SeqAlign (empty) → 0.1.0.0
raw patch · 7 files changed
+893/−0 lines, 7 filesdep +basedep +bytestringdep +vectorsetup-changed
Dependencies added: base, bytestring, vector
Files
- Alignment.hs +93/−0
- LICENSE +12/−0
- SeqAlign.cabal +20/−0
- Setup.hs +2/−0
- cbits/editdist.c +82/−0
- cbits/ksw.c +633/−0
- cbits/sw.c +51/−0
+ Alignment.hs view
@@ -0,0 +1,93 @@+{-# LANGUAGE OverloadedStrings #-}+module Alignment where++import Foreign.Ptr+import Foreign.ForeignPtr.Safe+import Foreign.ForeignPtr.Unsafe+import Foreign.Storable+import Foreign.Marshal.Alloc+import Foreign.C.Types+import Control.Applicative+import System.IO.Unsafe+import Data.Word+import qualified Data.ByteString.Internal as B+import qualified Data.ByteString.Char8 as B+import Data.ByteString.Unsafe+import qualified Data.Vector.Storable as V+import Data.Bits++foreign import ccall unsafe "c_degenshtein" cDist :: Ptr Word8 -> CSize -> Ptr Word8 -> CSize -> IO CInt++editDistance :: B.ByteString -> B.ByteString -> Int+editDistance b1@(B.PS ps1 s1 l1) b2@(B.PS ps2 s2 l2) = unsafePerformIO $ do + let p1 = unsafeForeignPtrToPtr ps1+ let p2 = unsafeForeignPtrToPtr ps2+ r <- cDist (castPtr p1 `plusPtr` s1) (fromIntegral l1) (castPtr p2 `plusPtr` s2) (fromIntegral l2)+ touchForeignPtr ps1+ touchForeignPtr ps2+ return (fromIntegral r)++data KSWR = KSWR {+ score :: CInt,+ targend :: CInt,+ querend :: CInt,+ score2 :: CInt,+ targend2 :: CInt,+ targbeg :: CInt,+ querbeg :: CInt } deriving (Show, Read, Eq)++instance Storable KSWR where+ sizeOf _ = 28+ alignment = sizeOf+ peek ptr = KSWR <$> pb 0 <*> pb 4 <*> pb 8 <*> pb 12 <*> pb 16 <*> pb 20 <*> pb 24 where + pb = peekByteOff ptr++foreign import ccall "default_align" cLocalAlign ::+ CInt -> Ptr Word8 -> CInt -> Ptr Word8 -> CInt -> CInt -> CInt -> Ptr KSWR -> IO ()++bs_align :: B.ByteString -> B.ByteString -> KSWR+bs_align (B.PS ptra offa lena) (B.PS ptrb offb lenb) = unsafePerformIO $ do+ let aptr = unsafeForeignPtrToPtr ptra `plusPtr` offa+ bptr = unsafeForeignPtrToPtr ptrb `plusPtr` offb+ kswrptr <- mallocBytes 28+ cLocalAlign (fromIntegral lena) aptr (fromIntegral lenb) bptr 5 2 (0x80000 + 0x40000) kswrptr+ kswr <- peek kswrptr+ touchForeignPtr ptra+ touchForeignPtr ptrb+ free kswrptr+ return kswr++foreign import ccall "cigar_align" cCigarAlign ::+ CInt -> Ptr Word8 -> CInt -> Ptr Word8 -> CInt -> CInt -> CInt -> Ptr CInt -> Ptr (Ptr CInt) -> IO CInt++foreign import ccall unsafe "static stdlib.h &free" free_finalizer+ :: FunPtr (Ptr a -> IO ())++cigar_align :: B.ByteString -> B.ByteString -> (Int, [(Char,Int)])+cigar_align (B.PS ptra offa lena) (B.PS ptrb offb lenb) = unsafePerformIO $ do+ let aptr = unsafeForeignPtrToPtr ptra `plusPtr` offa+ bptr = unsafeForeignPtrToPtr ptrb `plusPtr` offb+ ncigar_p <- mallocBytes 4+ cigar_pp <- mallocBytes 8+ r <- cCigarAlign (fromIntegral lena) aptr (fromIntegral lenb) bptr 1 1 10 ncigar_p cigar_pp+ ncigar <- peek ncigar_p+ cigar_p <- peek cigar_pp+ touchForeignPtr ptra+ touchForeignPtr ptrb+ free ncigar_p+ free cigar_pp+ fp <- newForeignPtr free_finalizer cigar_p+ let v = V.unsafeFromForeignPtr0 fp (fromIntegral ncigar)+ cigar = map pcigar $ V.toList v+ pcigar i = (code, fromIntegral $ i `shiftR` 4) where+ code = case i .&. 15 of+ 0 -> 'M'+ 1 -> 'I'+ 2 -> 'D'+ 3 -> 'N'+ 4 -> 'S'+ 5 -> 'H'+ 6 -> 'P'+ 7 -> '='+ 8 -> 'X'+ return (fromIntegral r, cigar)
+ LICENSE view
