; \
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+ } else { \
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+ __type *q = p->__head.p[1]; \
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+ if (q->__head.p[0] == 0) { /* ((1,2)3,4)5 => ((1)2,4)5; p=3,q=2 */ \
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+ q->__head.p[0] = p->__head.p[0]; \
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+ q->__head.balance = p->__head.balance; \
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+ path[d-1]->__head.p[dir[d-1]] = q; \
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+ path[d] = q, dir[d++] = 1; \
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+ q->__head.size = p->__head.size - 1; \
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+ } else { /* ((1,((.,2)3,4)5)6,7)8 => ((1,(2,4)5)3,7)8; p=6 */ \
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+ __type *r; \
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+ int e = d++; /* backup _d_ */\
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+ for (;;) { \
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+ dir[d] = 0; \
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+ path[d++] = q; \
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+ r = q->__head.p[0]; \
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+ if (r->__head.p[0] == 0) break; \
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+ q = r; \
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+ } \
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+ r->__head.p[0] = p->__head.p[0]; \
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+ q->__head.p[0] = r->__head.p[1]; \
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+ r->__head.p[1] = p->__head.p[1]; \
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+ r->__head.balance = p->__head.balance; \
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+ path[e-1]->__head.p[dir[e-1]] = r; \
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+ path[e] = r, dir[e] = 1; \
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+ for (i = e + 1; i < d; ++i) --path[i]->__head.size; \
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+ r->__head.size = p->__head.size - 1; \
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+ } \
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+ } \
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+ for (i = d - 1; i >= 0; --i) /* not sure why adding condition "path[i]->__head.s==p" doesn't work */ \
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+ krmq_update_min_##suf(path[i], path[i]->__head.p[0], path[i]->__head.p[1]); \
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+ while (--d > 0) { \
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+ __type *q = path[d]; \
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+ int which, other, b1 = 1, b2 = 2; \
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+ which = dir[d], other = 1 - which; \
308
+ if (which) b1 = -b1, b2 = -b2; \
309
+ q->__head.balance += b1; \
310
+ if (q->__head.balance == b1) break; \
311
+ else if (q->__head.balance == b2) { \
312
+ __type *r = q->__head.p[other]; \
313
+ if (r->__head.balance == -b1) { \
314
+ path[d-1]->__head.p[dir[d-1]] = krmq_rotate2_##suf(q, which); \
315
+ } else { \
316
+ path[d-1]->__head.p[dir[d-1]] = krmq_rotate1_##suf(q, which); \
317
+ if (r->__head.balance == 0) { \
318
+ r->__head.balance = -b1; \
319
+ q->__head.balance = b1; \
320
+ break; \
321
+ } else r->__head.balance = q->__head.balance = 0; \
322
+ } \
323
+ } \
324
+ } \
325
+ *root_ = fake.__head.p[0]; \
326
+ return p; \
327
+ }
328
+
329
+ #define krmq_free(__type, __head, __root, __free) do { \
330
+ __type *_p, *_q; \
331
+ for (_p = __root; _p; _p = _q) { \
332
+ if (_p->__head.p[0] == 0) { \
333
+ _q = _p->__head.p[1]; \
334
+ __free(_p); \
335
+ } else { \
336
+ _q = _p->__head.p[0]; \
337
+ _p->__head.p[0] = _q->__head.p[1]; \
338
+ _q->__head.p[1] = _p; \
339
+ } \
340
+ } \
341
+ } while (0)
342
+
343
+ #define __KRMQ_ITR(suf, __scope, __type, __head, __cmp) \
344
+ struct krmq_itr_##suf { \
345
+ const __type *stack[KRMQ_MAX_DEPTH], **top; \
346
+ }; \
347
+ __scope void krmq_itr_first_##suf(const __type *root, struct krmq_itr_##suf *itr) { \
348
+ const __type *p; \
349
+ for (itr->top = itr->stack - 1, p = root; p; p = p->__head.p[0]) \
350
+ *++itr->top = p; \
351
+ } \
352
+ __scope int krmq_itr_find_##suf(const __type *root, const __type *x, struct krmq_itr_##suf *itr) { \
353
+ const __type *p = root; \
354
+ itr->top = itr->stack - 1; \
355
+ while (p != 0) { \
356
+ int cmp; \
357
+ *++itr->top = p; \
358
+ cmp = __cmp(x, p); \
359
+ if (cmp < 0) p = p->__head.p[0]; \
360
+ else if (cmp > 0) p = p->__head.p[1]; \
361
+ else break; \
362
+ } \
363
+ return p? 1 : 0; \
364
+ } \
365
+ __scope int krmq_itr_next_bidir_##suf(struct krmq_itr_##suf *itr, int dir) { \
366
+ const __type *p; \
367
+ if (itr->top < itr->stack) return 0; \
368
+ dir = !!dir; \
369
+ p = (*itr->top)->__head.p[dir]; \
370
+ if (p) { /* go down */ \
371
+ for (; p; p = p->__head.p[!dir]) \
372
+ *++itr->top = p; \
373
+ return 1; \
374
+ } else { /* go up */ \
375
+ do { \
376
+ p = *itr->top--; \
377
+ } while (itr->top >= itr->stack && p == (*itr->top)->__head.p[dir]); \
378
+ return itr->top < itr->stack? 0 : 1; \
379
+ } \
380
+ } \
381
+
382
+ /**
383
+ * Insert a node to the tree
384
+ *
385
+ * @param suf name suffix used in KRMQ_INIT()
386
+ * @param proot pointer to the root of the tree (in/out: root may change)
387
+ * @param x node to insert (in)
388
+ * @param cnt number of nodes smaller than or equal to _x_; can be NULL (out)
389
+ *
390
+ * @return _x_ if not present in the tree, or the node equal to x.
