--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/samtools-0.1.16/kaln.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,486 @@
+/* The MIT License
+
+   Copyright (c) 2003-2006, 2008, 2009, by Heng Li <lh3lh3@gmail.com>
+
+   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 <stdio.h>
+#include <string.h>
+#include <stdint.h>
+#include <math.h>
+#include "kaln.h"
+
+#define FROM_M 0
+#define FROM_I 1
+#define FROM_D 2
+
+typedef struct {
+	int i, j;
+	unsigned char ctype;
+} path_t;
+
+int aln_sm_blosum62[] = {
+/*	 A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  *  X */
+	 4,-1,-2,-2, 0,-1,-1, 0,-2,-1,-1,-1,-1,-2,-1, 1, 0,-3,-2, 0,-4, 0,
+	-1, 5, 0,-2,-3, 1, 0,-2, 0,-3,-2, 2,-1,-3,-2,-1,-1,-3,-2,-3,-4,-1,
+	-2, 0, 6, 1,-3, 0, 0, 0, 1,-3,-3, 0,-2,-3,-2, 1, 0,-4,-2,-3,-4,-1,
+	-2,-2, 1, 6,-3, 0, 2,-1,-1,-3,-4,-1,-3,-3,-1, 0,-1,-4,-3,-3,-4,-1,
+	 0,-3,-3,-3, 9,-3,-4,-3,-3,-1,-1,-3,-1,-2,-3,-1,-1,-2,-2,-1,-4,-2,
+	-1, 1, 0, 0,-3, 5, 2,-2, 0,-3,-2, 1, 0,-3,-1, 0,-1,-2,-1,-2,-4,-1,
+	-1, 0, 0, 2,-4, 2, 5,-2, 0,-3,-3, 1,-2,-3,-1, 0,-1,-3,-2,-2,-4,-1,
+	 0,-2, 0,-1,-3,-2,-2, 6,-2,-4,-4,-2,-3,-3,-2, 0,-2,-2,-3,-3,-4,-1,
+	-2, 0, 1,-1,-3, 0, 0,-2, 8,-3,-3,-1,-2,-1,-2,-1,-2,-2, 2,-3,-4,-1,
+	-1,-3,-3,-3,-1,-3,-3,-4,-3, 4, 2,-3, 1, 0,-3,-2,-1,-3,-1, 3,-4,-1,
+	-1,-2,-3,-4,-1,-2,-3,-4,-3, 2, 4,-2, 2, 0,-3,-2,-1,-2,-1, 1,-4,-1,
+	-1, 2, 0,-1,-3, 1, 1,-2,-1,-3,-2, 5,-1,-3,-1, 0,-1,-3,-2,-2,-4,-1,
+	-1,-1,-2,-3,-1, 0,-2,-3,-2, 1, 2,-1, 5, 0,-2,-1,-1,-1,-1, 1,-4,-1,
+	-2,-3,-3,-3,-2,-3,-3,-3,-1, 0, 0,-3, 0, 6,-4,-2,-2, 1, 3,-1,-4,-1,
+	-1,-2,-2,-1,-3,-1,-1,-2,-2,-3,-3,-1,-2,-4, 7,-1,-1,-4,-3,-2,-4,-2,
+	 1,-1, 1, 0,-1, 0, 0, 0,-1,-2,-2, 0,-1,-2,-1, 4, 1,-3,-2,-2,-4, 0,
+	 0,-1, 0,-1,-1,-1,-1,-2,-2,-1,-1,-1,-1,-2,-1, 1, 5,-2,-2, 0,-4, 0,
+	-3,-3,-4,-4,-2,-2,-3,-2,-2,-3,-2,-3,-1, 1,-4,-3,-2,11, 2,-3,-4,-2,
+	-2,-2,-2,-3,-2,-1,-2,-3, 2,-1,-1,-2,-1, 3,-3,-2,-2, 2, 7,-1,-4,-1,
+	 0,-3,-3,-3,-1,-2,-2,-3,-3, 3, 1,-2, 1,-1,-2,-2, 0,-3,-1, 4,-4,-1,
+	-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4, 1,-4,
+	 0,-1,-1,-1,-2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-2, 0, 0,-2,-1,-1,-4,-1
+};
+
+int aln_sm_blast[] = {
+	1, -3, -3, -3, -2,
+	-3, 1, -3, -3, -2,
+	-3, -3, 1, -3, -2,
+	-3, -3, -3, 1, -2,
+	-2, -2, -2, -2, -2
+};
+
+int aln_sm_qual[] = {
+	  0, -23, -23, -23, 0,
+	-23,   0, -23, -23, 0,
+	-23, -23,   0, -23, 0,
+	-23, -23, -23,   0, 0,