@@ -0,0 +1,12 @@+Copyright (c) 2014-2015, Rob O'Callahan+All rights reserved.++Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:++1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.++2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.++3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.++THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ SeqAlign.cabal view
@@ -0,0 +1,20 @@+name: SeqAlign+version: 0.1.0.0+synopsis: Sequence Alignment+description: FFI wrappers for global and local string alignment functions+license: BSD3+license-file: LICENSE+author: Rob O'Callahan+maintainer: rcallahan@eurekagenomics.com+copyright: (c) 2014-2015 Rob O'Callahan+build-type: Simple+cabal-version: >=1.10++library+ exposed-modules: Alignment+ other-extensions: OverloadedStrings+ build-depends: base >=4.6 && <5, bytestring, vector+ c-sources: cbits/editdist.c cbits/ksw.c cbits/sw.c+ include-dirs: cbits+ default-language: Haskell2010+ cc-options: -O3 -fPIC
+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ cbits/editdist.c view
@@ -0,0 +1,82 @@+#define MIN2(a,b) (((a) < (b)) ? (a) : (b))+#define MIN3(x, y, z) MIN2(z, MIN2(x,y))+#define MIN5(v, w, x, y, z) MIN3(x, MIN2(y,z), MIN2(v,w))+#include <stdlib.h>+#include <stdint.h>++int c_hamming(const char *s1, const char *s2, int sz) {+ int dif = 0;+ int i;+ for (i=0; i<sz; i++)+ if (s1[i] != s2[i]) + dif++;+ + return dif;+}++int c_levenshtein(const char *s1, int sz1, const char *s2, int sz2) {+ int i, j;++ int matrix[sz1+1][sz2+1];++ for(i=0;i<=sz1;i++){+ matrix[0][i]=i;+ }++ for(i=0;i<=sz2;i++){+ matrix[i][0]=i;+ }++ for(i=1; i<=sz1; i++){+ for (j=1; j<=sz2;j++){+ matrix[i][j]=MIN3(matrix[i-1][j]+1 , matrix[i][j-1]+1, matrix[i-1][j-1]+ ((s1[i-1]==s2[j-1])?0:1 ) );+ }+ }++ return matrix[sz1][sz2];+}++static const uint8_t degeneracies[256] = {+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,+ 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 1, 14, 2, 13, 0, 0, 4, 11, 15, 0, 12, 0, 3, 15, 0, + 0, 0, 5, 6, 8, 8, 7, 9, 0, 10, 0, 0, 0, 0, 0, 0, + 0, 1, 14, 2, 13, 0, 0, 4, 11, 15, 0, 12, 0, 3, 15, 0, + 0, 0, 5, 6, 8, 8, 7, 9, 0, 10, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, + 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0+};++inline int degen_eq(char a, char b) {+ return !(degeneracies[a] & degeneracies[b]);+}++int c_degenshtein(const char *s1, int sz1, const char *s2, int sz2){+ int i, j;++ int matrix[sz1+1][sz2+1];++ for(i=0;i<=sz1;i++){+ matrix[0][i]=i;+ }++ for(i=0;i<=sz2;i++){+ matrix[i][0]=i;+ }++ for(i=1; i<=sz1; i++){+ for (j=1; j<=sz2;j++){+ matrix[i][j]=MIN3(matrix[i-1][j]+1 , matrix[i][j-1]+1, matrix[i-1][j-1]+ degen_eq(s1[i-1], s2[j-1]));+ }+ }++ return matrix[sz1][sz2];+}
+ cbits/ksw.c view
@@ -0,0 +1,633 @@+/* The MIT License++ Copyright (c) 2011 by Attractive Chaos <attractor@live.co.uk>++ Permission is hereby granted, free of charge, to any person obtaining+ a copy of this software and associated documentation files (the+ "Software"), to deal in the Software without restriction, including+ without limitation the rights to use, copy, modify, merge, publish,+ distribute, sublicense, and/or sell copies of the Software, and to+ permit persons to whom the Software is furnished to do so, subject to+ the following conditions:++ The above copyright notice and this permission notice shall be+ included in all copies or substantial portions of the Software.++ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS+ BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN+ ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE+ SOFTWARE.