minimap2 0.2.22.0 → 0.2.24.1
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.
- checksums.yaml +4 -4
- data/README.md +60 -76
- data/ext/Rakefile +55 -0
- data/ext/cmappy/cmappy.c +129 -0
- data/ext/cmappy/cmappy.h +44 -0
- data/ext/minimap2/FAQ.md +46 -0
- data/ext/minimap2/LICENSE.txt +24 -0
- data/ext/minimap2/MANIFEST.in +10 -0
- data/ext/minimap2/Makefile +132 -0
- data/ext/minimap2/Makefile.simde +97 -0
- data/ext/minimap2/NEWS.md +821 -0
- data/ext/minimap2/README.md +403 -0
- data/ext/minimap2/align.c +1020 -0
- data/ext/minimap2/bseq.c +169 -0
- data/ext/minimap2/bseq.h +64 -0
- data/ext/minimap2/code_of_conduct.md +30 -0
- data/ext/minimap2/cookbook.md +243 -0
- data/ext/minimap2/esterr.c +64 -0
- data/ext/minimap2/example.c +63 -0
- data/ext/minimap2/format.c +559 -0
- data/ext/minimap2/hit.c +466 -0
- data/ext/minimap2/index.c +775 -0
- data/ext/minimap2/kalloc.c +205 -0
- data/ext/minimap2/kalloc.h +76 -0
- data/ext/minimap2/kdq.h +132 -0
- data/ext/minimap2/ketopt.h +120 -0
- data/ext/minimap2/khash.h +615 -0
- data/ext/minimap2/krmq.h +474 -0
- data/ext/minimap2/kseq.h +256 -0
- data/ext/minimap2/ksort.h +153 -0
- data/ext/minimap2/ksw2.h +184 -0
- data/ext/minimap2/ksw2_dispatch.c +96 -0
- data/ext/minimap2/ksw2_extd2_sse.c +402 -0
- data/ext/minimap2/ksw2_exts2_sse.c +416 -0
- data/ext/minimap2/ksw2_extz2_sse.c +313 -0
- data/ext/minimap2/ksw2_ll_sse.c +152 -0
- data/ext/minimap2/kthread.c +159 -0
- data/ext/minimap2/kthread.h +15 -0
- data/ext/minimap2/kvec.h +105 -0
- data/ext/minimap2/lchain.c +369 -0
- data/ext/minimap2/main.c +459 -0
- data/ext/minimap2/map.c +714 -0
- data/ext/minimap2/minimap.h +410 -0
- data/ext/minimap2/minimap2.1 +725 -0
- data/ext/minimap2/misc/README.md +179 -0
- data/ext/minimap2/misc/mmphase.js +335 -0
- data/ext/minimap2/misc/paftools.js +3149 -0
- data/ext/minimap2/misc.c +162 -0
- data/ext/minimap2/mmpriv.h +132 -0
- data/ext/minimap2/options.c +234 -0
- data/ext/minimap2/pe.c +177 -0
- data/ext/minimap2/python/README.rst +196 -0
- data/ext/minimap2/python/cmappy.h +152 -0
- data/ext/minimap2/python/cmappy.pxd +153 -0
- data/ext/minimap2/python/mappy.pyx +273 -0
- data/ext/minimap2/python/minimap2.py +39 -0
- data/ext/minimap2/sdust.c +213 -0
- data/ext/minimap2/sdust.h +25 -0
- data/ext/minimap2/seed.c +131 -0
- data/ext/minimap2/setup.py +55 -0
- data/ext/minimap2/sketch.c +143 -0
- data/ext/minimap2/splitidx.c +84 -0
- data/ext/minimap2/sse2neon/emmintrin.h +1689 -0
- data/ext/minimap2/test/MT-human.fa +278 -0
- data/ext/minimap2/test/MT-orang.fa +276 -0
- data/ext/minimap2/test/q-inv.fa +4 -0
- data/ext/minimap2/test/q2.fa +2 -0
- data/ext/minimap2/test/t-inv.fa +127 -0
- data/ext/minimap2/test/t2.fa +2 -0
- data/ext/minimap2/tex/Makefile +21 -0
- data/ext/minimap2/tex/bioinfo.cls +930 -0