+	  0,   0,   0,   0, 0
+};
+
+ka_param_t ka_param_blast = {  5,  2,   5, 2, aln_sm_blast, 5, 50 };
+ka_param_t ka_param_aa2aa = { 10,  2,  10, 2, aln_sm_blosum62, 22, 50 };
+
+ka_param2_t ka_param2_qual  = { 37, 11, 37, 11, 37, 11, 0, 0, aln_sm_qual, 5, 50 };
+
+static uint32_t *ka_path2cigar32(const path_t *path, int path_len, int *n_cigar)
+{
+	int i, n;
+	uint32_t *cigar;
+	unsigned char last_type;
+
+	if (path_len == 0 || path == 0) {
+		*n_cigar = 0;
+		return 0;
+	}
+
+	last_type = path->ctype;
+	for (i = n = 1; i < path_len; ++i) {
+		if (last_type != path[i].ctype) ++n;
+		last_type = path[i].ctype;
+	}
+	*n_cigar = n;
+	cigar = (uint32_t*)calloc(*n_cigar, 4);
+
+	cigar[0] = 1u << 4 | path[path_len-1].ctype;
+	last_type = path[path_len-1].ctype;
+	for (i = path_len - 2, n = 0; i >= 0; --i) {
+		if (path[i].ctype == last_type) cigar[n] += 1u << 4;
+		else {
+			cigar[++n] = 1u << 4 | path[i].ctype;
+			last_type = path[i].ctype;
+		}
+	}
+
+	return cigar;
+}
+
+/***************************/
+/* START OF common_align.c */
+/***************************/
+
+#define SET_INF(s) (s).M = (s).I = (s).D = MINOR_INF;
+
+#define set_M(MM, cur, p, sc)							\
+{														\
+	if ((p)->M >= (p)->I) {								\
+		if ((p)->M >= (p)->D) {							\
+			(MM) = (p)->M + (sc); (cur)->Mt = FROM_M;	\
+		} else {										\
+			(MM) = (p)->D + (sc); (cur)->Mt = FROM_D;	\
+		}												\
+	} else {											\
+		if ((p)->I > (p)->D) {							\
+			(MM) = (p)->I + (sc); (cur)->Mt = FROM_I;	\
+		} else {										\
+			(MM) = (p)->D + (sc); (cur)->Mt = FROM_D;	\
+		}												\
+	}													\
+}
+#define set_I(II, cur, p)								\
+{														\
+	if ((p)->M - gap_open > (p)->I) {					\
+		(cur)->It = FROM_M;								\
+		(II) = (p)->M - gap_open - gap_ext;				\
+	} else {											\
+		(cur)->It = FROM_I;								\
+		(II) = (p)->I - gap_ext;						\
+	}													\
+}
+#define set_end_I(II, cur, p)							\
+{														\
+	if (gap_end_ext >= 0) {								\
+		if ((p)->M - gap_end_open > (p)->I) {			\
+			(cur)->It = FROM_M;							\
+			(II) = (p)->M - gap_end_open - gap_end_ext;	\
+		} else {										\
+			(cur)->It = FROM_I;							\
+			(II) = (p)->I - gap_end_ext;				\
+		}												\
+	} else set_I(II, cur, p);							\
+}
+#define set_D(DD, cur, p)								\
+{														\
+	if ((p)->M - gap_open > (p)->D) {					\
+		(cur)->Dt = FROM_M;								\