+*/++#include <stdlib.h>+#include <stdint.h>+#include <emmintrin.h>+#include "ksw.h"++#ifdef __GNUC__+#define LIKELY(x) __builtin_expect((x),1)+#define UNLIKELY(x) __builtin_expect((x),0)+#else+#define LIKELY(x) (x)+#define UNLIKELY(x) (x)+#endif++const kswr_t g_defr = { 0, -1, -1, -1, -1, -1, -1 };++struct _kswq_t {+ int qlen, slen;+ uint8_t shift, mdiff, max, size;+ __m128i *qp, *H0, *H1, *E, *Hmax;+};++/**+ * Initialize the query data structure+ *+ * @param size Number of bytes used to store a score; valid valures are 1 or 2+ * @param qlen Length of the query sequence+ * @param query Query sequence+ * @param m Size of the alphabet+ * @param mat Scoring matrix in a one-dimension array+ *+ * @return Query data structure+ */+kswq_t *ksw_qinit(int size, int qlen, const uint8_t *query, int m, const int8_t *mat)+{+ kswq_t *q;+ int slen, a, tmp, p;++ size = size > 1? 2 : 1;+ p = 8 * (3 - size); // # values per __m128i+ slen = (qlen + p - 1) / p; // segmented length+ q = (kswq_t*)malloc(sizeof(kswq_t) + 256 + 16 * slen * (m + 4)); // a single block of memory+ q->qp = (__m128i*)(((size_t)q + sizeof(kswq_t) + 15) >> 4 << 4); // align memory+ q->H0 = q->qp + slen * m;+ q->H1 = q->H0 + slen;+ q->E = q->H1 + slen;+ q->Hmax = q->E + slen;+ q->slen = slen; q->qlen = qlen; q->size = size;+ // compute shift+ tmp = m * m;+ for (a = 0, q->shift = 127, q->mdiff = 0; a < tmp; ++a) { // find the minimum and maximum score+ if (mat[a] < (int8_t)q->shift) q->shift = mat[a];+ if (mat[a] > (int8_t)q->mdiff) q->mdiff = mat[a];+ }+ q->max = q->mdiff;+ q->shift = 256 - q->shift; // NB: q->shift is uint8_t+ q->mdiff += q->shift; // this is the difference between the min and max scores+ // An example: p=8, qlen=19, slen=3 and segmentation:+ // {{0,3,6,9,12,15,18,-1},{1,4,7,10,13,16,-1,-1},{2,5,8,11,14,17,-1,-1}}+ if (size == 1) {+ int8_t *t = (int8_t*)q->qp;+ for (a = 0; a < m; ++a) {+ int i, k, nlen = slen * p;+ const int8_t *ma = mat + a * m;+ for (i = 0; i < slen; ++i)+ for (k = i; k < nlen; k += slen) // p iterations+ *t++ = (k >= qlen? 0 : ma[query[k]]) + q->shift;+ }+ } else {+ int16_t *t = (int16_t*)q->qp;+ for (a = 0; a < m; ++a) {+ int i, k, nlen = slen * p;+ const int8_t *ma = mat + a * m;+ for (i = 0; i < slen; ++i)+ for (k = i; k < nlen; k += slen) // p iterations+ *t++ = (k >= qlen? 0 : ma[query[k]]);+ }+ }+ return q;+}++kswr_t ksw_u8(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e)+{+ int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;+ uint64_t *b;+ __m128i zero, gapoe, gape, shift, *H0, *H1, *E, *Hmax;+ kswr_t r;++#define __max_16(ret, xx) do { \+ (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 8)); \+ (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 4)); \+ (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 2)); \+ (xx) = _mm_max_epu8((xx), _mm_srli_si128((xx), 1)); \+ (ret) = _mm_extract_epi16((xx), 0) & 0x00ff; \+ } while (0)++ // initialization+ r = g_defr;+ minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;+ endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;+ m_b = n_b = 0; b = 0;+ zero = _mm_set1_epi32(0);+ gapoe = _mm_set1_epi8(_gapo + _gape);+ gape = _mm_set1_epi8(_gape);+ shift = _mm_set1_epi8(q->shift);+ H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;+ slen = q->slen;+ for (i = 0; i < slen; ++i) {+ _mm_store_si128(E + i, zero);+ _mm_store_si128(H0 + i, zero);+ _mm_store_si128(Hmax + i, zero);+ }+ // the core loop+ for (i = 0; i < tlen; ++i) {+ int j, k, cmp, imax;+ __m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector+ h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example+ h = _mm_slli_si128(h, 1); // h=H(i-1,-1); << instead of >> because x64 is little-endian+ for (j = 0; LIKELY(j < slen); ++j) {+ /* SW cells are computed in the following order:+ * H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}+ * E(i+1,j) = max{H(i,j)-q, E(i,j)-r}+ * F(i,j+1) = max{H(i,j)-q, F(i,j)-r}+ */+ // compute H'(i,j); note that at the beginning, h=H'(i-1,j-1)+ h = _mm_adds_epu8(h, _mm_load_si128(S + j));+ h = _mm_subs_epu8(h, shift); // h=H'(i-1,j-1)+S(i,j)+ e = _mm_load_si128(E + j); // e=E'(i,j)+ h = _mm_max_epu8(h, e);+ h = _mm_max_epu8(h, f); // h=H'(i,j)+ max = _mm_max_epu8(max, h); // set max+ _mm_store_si128(H1 + j, h); // save to H'(i,j)+ // now compute E'(i+1,j)+ h = _mm_subs_epu8(h, gapoe); // h=H'(i,j)-gapo+ e = _mm_subs_epu8(e, gape); // e=E'(i,j)-gape+ e = _mm_max_epu8(e, h); // e=E'(i+1,j)+ _mm_store_si128(E + j, e); // save to E'(i+1,j)+ // now compute F'(i,j+1)+ f = _mm_subs_epu8(f, gape);+ f = _mm_max_epu8(f, h);+ // get H'(i-1,j) and prepare for the next j+ h = _mm_load_si128(H0 + j); // h=H'(i-1,j)+ }+ // NB: we do not need to set E(i,j) as we disallow adjecent insertion and then deletion+ for (k = 0; LIKELY(k < 16); ++k) { // this block mimics SWPS3; NB: H(i,j) updated in the lazy-F loop cannot exceed max+ f = _mm_slli_si128(f, 1);+ for (j = 0; LIKELY(j < slen); ++j) {+ h = _mm_load_si128(H1 + j);+ h = _mm_max_epu8(h, f); // h=H'(i,j)+ _mm_store_si128(H1 + j, h);+ h = _mm_subs_epu8(h, gapoe);+ f = _mm_subs_epu8(f, gape);+ cmp = _mm_movemask_epi8(_mm_cmpeq_epi8(_mm_subs_epu8(f, h), zero));+ if (UNLIKELY(cmp == 0xffff)) goto end_loop16;+ }+ }+end_loop16:+ //int k;for (k=0;k<16;++k)printf("%d ", ((uint8_t*)&max)[k]);printf("\n");+ __max_16(imax, max); // imax is the maximum number in max+ if (imax >= minsc) { // write the b array; this condition adds branching unfornately+ if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) { // then append+ if (n_b == m_b) {+ m_b = m_b? m_b<<1 : 8;+ b = (uint64_t*)realloc(b, 8 * m_b);+ }+ b[n_b++] = (uint64_t)imax<<32 | i;+ } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last+ }+ if (imax > gmax) {+ gmax = imax; te = i; // te is the end position on the target+ for (j = 0; LIKELY(j < slen); ++j) // keep the H1 vector+ _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));+ if (gmax + q->shift >= 255 || gmax >= endsc) break;+ }+ S = H1; H1 = H0; H0 = S; // swap H0 and H1+ }+ r.score = gmax + q->shift < 255? gmax : 255;+ r.te = te;+ if (r.score != 255) { // get a->qe, the end of query match; find the 2nd best score+ int max = -1, low, high, qlen = slen * 16;+ uint8_t *t = (uint8_t*)Hmax;+ for (i = 0; i < qlen; ++i, ++t)+ if ((int)*t > max) max = *t, r.qe = i / 16 + i % 16 * slen;+ //printf("%d,%d\n", max, gmax);+ if (b) {+ i = (r.score + q->max - 1) / q->max;+ low = te - i; high = te + i;+ for (i = 0; i < n_b; ++i) {+ int e = (int32_t)b[i];+ if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)+ r.score2 = b[i]>>32, r.te2 = e;+ }+ }+ }+ free(b);+ return r;+}++kswr_t ksw_i16(kswq_t *q, int tlen, const uint8_t *target, int _gapo, int _gape, int xtra) // the first gap costs -(_o+_e)+{+ int slen, i, m_b, n_b, te = -1, gmax = 0, minsc, endsc;+ uint64_t *b;+ __m128i