- data/ext/minimap2/tex/blasr-mc.eval +17 -0
- data/ext/minimap2/tex/bowtie2-s3.sam.eval +28 -0
- data/ext/minimap2/tex/bwa-s3.sam.eval +52 -0
- data/ext/minimap2/tex/bwa.eval +55 -0
- data/ext/minimap2/tex/eval2roc.pl +33 -0
- data/ext/minimap2/tex/graphmap.eval +4 -0
- data/ext/minimap2/tex/hs38-simu.sh +10 -0
- data/ext/minimap2/tex/minialign.eval +49 -0
- data/ext/minimap2/tex/minimap2.bib +460 -0
- data/ext/minimap2/tex/minimap2.tex +724 -0
- data/ext/minimap2/tex/mm2-s3.sam.eval +62 -0
- data/ext/minimap2/tex/mm2-update.tex +240 -0
- data/ext/minimap2/tex/mm2.approx.eval +12 -0
- data/ext/minimap2/tex/mm2.eval +13 -0
- data/ext/minimap2/tex/natbib.bst +1288 -0
- data/ext/minimap2/tex/natbib.sty +803 -0
- data/ext/minimap2/tex/ngmlr.eval +38 -0
- data/ext/minimap2/tex/roc.gp +60 -0
- data/ext/minimap2/tex/snap-s3.sam.eval +62 -0
- data/ext/minimap2.patch +19 -0
- data/lib/minimap2/aligner.rb +4 -4
- data/lib/minimap2/alignment.rb +11 -11
- data/lib/minimap2/ffi/constants.rb +20 -16
- data/lib/minimap2/ffi/functions.rb +5 -0
- data/lib/minimap2/ffi.rb +4 -5
- data/lib/minimap2/version.rb +2 -2
- data/lib/minimap2.rb +51 -15
- metadata +97 -79
- data/lib/minimap2/ffi_helper.rb +0 -53
- data/vendor/libminimap2.so +0 -0
data/ext/minimap2/kvec.h
ADDED
@@ -0,0 +1,105 @@
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/* The MIT License
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Copyright (c) 2008, by Attractive Chaos <attractor@live.co.uk>
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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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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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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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#include "kvec.h"
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int main() {
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kvec_t(int) array;
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kv_init(array);
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kv_push(int, array, 10); // append
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kv_a(int, array, 20) = 5; // dynamic
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kv_A(array, 20) = 4; // static
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kv_destroy(array);
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return 0;
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}
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*/
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/*
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2008-09-22 (0.1.0):
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* The initial version.