391
+ */
392
+ #define krmq_insert(suf, proot, x, cnt) krmq_insert_##suf(proot, x, cnt)
393
+
394
+ /**
395
+ * Find a node in the tree
396
+ *
397
+ * @param suf name suffix used in KRMQ_INIT()
398
+ * @param root root of the tree
399
+ * @param x node value to find (in)
400
+ * @param cnt number of nodes smaller than or equal to _x_; can be NULL (out)
401
+ *
402
+ * @return node equal to _x_ if present, or NULL if absent
403
+ */
404
+ #define krmq_find(suf, root, x, cnt) krmq_find_##suf(root, x, cnt)
405
+ #define krmq_interval(suf, root, x, lower, upper) krmq_interval_##suf(root, x, lower, upper)
406
+ #define krmq_rmq(suf, root, lo, up) krmq_rmq_##suf(root, lo, up)
407
+
408
+ /**
409
+ * Delete a node from the tree
410
+ *
411
+ * @param suf name suffix used in KRMQ_INIT()
412
+ * @param proot pointer to the root of the tree (in/out: root may change)
413
+ * @param x node value to delete; if NULL, delete the first node (in)
414
+ *
415
+ * @return node removed from the tree if present, or NULL if absent
416
+ */
417
+ #define krmq_erase(suf, proot, x, cnt) krmq_erase_##suf(proot, x, cnt)
418
+ #define krmq_erase_first(suf, proot) krmq_erase_##suf(proot, 0, 0)
419
+
420
+ #define krmq_itr_t(suf) struct krmq_itr_##suf
421
+
422
+ /**
423
+ * Place the iterator at the smallest object
424
+ *
425
+ * @param suf name suffix used in KRMQ_INIT()
426
+ * @param root root of the tree
427
+ * @param itr iterator
428
+ */
429
+ #define krmq_itr_first(suf, root, itr) krmq_itr_first_##suf(root, itr)
430
+
431
+ /**
432
+ * Place the iterator at the object equal to or greater than the query
433
+ *
434
+ * @param suf name suffix used in KRMQ_INIT()
435
+ * @param root root of the tree
436
+ * @param x query (in)
437
+ * @param itr iterator (out)
438
+ *
439
+ * @return 1 if find; 0 otherwise. krmq_at(itr) is NULL if and only if query is
440
+ * larger than all objects in the tree
441
+ */
442
+ #define krmq_itr_find(suf, root, x, itr) krmq_itr_find_##suf(root, x, itr)
443
+
444
+ /**
445
+ * Move to the next object in order
446
+ *
447
+ * @param itr iterator (modified)
448
+ *
449
+ * @return 1 if there is a next object; 0 otherwise
450
+ */
451
+ #define krmq_itr_next(suf, itr) krmq_itr_next_bidir_##suf(itr, 1)
452
+ #define krmq_itr_prev(suf, itr) krmq_itr_next_bidir_##suf(itr, 0)
453
+
454
+ /**
455
+ * Return the pointer at the iterator
456
+ *
457
+ * @param itr iterator
458
+ *
459
+ * @return pointer if present; NULL otherwise
460
+ */
461
+ #define krmq_at(itr) ((itr)->top < (itr)->stack? 0 : *(itr)->top)
462
+
463
+ #define KRMQ_INIT2(suf, __scope, __type, __head, __cmp, __lt2) \
464
+ __KRMQ_FIND(suf, __scope, __type, __head, __cmp) \
465
+ __KRMQ_RMQ(suf, __scope, __type, __head, __cmp, __lt2) \
466
+ __KRMQ_ROTATE(suf, __type, __head, __lt2) \
467
+ __KRMQ_INSERT(suf, __scope, __type, __head, __cmp, __lt2) \
468
+ __KRMQ_ERASE(suf, __scope, __type, __head, __cmp, __lt2) \
469
+ __KRMQ_ITR(suf, __scope, __type, __head, __cmp)
470
+
471
+ #define KRMQ_INIT(suf, __type, __head, __cmp, __lt2) \
472
+ KRMQ_INIT2(suf,, __type, __head, __cmp, __lt2)
473
+
474
+ #endif