zero, gapoe, gape, *H0, *H1, *E, *Hmax;+ kswr_t r;++#define __max_8(ret, xx) do { \+ (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 8)); \+ (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 4)); \+ (xx) = _mm_max_epi16((xx), _mm_srli_si128((xx), 2)); \+ (ret) = _mm_extract_epi16((xx), 0); \+ } while (0)++ // initialization+ r = g_defr;+ minsc = (xtra&KSW_XSUBO)? xtra&0xffff : 0x10000;+ endsc = (xtra&KSW_XSTOP)? xtra&0xffff : 0x10000;+ m_b = n_b = 0; b = 0;+ zero = _mm_set1_epi32(0);+ gapoe = _mm_set1_epi16(_gapo + _gape);+ gape = _mm_set1_epi16(_gape);+ H0 = q->H0; H1 = q->H1; E = q->E; Hmax = q->Hmax;+ slen = q->slen;+ for (i = 0; i < slen; ++i) {+ _mm_store_si128(E + i, zero);+ _mm_store_si128(H0 + i, zero);+ _mm_store_si128(Hmax + i, zero);+ }+ // the core loop+ for (i = 0; i < tlen; ++i) {+ int j, k, imax;+ __m128i e, h, f = zero, max = zero, *S = q->qp + target[i] * slen; // s is the 1st score vector+ h = _mm_load_si128(H0 + slen - 1); // h={2,5,8,11,14,17,-1,-1} in the above example+ h = _mm_slli_si128(h, 2);+ for (j = 0; LIKELY(j < slen); ++j) {+ h = _mm_adds_epi16(h, *S++);+ e = _mm_load_si128(E + j);+ h = _mm_max_epi16(h, e);+ h = _mm_max_epi16(h, f);+ max = _mm_max_epi16(max, h);+ _mm_store_si128(H1 + j, h);+ h = _mm_subs_epu16(h, gapoe);+ e = _mm_subs_epu16(e, gape);+ e = _mm_max_epi16(e, h);+ _mm_store_si128(E + j, e);+ f = _mm_subs_epu16(f, gape);+ f = _mm_max_epi16(f, h);+ h = _mm_load_si128(H0 + j);+ }+ for (k = 0; LIKELY(k < 16); ++k) {+ f = _mm_slli_si128(f, 2);+ for (j = 0; LIKELY(j < slen); ++j) {+ h = _mm_load_si128(H1 + j);+ h = _mm_max_epi16(h, f);+ _mm_store_si128(H1 + j, h);+ h = _mm_subs_epu16(h, gapoe);+ f = _mm_subs_epu16(f, gape);+ if(UNLIKELY(!_mm_movemask_epi8(_mm_cmpgt_epi16(f, h)))) goto end_loop8;+ }+ }+end_loop8:+ __max_8(imax, max);+ if (imax >= minsc) {+ if (n_b == 0 || (int32_t)b[n_b-1] + 1 != i) {+ if (n_b == m_b) {+ m_b = m_b? m_b<<1 : 8;+ b = (uint64_t*)realloc(b, 8 * m_b);+ }+ b[n_b++] = (uint64_t)imax<<32 | i;+ } else if ((int)(b[n_b-1]>>32) < imax) b[n_b-1] = (uint64_t)imax<<32 | i; // modify the last+ }+ if (imax > gmax) {+ gmax = imax; te = i;+ for (j = 0; LIKELY(j < slen); ++j)+ _mm_store_si128(Hmax + j, _mm_load_si128(H1 + j));+ if (gmax >= endsc) break;+ }+ S = H1; H1 = H0; H0 = S;+ }+ r.score = gmax; r.te = te;+ {+ int max = -1, low, high, qlen = slen * 8;+ uint16_t *t = (uint16_t*)Hmax;+ for (i = 0, r.qe = -1; i < qlen; ++i, ++t)+ if ((int)*t > max) max = *t, r.qe = i / 8 + i % 8 * slen;+ if (b) {+ i = (r.score + q->max - 1) / q->max;+ low = te - i; high = te + i;+ for (i = 0; i < n_b; ++i) {+ int e = (int32_t)b[i];+ if ((e < low || e > high) && (int)(b[i]>>32) > r.score2)+ r.score2 = b[i]>>32, r.te2 = e;+ }+ }+ }+ free(b);+ return r;+}++static void revseq(int l, uint8_t *s)+{+ int i, t;+ for (i = 0; i < l>>1; ++i)+ t = s[i], s[i] = s[l - 1 - i], s[l - 1 - i] = t;+}++kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry)+{+ int size;+ kswq_t *q;+ kswr_t r, rr;+ kswr_t (*func)(kswq_t*, int, const uint8_t*, int, int, int);++ q = (qry && *qry)? *qry : ksw_qinit((xtra&KSW_XBYTE)? 