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*/
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#ifndef AC_KVEC_H
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#define AC_KVEC_H
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#include <stdlib.h>
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#include "kalloc.h"
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#define kv_roundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))
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#define kvec_t(type) struct { size_t n, m; type *a; }
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#define kv_init(v) ((v).n = (v).m = 0, (v).a = 0)
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#define kv_destroy(v) free((v).a)
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#define kv_A(v, i) ((v).a[(i)])
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#define kv_pop(v) ((v).a[--(v).n])
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#define kv_size(v) ((v).n)
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#define kv_max(v) ((v).m)
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#define kv_resize(type, km, v, s) do { \
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if ((v).m < (s)) { \
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(v).m = (s); \
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kv_roundup32((v).m); \
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(v).a = (type*)krealloc((km), (v).a, sizeof(type) * (v).m); \
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} \
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} while (0)
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#define kv_copy(type, km, v1, v0) do { \
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if ((v1).m < (v0).n) kv_resize(type, (km), (v1), (v0).n); \
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(v1).n = (v0).n; \
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memcpy((v1).a, (v0).a, sizeof(type) * (v0).n); \
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} while (0) \
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#define kv_push(type, km, v, x) do { \
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if ((v).n == (v).m) { \
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(v).m = (v).m? (v).m<<1 : 2; \
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(v).a = (type*)krealloc((km), (v).a, sizeof(type) * (v).m); \
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} \
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(v).a[(v).n++] = (x); \
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} while (0)
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#define kv_pushp(type, km, v, p) do { \
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if ((v).n == (v).m) { \
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(v).m = (v).m? (v).m<<1 : 2; \
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(v).a = (type*)krealloc((km), (v).a, sizeof(type) * (v).m); \
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} \
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*(p) = &(v).a[(v).n++]; \
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} while (0)
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#define kv_reverse(type, v, start) do { \
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if ((v).m > 0 && (v).n > (start)) { \
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size_t __i, __end = (v).n - (start); \
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type *__a = (v).a + (start); \
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for (__i = 0; __i < __end>>1; ++__i) { \
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type __t = __a[__end - 1 - __i]; \
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__a[__end - 1 - __i] = __a[__i]; __a[__i] = __t; \
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} \
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} \
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} while (0)
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#endif
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#include <stdint.h>
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#include <string.h>
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#include <stdio.h>
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#include <assert.h>
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#include "mmpriv.h"
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#include "kalloc.h"
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#include "krmq.h"
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static int64_t mg_chain_bk_end(int32_t max_drop, const mm128_t *z, const int32_t *f, const int64_t *p, int32_t *t, int64_t k)
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{
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int64_t i = z[k].y, end_i = -1, max_i = i;
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int32_t max_s = 0;
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if (i < 0 || t[i] != 0) return i;
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do {
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int32_t s;
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t[i] = 2;
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end_i = i = p[i];
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s = i < 0? z[k].x : (int32_t)z[k].x - f[i];
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if (s > max_s) max_s = s, max_i = i;
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else if (max_s - s > max_drop) break;
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} while (i >= 0 && t[i] == 0);
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for (i = z[k].y; i >= 0 && i != end_i; i = p[i]) // reset modified t[]
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t[i] = 0;
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return max_i;
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}
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uint64_t *mg_chain_backtrack(void *km, int64_t n, const int32_t *f, const int64_t *p, int32_t *v, int32_t *t, int32_t min_cnt, int32_t min_sc, int32_t max_drop, int32_t *n_u_, int32_t *n_v_)
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{
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mm128_t *z;
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uint64_t *u;
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int64_t i, k, n_z, n_v;
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int32_t n_u;
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*n_u_ = *n_v_ = 0;
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for (i = 0, n_z = 0; i < n; ++i) // precompute n_z
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if (f[i] >= min_sc) ++n_z;
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if (n_z == 0) return 0;
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KMALLOC(km, z, n_z);
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for (i = 0, k = 0; i < n; ++i) // populate z[]
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if (f[i] >= min_sc) z[k].x = f[i], z[k++].y = i;
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radix_sort_128x(z, z + n_z);
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memset(t, 0, n * 4);
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for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // precompute n_u
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if (t[z[k].y] == 0) {
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int64_t n_v0 = n_v, end_i;
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int32_t sc;
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end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
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for (i = z[k].y; i != end_i; i = p[i])
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++n_v, t[i] = 1;