1 : 2, qlen, query, m, mat);+ if (qry && *qry == 0) *qry = q;+ func = q->size == 2? ksw_i16 : ksw_u8;+ size = q->size;+ r = func(q, tlen, target, gapo, gape, xtra);+ if (qry == 0) free(q);+ if ((xtra&KSW_XSTART) == 0 || ((xtra&KSW_XSUBO) && r.score < (xtra&0xffff))) return r;+ revseq(r.qe + 1, query); revseq(r.te + 1, target); // +1 because qe/te points to the exact end, not the position after the end+ q = ksw_qinit(size, r.qe + 1, query, m, mat);+ rr = func(q, tlen, target, gapo, gape, KSW_XSTOP | r.score);+ revseq(r.qe + 1, query); revseq(r.te + 1, target);+ free(q);+ if (r.score == rr.score)+ r.tb = r.te - rr.te, r.qb = r.qe - rr.qe;+ return r;+}++/********************+ *** SW extension ***+ ********************/++typedef struct {+ int32_t h, e;+} eh_t;++int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle)+{+ eh_t *eh; // score array+ int8_t *qp; // query profile+ int i, j, k, gapoe = gapo + gape, beg, end, max, max_i, max_j, max_gap;+ if (h0 < 0) h0 = 0;+ // allocate memory+ qp = malloc(qlen * m);+ eh = calloc(qlen + 1, 8);+ // generate the query profile+ for (k = i = 0; k < m; ++k) {+ const int8_t *p = &mat[k * m];+ for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];+ }+ // fill the first row+ eh[0].h = h0; eh[1].h = h0 > gapoe? h0 - gapoe : 0;+ for (j = 2; j <= qlen && eh[j-1].h > gape; ++j)+ eh[j].h = eh[j-1].h - gape;+ // adjust $w if it is too large+ k = m * m;+ for (i = 0, max = 0; i < k; ++i) // get the max score+ max = max > mat[i]? max : mat[i];+ max_gap = (int)((double)(qlen * max - gapo) / gape + 1.);+ max_gap = max_gap > 1? max_gap : 1;+ w = w < max_gap? w : max_gap;+ // DP loop+ max = h0, max_i = max_j = -1;+ beg = 0, end = qlen;+ for (i = 0; LIKELY(i < tlen); ++i) {+ int f = 0, h1, m = 0, mj = -1;+ int8_t *q = &qp[target[i] * qlen];+ // compute the first column+ h1 = h0 - (gapo + gape * (i + 1));+ if (h1 < 0) h1 = 0;+ // apply the band and the constraint (if provided)+ if (beg < i - w) beg = i - w;+ if (end > i + w + 1) end = i + w + 1;+ if (end > qlen) end = qlen;+ for (j = beg; LIKELY(j < end); ++j) {+ // At the beginning of the loop: eh[j] = { H(i-1,j-1), E(i,j) }, f = F(i,j) and h1 = H(i,j-1)+ // Similar to SSE2-SW, cells are computed in the following order:+ // H(i,j) = max{H(i-1,j-1)+S(i,j), E(i,j), F(i,j)}+ // E(i+1,j) = max{H(i,j)-gapo, E(i,j)} - gape+ // F(i,j+1) = max{H(i,j)-gapo, F(i,j)} - gape+ eh_t *p = &eh[j];+ int h = p->h, e = p->e; // get H(i-1,j-1) and E(i-1,j)+ p->h = h1; // set H(i,j-1) for the next row+ h += q[j];+ h = h > e? h : e;+ h = h > f? h : f;+ h1 = h; // save H(i,j) to h1 for the next column+ mj = m > h? mj : j;+ m = m > h? m : h; // m is stored at eh[mj+1]+ h -= gapoe;+ h = h > 0? h : 0;+ e -= gape;+ e = e > h? e : h; // computed E(i+1,j)+ p->e = e; // save E(i+1,j) for the next row+ f -= gape;+ f = f > h? f : h; // computed F(i,j+1)+ }+ eh[end].h = h1; eh[end].e = 0;+ if (m == 0) break;+ if (m > max) max = m, max_i = i, max_j = mj;+ // update beg and end for the next round+ for (j = mj; j >= beg && eh[j].h; --j);+ beg = j + 1;+ for (j = mj + 2; j <= end && eh[j].h; ++j);+ end = j;+ //beg = 0; end = qlen; // uncomment this line for debugging+ }+ free(eh); free(qp);+ if (_qle) *_qle = max_j + 1;+ if (_tle) *_tle = max_i + 1;+ return max;+}++/********************+ * Global alignment *+ ********************/++#define MINUS_INF -0x40000000++static inline uint32_t *push_cigar(int *n_cigar, int *m_cigar, uint32_t *cigar, int op, int len)+{+ if (*n_cigar == 0 || op != (cigar[(*n_cigar) - 1]&0xf)) {+ if (*n_cigar == *m_cigar) {+ *m_cigar = *m_cigar? (*m_cigar)<<1 : 4;+ cigar = realloc(cigar, (*m_cigar) << 2);+ }+ cigar[(*n_cigar)++] = len<<4 | op;+ } else cigar[(*n_cigar)-1] += len<<4;+ return cigar;+}++int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar_, uint32_t **cigar_)+{+ eh_t *eh;+ int8_t *qp; // query profile+ int i, j, k, gapoe = gapo + gape, score, n_col;+ uint8_t *z; // backtrack matrix; in each cell: f<<4|e<<2|h; in principle, we can halve the memory, but backtrack will be a little more complex+ if (n_cigar_) *n_cigar_ = 0;+ // allocate memory+ n_col = qlen < 2*w+1? qlen : 2*w+1; // maximum #columns of the backtrack matrix+ z = malloc(n_col * tlen);+ qp = malloc(qlen * m);+ eh = calloc(qlen + 1, 8);+ // generate the query profile+ for (k = i = 0; k < m; ++k) {+ const int8_t *p = &mat[k * m];+ for (j = 0; j < qlen; ++j) qp[i++] = p[query[j]];+ }+ // fill the first row+ eh[0].h = 0; eh[0].e = MINUS_INF;+ for (j = 1; j <= qlen && j <= w; ++j)+ eh[j].h = -(gapo + gape * j), eh[j].e = MINUS_INF;+ for (; j <= qlen; ++j) eh[j].h = eh[j].e = MINUS_INF; // everything is -inf outside the band+ // DP loop+ for (i = 0; LIKELY(i < tlen); ++i) { // target sequence is in the outer loop+ int32_t f = MINUS_INF, h1, beg, end;+ int8_t *q = &qp[target[i] * qlen];+ uint8_t *zi = &z[i * n_col];+ beg = i > w? i - w : 0;+ end = i + w + 1 < qlen? i + w + 1 : qlen; // only loop through [beg,end) of the query sequence+ h1 = beg == 0? -(gapo + gape * (i + 1)) : MINUS_INF;+ for (j = beg; LIKELY(j < end); ++j) {+ // This loop is organized in a similar way to ksw_extend() and ksw_sse2(), except:+ // 1) not checking h>0; 2) recording direction for backtracking+ eh_t *p = &eh[j];+ int32_t h = p->h, e = p->e;+ uint8_t d; // direction+ p->h = h1;+ h += q[j];+ d = h > e? 0 : 1;+ h = h > e? h : e;+ d = h > f? d : 2;+ h = h > f? h : f;+ h1 = h;+ h -= gapoe;+ e -= gape;+ d |= e > h? 1<<2 : 0;+ e = e > h? e : h;+ p->e = e;+ f -= gape;+ d |= f > h? 2<<4 : 0; // if we want to halve the memory, use one bit only, instead of two+ f = f > h? f : h;+ zi[j - beg] = d; // z[i,j] keeps h for the current cell and e/f for the next cell+ }+ eh[end].h = h1; eh[end].e = MINUS_INF;+ }+ score = eh[qlen].h;+ if (n_cigar_ && cigar_) { // backtrack+ int n_cigar = 0, m_cigar = 0, which = 0;+ uint32_t *cigar = 0, tmp;+ i = tlen - 1; k = (i + w + 1 < qlen? i + w + 1 : qlen) - 1; // (i,k) points to the last cell+ while (i >= 0 && k >= 0) {+ which = z[i * n_col + (k - (i > w? i - w : 0))] >> (which<<1) & 3;+ if (which == 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 0, 1), --i, --k;+ else if (which == 1) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, 1), --i;+ else cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, 1), --k;+ }+ if (i >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 2, i + 1);+ if (k >= 0) cigar = push_cigar(&n_cigar, &m_cigar, cigar, 1, k + 1);+ for (i = 0; i < n_cigar>>1; ++i) // reverse CIGAR+ tmp = cigar[i], cigar[i] = cigar[n_cigar-1-i], cigar[n_cigar-1-i] = tmp;+ *n_cigar_ = n_cigar, *cigar_ = cigar;+ }+ free(eh); free(qp); free(z);+ return score;+}++/*******************************************+ * Main function (not compiled by default) *+ *******************************************/++#ifdef _KSW_MAIN++#include <unistd.h>+#include <stdio.h>+#include <zlib.h>+#include "kseq.h"+KSEQ_INIT(gzFile, gzread)++unsigned char seq_nt4_table[256] = {+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4+};++int main(int argc, char *argv[])+{+ int c, sa = 1, sb = 3, i, j, k, forward_only = 0, max_rseq = 0;+ int8_t mat[25];+ int gapo = 5, gape = 2, minsc = 0, xtra = KSW_XSTART;+ uint8_t *rseq = 0;+ gzFile fpt, fpq;+ kseq_t *kst, *ksq;++ // parse