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sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
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if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
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++n_u;
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else n_v = n_v0;
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}
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}
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KMALLOC(km, u, n_u);
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memset(t, 0, n * 4);
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for (k = n_z - 1, n_v = n_u = 0; k >= 0; --k) { // populate u[]
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if (t[z[k].y] == 0) {
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int64_t n_v0 = n_v, end_i;
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int32_t sc;
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end_i = mg_chain_bk_end(max_drop, z, f, p, t, k);
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for (i = z[k].y; i != end_i; i = p[i])
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v[n_v++] = i, t[i] = 1;
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sc = i < 0? z[k].x : (int32_t)z[k].x - f[i];
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if (sc >= min_sc && n_v > n_v0 && n_v - n_v0 >= min_cnt)
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u[n_u++] = (uint64_t)sc << 32 | (n_v - n_v0);
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else n_v = n_v0;
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}
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}
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kfree(km, z);
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assert(n_v < INT32_MAX);
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*n_u_ = n_u, *n_v_ = n_v;
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return u;
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}
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static mm128_t *compact_a(void *km, int32_t n_u, uint64_t *u, int32_t n_v, int32_t *v, mm128_t *a)
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{
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mm128_t *b, *w;
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uint64_t *u2;
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int64_t i, j, k;
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// write the result to b[]
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KMALLOC(km, b, n_v);
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for (i = 0, k = 0; i < n_u; ++i) {
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int32_t k0 = k, ni = (int32_t)u[i];
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for (j = 0; j < ni; ++j)
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b[k++] = a[v[k0 + (ni - j - 1)]];
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}
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kfree(km, v);
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// sort u[] and a[] by the target position, such that adjacent chains may be joined
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KMALLOC(km, w, n_u);
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for (i = k = 0; i < n_u; ++i) {
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w[i].x = b[k].x, w[i].y = (uint64_t)k<<32|i;
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k += (int32_t)u[i];
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}
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radix_sort_128x(w, w + n_u);
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KMALLOC(km, u2, n_u);
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for (i = k = 0; i < n_u; ++i) {
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int32_t j = (int32_t)w[i].y, n = (int32_t)u[j];
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u2[i] = u[j];
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memcpy(&a[k], &b[w[i].y>>32], n * sizeof(mm128_t));
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k += n;
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}
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memcpy(u, u2, n_u * 8);
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memcpy(b, a, k * sizeof(mm128_t)); // write _a_ to _b_ and deallocate _a_ because _a_ is oversized, sometimes a lot
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kfree(km, a); kfree(km, w); kfree(km, u2);
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return b;
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}
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static inline int32_t comput_sc(const mm128_t *ai, const mm128_t *aj, int32_t max_dist_x, int32_t max_dist_y, int32_t bw, float chn_pen_gap, float chn_pen_skip, int is_cdna, int n_seg)
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{
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int32_t dq = (int32_t)ai->y - (int32_t)aj->y, dr, dd, dg, q_span, sc;
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int32_t sidi = (ai->y & MM_SEED_SEG_MASK) >> MM_SEED_SEG_SHIFT;
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int32_t sidj = (aj->y & MM_SEED_SEG_MASK) >> MM_SEED_SEG_SHIFT;
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if (dq <= 0 || dq > max_dist_x) return INT32_MIN;
|
119
|
+
dr = (int32_t)(ai->x - aj->x);
|
120
|
+
if (sidi == sidj && (dr == 0 || dq > max_dist_y)) return INT32_MIN;
|
121
|
+
dd = dr > dq? dr - dq : dq - dr;
|
122
|
+
if (sidi == sidj && dd > bw) return INT32_MIN;
|
123
|
+
if (n_seg > 1 && !is_cdna && sidi == sidj && dr > max_dist_y) return INT32_MIN;
|
124
|
+
dg = dr < dq? dr : dq;
|
125
|
+
q_span = aj->y>>32&0xff;
|
126
|
+
sc = q_span < dg? q_span : dg;
|
127
|
+
if (dd || dg > q_span) {
|
128
|
+
float lin_pen, log_pen;
|
129
|
+
lin_pen = chn_pen_gap * (float)dd + chn_pen_skip * (float)dg;
|
130
|
+
log_pen = dd >= 1? mg_log2(dd + 1) : 0.0f; // mg_log2() only works for dd>=2
|
131
|
+
if (is_cdna || sidi != sidj) {
|
132
|
+
if (sidi != sidj && dr == 0) ++sc; // possibly due to overlapping paired ends; give a minor bonus
|
133
|
+
else if (dr > dq || sidi != sidj) sc -= (int)(lin_pen < log_pen? lin_pen : log_pen); // deletion or jump between paired ends
|
134
|
+
else sc -= (int)(lin_pen + .5f * log_pen);
|
135
|
+
} else sc -= (int)(lin_pen + .5f * log_pen);
|
136
|
+
}
|
137
|
+
return sc;
|
138
|
+
}
|
139
|
+
|
140
|
+
/* Input:
|
141
|
+
* a[].x: tid<<33 | rev<<32 | tpos
|
142
|
+
* a[].y: flags<<40 | q_span<<32 | q_pos
|
143
|
+
* Output:
|
144
|
+
* n_u: #chains
|
145
|
+
* u[]: score<<32 | #anchors (sum of lower 32 bits of u[] is the returned length of a[])
|
146
|
+
* input a[] is deallocated on return
|
147
|
+
*/
|
148
|
+
mm128_t *mg_lchain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
|
149
|
+
int is_cdna, int n_seg, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
|
150
|
+
{ // TODO: make sure this works when n has more than 32 bits
|
151
|
+
int32_t *f, *t, *v, n_u, n_v, mmax_f = 0, max_drop = bw;
|
152
|
+
int64_t *p, i, j, max_ii, st = 0, n_iter = 0;
|
153
|
+
uint64_t *u;
|
154
|
+
|
155
|
+
if (_u) *_u = 0, *n_u_ = 0;
|
156
|
+
if (n == 0 || a == 0) {
|
157
|
+
kfree(km, a);
|
158
|
+
return 0;
|
159
|
+
}
|
160
|
+
if (max_dist_x < bw) max_dist_x = bw;
|
161
|
+
if (max_dist_y < bw && !is_cdna) max_dist_y = bw;
|
162
|
+
if (is_cdna) max_drop = INT32_MAX;
|
163
|
+
KMALLOC(km, p, n);
|
164
|
+
KMALLOC(km, f, n);
|
165
|
+
KMALLOC(km, v, n);
|
166
|
+
KCALLOC(km, t, n);
|
167
|
+
|
168
|
+
// fill the score and backtrack arrays
|
169
|
+
for (i = 0, max_ii = -1; i < n; ++i) {
|
170
|
+
int64_t max_j = -1, end_j;
|
171
|
+
int32_t max_f = a[i].y>>32&0xff, n_skip = 0;
|
172
|
+
while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist_x)) ++st;
|
173
|
+
if (i - st > max_iter) st = i - max_iter;
|
174
|
+
for (j = i - 1; j >= st; --j) {
|
175
|
+
int32_t sc;
|
176
|
+