command line+ while ((c = getopt(argc, argv, "a:b:q:r:ft:1")) >= 0) {+ switch (c) {+ case 'a': sa = atoi(optarg); break;+ case 'b': sb = atoi(optarg); break;+ case 'q': gapo = atoi(optarg); break;+ case 'r': gape = atoi(optarg); break;+ case 't': minsc = atoi(optarg); break;+ case 'f': forward_only = 1; break;+ case '1': xtra |= KSW_XBYTE; break;+ }+ }+ if (optind + 2 > argc) {+ fprintf(stderr, "Usage: ksw [-1] [-f] [-a%d] [-b%d] [-q%d] [-r%d] [-t%d] <target.fa> <query.fa>\n", sa, sb, gapo, gape, minsc);+ return 1;+ }+ if (minsc > 0xffff) minsc = 0xffff;+ xtra |= KSW_XSUBO | minsc;+ // initialize scoring matrix+ for (i = k = 0; i < 4; ++i) {+ for (j = 0; j < 4; ++j)+ mat[k++] = i == j? sa : -sb;+ mat[k++] = 0; // ambiguous base+ }+ for (j = 0; j < 5; ++j) mat[k++] = 0;+ // open file+ fpt = gzopen(argv[optind], "r"); kst = kseq_init(fpt);+ fpq = gzopen(argv[optind+1], "r"); ksq = kseq_init(fpq);+ // all-pair alignment+ while (kseq_read(ksq) > 0) {+ kswq_t *q[2] = {0, 0};+ kswr_t r;+ for (i = 0; i < (int)ksq->seq.l; ++i) ksq->seq.s[i] = seq_nt4_table[(int)ksq->seq.s[i]];+ if (!forward_only) { // reverse+ if ((int)ksq->seq.m > max_rseq) {+ max_rseq = ksq->seq.m;+ rseq = (uint8_t*)realloc(rseq, max_rseq);+ }+ for (i = 0, j = ksq->seq.l - 1; i < (int)ksq->seq.l; ++i, --j)+ rseq[j] = ksq->seq.s[i] == 4? 4 : 3 - ksq->seq.s[i];+ }+ gzrewind(fpt); kseq_rewind(kst);+ while (kseq_read(kst) > 0) {+ for (i = 0; i < (int)kst->seq.l; ++i) kst->seq.s[i] = seq_nt4_table[(int)kst->seq.s[i]];+ r = ksw_align(ksq->seq.l, (uint8_t*)ksq->seq.s, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[0]);+ if (r.score >= minsc)+ printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, r.qb, r.qe+1, r.score, r.score2, r.te2);+ if (rseq) {+ r = ksw_align(ksq->seq.l, rseq, kst->seq.l, (uint8_t*)kst->seq.s, 5, mat, gapo, gape, xtra, &q[1]);+ if (r.score >= minsc)+ printf("%s\t%d\t%d\t%s\t%d\t%d\t%d\t%d\t%d\n", kst->name.s, r.tb, r.te+1, ksq->name.s, (int)ksq->seq.l - r.qb, (int)ksq->seq.l - 1 - r.qe, r.score, r.score2, r.te2);+ }+ }+ free(q[0]); free(q[1]);+ }+ free(rseq);+ kseq_destroy(kst); gzclose(fpt);+ kseq_destroy(ksq); gzclose(fpq);+ return 0;+}+#endif
+ cbits/sw.c view
@@ -0,0 +1,51 @@+#include <stdlib.h>+#include <stdint.h>+#include "ksw.h"++static const int8_t default_mat[25] = {+ 1, -1, -1, -1, 0,+ -1, 1, -1, -1, 0,+ -1, -1, 1, -1, 0,+ -1, -1, -1, 1, 0,+ 0, 0, 0, 0, 0+};++static const uint8_t seq_nt4_table[256] = {+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4,+ 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 0, 4, 1, 4, 4, 4, 2, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, + 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4+};++inline void trans_nt4(char* qsq, uint8_t* qnt, int qlen) {+ int i;+ for (i = 0; i < qlen; i++) qnt[i] = seq_nt4_table[qsq[i]];+}++void default_align(int qlen, char *query, int tlen, char *target, int gapo, int gape, int xtra, kswr_t* ret) {+ uint8_t qnt4[qlen];+ trans_nt4(query, qnt4, qlen);+ uint8_t tnt4[tlen];+ trans_nt4(target, tnt4, tlen);+ *ret = ksw_align(qlen, qnt4, tlen, tnt4, 5, default_mat, gapo, gape, xtra, 0);+}++int cigar_align(int qlen, char *query, int tlen, char *target, int gapo, int gape, int w, int *n_cigar, uint32_t **cigar) {+ uint8_t qnt4[qlen];+ trans_nt4(query, qnt4, qlen);+ uint8_t tnt4[tlen];+ trans_nt4(target, tnt4, tlen);+ return ksw_global(qlen, qnt4, tlen, tnt4, 5, default_mat, gapo, gape, w, n_cigar, cigar);+}