sc = comput_sc(&a[i], &a[j], max_dist_x, max_dist_y, bw, chn_pen_gap, chn_pen_skip, is_cdna, n_seg);
|
177
|
+
++n_iter;
|
178
|
+
if (sc == INT32_MIN) continue;
|
179
|
+
sc += f[j];
|
180
|
+
if (sc > max_f) {
|
181
|
+
max_f = sc, max_j = j;
|
182
|
+
if (n_skip > 0) --n_skip;
|
183
|
+
} else if (t[j] == (int32_t)i) {
|
184
|
+
if (++n_skip > max_skip)
|
185
|
+
break;
|
186
|
+
}
|
187
|
+
if (p[j] >= 0) t[p[j]] = i;
|
188
|
+
}
|
189
|
+
end_j = j;
|
190
|
+
if (max_ii < 0 || a[i].x - a[max_ii].x > (int64_t)max_dist_x) {
|
191
|
+
int32_t max = INT32_MIN;
|
192
|
+
max_ii = -1;
|
193
|
+
for (j = i - 1; j >= st; --j)
|
194
|
+
if (max < f[j]) max = f[j], max_ii = j;
|
195
|
+
}
|
196
|
+
if (max_ii >= 0 && max_ii < end_j) {
|
197
|
+
int32_t tmp;
|
198
|
+
tmp = comput_sc(&a[i], &a[max_ii], max_dist_x, max_dist_y, bw, chn_pen_gap, chn_pen_skip, is_cdna, n_seg);
|
199
|
+
if (tmp != INT32_MIN && max_f < tmp + f[max_ii])
|
200
|
+
max_f = tmp + f[max_ii], max_j = max_ii;
|
201
|
+
}
|
202
|
+
f[i] = max_f, p[i] = max_j;
|
203
|
+
v[i] = max_j >= 0 && v[max_j] > max_f? v[max_j] : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
|
204
|
+
if (max_ii < 0 || (a[i].x - a[max_ii].x <= (int64_t)max_dist_x && f[max_ii] < f[i]))
|
205
|
+
max_ii = i;
|
206
|
+
if (mmax_f < max_f) mmax_f = max_f;
|
207
|
+
}
|
208
|
+
|
209
|
+
u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
|
210
|
+
*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
|
211
|
+
kfree(km, p); kfree(km, f); kfree(km, t);
|
212
|
+
if (n_u == 0) {
|
213
|
+
kfree(km, a); kfree(km, v);
|
214
|
+
return 0;
|
215
|
+
}
|
216
|
+
return compact_a(km, n_u, u, n_v, v, a);
|
217
|
+
}
|
218
|
+
|
219
|
+
typedef struct lc_elem_s {
|
220
|
+
int32_t y;
|
221
|
+
int64_t i;
|
222
|
+
double pri;
|
223
|
+
KRMQ_HEAD(struct lc_elem_s) head;
|
224
|
+
} lc_elem_t;
|
225
|
+
|
226
|
+
#define lc_elem_cmp(a, b) ((a)->y < (b)->y? -1 : (a)->y > (b)->y? 1 : ((a)->i > (b)->i) - ((a)->i < (b)->i))
|
227
|
+
#define lc_elem_lt2(a, b) ((a)->pri < (b)->pri)
|
228
|
+
KRMQ_INIT(lc_elem, lc_elem_t, head, lc_elem_cmp, lc_elem_lt2)
|
229
|
+
|
230
|
+
KALLOC_POOL_INIT(rmq, lc_elem_t)
|
231
|
+
|
232
|
+
static inline int32_t comput_sc_simple(const mm128_t *ai, const mm128_t *aj, float chn_pen_gap, float chn_pen_skip, int32_t *exact, int32_t *width)
|
233
|
+
{
|
234
|
+
int32_t dq = (int32_t)ai->y - (int32_t)aj->y, dr, dd, dg, q_span, sc;
|
235
|
+
dr = (int32_t)(ai->x - aj->x);
|
236
|
+
*width = dd = dr > dq? dr - dq : dq - dr;
|
237
|
+
dg = dr < dq? dr : dq;
|
238
|
+
q_span = aj->y>>32&0xff;
|
239
|
+
sc = q_span < dg? q_span : dg;
|
240
|
+
if (exact) *exact = (dd == 0 && dg <= q_span);
|
241
|
+
if (dd || dq > q_span) {
|
242
|
+
float lin_pen, log_pen;
|
243
|
+
lin_pen = chn_pen_gap * (float)dd + chn_pen_skip * (float)dg;
|
244
|
+
log_pen = dd >= 1? mg_log2(dd + 1) : 0.0f; // mg_log2() only works for dd>=2
|
245
|
+
sc -= (int)(lin_pen + .5f * log_pen);
|
246
|
+
}
|
247
|
+
return sc;
|
248
|
+
}
|
249
|
+
|
250
|
+
mm128_t *mg_lchain_rmq(int max_dist, int max_dist_inner, int bw, int max_chn_skip, int cap_rmq_size, int min_cnt, int min_sc, float chn_pen_gap, float chn_pen_skip,
|
251
|
+
int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
|
252
|
+
{
|
253
|
+
int32_t *f,*t, *v, n_u, n_v, mmax_f = 0, max_rmq_size = 0, max_drop = bw;
|
254
|
+
int64_t *p, i, i0, st = 0, st_inner = 0, n_iter = 0;
|
255
|
+
uint64_t *u;
|
256
|
+
lc_elem_t *root = 0, *root_inner = 0;
|
257
|
+
void *mem_mp = 0;
|
258
|
+
kmp_rmq_t *mp;
|
259
|
+
|
260
|
+
if (_u) *_u = 0, *n_u_ = 0;
|
261
|
+
if (n == 0 || a == 0) {
|
262
|
+
kfree(km, a);
|
263
|
+
return 0;
|
264
|
+
}
|
265
|
+
if (max_dist < bw) max_dist = bw;
|
266
|
+
if (max_dist_inner <= 0 || max_dist_inner >= max_dist) max_dist_inner = 0;
|
267
|
+
KMALLOC(km, p, n);
|
268
|
+
KMALLOC(km, f, n);
|
269
|
+
KCALLOC(km, t, n);
|
270
|
+
KMALLOC(km, v, n);
|
271
|
+
mem_mp = km_init2(km, 0x10000);
|
272
|
+
mp = kmp_init_rmq(mem_mp);
|
273
|
+
|
274
|
+
// fill the score and backtrack arrays
|
275
|
+
for (i = i0 = 0; i < n; ++i) {
|
276
|
+
int64_t max_j = -1;
|
277
|
+
int32_t q_span = a[i].y>>32&0xff, max_f = q_span;
|
278
|
+
lc_elem_t s, *q, *r, lo, hi;
|
279
|
+
// add in-range anchors
|
280
|
+
if (i0 < i && a[i0].x != a[i].x) {
|
281
|
+
int64_t j;
|
282
|
+
for (j = i0; j < i; ++j) {
|
283
|
+
q = kmp_alloc_rmq(mp);
|
284
|
+
q->y = (int32_t)a[j].y, q->i = j, q->pri = -(f[j] + 0.5 * chn_pen_gap * ((int32_t)a[j].x + (int32_t)a[j].y));
|
285
|
+
krmq_insert(lc_elem, &root, q, 0);
|
286
|
+
if (max_dist_inner > 0) {
|
287
|
+
r = kmp_alloc_rmq(mp);
|
288
|
+
*r = *q;
|
289
|
+
krmq_insert(lc_elem, &root_inner, r, 0);
|
290
|
+
}
|
291
|
+
}
|
292
|
+
i0 = i;
|
293
|
+
}
|
294
|
+
// get rid of active chains out of range
|
295
|
+
while (st < i && (a[i].x>>32 != a[st].x>>32 || a[i].x > a[st].x + max_dist || krmq_size(head, root) > cap_rmq_size)) {
|
296
|
+
s.y = (int32_t)a[st].y, s.i = st;
|
297
|
+
if ((q = krmq_find(lc_elem, root, &s, 0)) != 0) {
|
298
|
+
q = krmq_erase(lc_elem, &root, q, 0);
|
299
|
+
kmp_free_rmq(mp, q);
|
300
|
+
}
|
301
|
+
++st;
|
302
|
+
}
|
303
|
+
if (max_dist_inner > 0) { // similar to the block above, but applied to the inner tree
|
304
|
+
while (st_inner < i && (a[i].x>>32 != a[st_inner].x>>32 || a[i].x > a[st_inner].x + max_dist_inner || krmq_size(head, root_inner) > cap_rmq_size)) {
|
305
|
+
s.y = (int32_t)a[st_inner].y, s.i = st_inner;
|
306
|
+
if ((q = krmq_find(lc_elem, root_inner, &s, 0)) != 0) {
|
307
|
+
q = krmq_erase(lc_elem, &root_inner, q, 0);
|
308
|
+
kmp_free_rmq(mp, q);
|
309
|
+
}
|
310
|
+
++st_inner;
|
311
|
+
}
|
312
|
+
}
|
313
|
+
// RMQ
|
314
|
+
lo.i = INT32_MAX, lo.y = (int32_t)a[i].y - max_dist;
|
315
|
+
hi.i = 0, hi.y = (int32_t)a[i].y;
|
316
|
+
if ((q = krmq_rmq(lc_elem, root, &lo, &hi)) != 0) {
|
317
|
+
int32_t sc, exact, width, n_skip = 0;
|
318
|
+
int64_t j = q->i;
|
319
|
+
assert(q->y >= lo.y && q->y <= hi.y);
|
320
|
+
sc = f[j] + comput_sc_simple(&a[i], &a[j], chn_pen_gap, chn_pen_skip, &exact, &width);
|
321
|
+
if (width <= bw && sc > max_f) max_f = sc, max_j = j;
|
322
|
+
if (!exact && root_inner && (int32_t)a[i].y > 0) {
|
323
|
+
lc_elem_t *lo, *hi;
|
324
|
+
s.y = (int32_t)a[i].y - 1, s.i = n;
|
325
|
+
krmq_interval(lc_elem, root_inner, &s, &lo, &hi);
|
326
|
+
if (lo) {
|
327
|
+
const lc_elem_t *q;
|
328
|
+
int32_t width, n_rmq_iter = 0;
|
329
|
+
krmq_itr_t(lc_elem) itr;
|
330
|
+
krmq_itr_find(lc_elem, root_inner, lo, &itr);
|
331
|
+
while ((q = krmq_at(&itr)) != 0) {
|
332
|
+
if (q->y < (int32_t)a[i].y - max_dist_inner) break;
|
333
|
+
++n_rmq_iter;
|
334
|
+
j = q->i;
|
335
|
+
sc = f[j] + comput_sc_simple(&a[i], &a[j], chn_pen_gap, chn_pen_skip, 0, &width);
|
336
|
+
if (width <= bw) {
|
337
|
+
if (sc > max_f) {
|
338
|
+
max_f = sc, max_j = j;
|
339
|
+
if (n_skip > 0) --n_skip;
|
340
|
+
} else if (t[j] == (int32_t)i) {
|
341
|
+
if (++n_skip > max_chn_skip)
|
342
|
+
break;
|
343
|
+
}
|
344
|
+
if (p[j] >= 0) t[p[j]] = i;
|
345
|
+
}
|
346
|
+
if (!krmq_itr_prev(lc_elem, &itr)) break;
|
347
|
+
}
|
348
|
+
n_iter += n_rmq_iter;
|
349
|
+
}
|
350
|
+
}
|
351
|
+
}
|
352
|
+
// set max
|
353
|
+
assert(max_j < 0 || (a[max_j].x < a[i].x && (int32_t)a[max_j].y < (int32_t)a[i].y));
|
354
|
+
f[i] = max_f, p[i] = max_j;
|
355
|
+
v[i] = max_j >= 0 && v[max_j] > max_f? v[max_j] : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
|
356
|
+
if (mmax_f < max_f) mmax_f = max_f;
|
357
|
+
if (max_rmq_size < krmq_size(head, root)) max_rmq_size = krmq_size(head, root);
|
358
|
+
}
|
359
|
+
km_destroy(mem_mp);
|
360
|
+
|
361
|
+
u = mg_chain_backtrack(km, n, f, p, v, t, min_cnt, min_sc, max_drop, &n_u, &n_v);
|
362
|
+
*n_u_ = n_u, *_u = u; // NB: note that u[] may not be sorted by score here
|
363
|
+
kfree(km, p); kfree(km, f); kfree(km, t);
|
364
|
+
if (n_u == 0) {
|
365
|
+
kfree(km, a); kfree(km, v);
|
366
|
+
return 0;
|
367
|
+
}
|
368
|
+
return compact_a(km, n_u, u, n_v, v, a);
|
369
|
+
}
|