+		(DD) = (p)->M - gap_open - gap_ext;				\
+	} else {											\
+		(cur)->Dt = FROM_D;								\
+		(DD) = (p)->D - gap_ext;						\
+	}													\
+}
+#define set_end_D(DD, cur, p)							\
+{														\
+	if (gap_end_ext >= 0) {								\
+		if ((p)->M - gap_end_open > (p)->D) {			\
+			(cur)->Dt = FROM_M;							\
+			(DD) = (p)->M - gap_end_open - gap_end_ext;	\
+		} else {										\
+			(cur)->Dt = FROM_D;							\
+			(DD) = (p)->D - gap_end_ext;				\
+		}												\
+	} else set_D(DD, cur, p);							\
+}
+
+typedef struct {
+	uint8_t Mt:3, It:2, Dt:3;
+} dpcell_t;
+
+typedef struct {
+	int M, I, D;
+} dpscore_t;
+
+/***************************
+ * banded global alignment *
+ ***************************/
+uint32_t *ka_global_core(uint8_t *seq1, int len1, uint8_t *seq2, int len2, const ka_param_t *ap, int *_score, int *n_cigar)
+{
+	int i, j;
+	dpcell_t **dpcell, *q;
+	dpscore_t *curr, *last, *s;
+	int b1, b2, tmp_end;
+	int *mat, end, max = 0;
+	uint8_t type, ctype;
+	uint32_t *cigar = 0;
+
+	int gap_open, gap_ext, gap_end_open, gap_end_ext, b;
+	int *score_matrix, N_MATRIX_ROW;
+
+	/* initialize some align-related parameters. just for compatibility */
+	gap_open = ap->gap_open;
+	gap_ext = ap->gap_ext;
+	gap_end_open = ap->gap_end_open;
+	gap_end_ext = ap->gap_end_ext;
+	b = ap->band_width;
+	score_matrix = ap->matrix;
+	N_MATRIX_ROW = ap->row;
+
+	if (n_cigar) *n_cigar = 0;
+	if (len1 == 0 || len2 == 0) return 0;
+
+	/* calculate b1 and b2 */
+	if (len1 > len2) {
+		b1 = len1 - len2 + b;
+		b2 = b;
+	} else {
+		b1 = b;
+		b2 = len2 - len1 + b;
+	}
+	if (b1 > len1) b1 = len1;
+	if (b2 > len2) b2 = len2;
+	--seq1; --seq2;
+
+	/* allocate memory */
+	end = (b1 + b2 <= len1)? (b1 + b2 + 1) : (len1 + 1);
+	dpcell = (dpcell_t**)malloc(sizeof(dpcell_t*) * (len2 + 1));
+	for (j = 0; j <= len2; ++j)
+		dpcell[j] = (dpcell_t*)malloc(sizeof(dpcell_t) * end);
+	for (j = b2 + 1; j <= len2; ++j)
+		dpcell[j] -= j - b2;
+	curr = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
+	last = (dpscore_t*)malloc(sizeof(dpscore_t) * (len1 + 1));
+	
+	/* set first row */
+	SET_INF(*curr); curr->M = 0;
+	for (i = 1, s = curr + 1; i < b1; ++i, ++s) {
+		SET_INF(*s);
+		set_end_D(s->D, dpcell[0] + i, s - 1);
+	}
+	s = curr; curr = last; last = s;
+
+	/* core dynamic programming, part 1 */
+	tmp_end = (b2 < len2)? b2 : len2 - 1;
+	for (j = 1; j <= tmp_end; ++j) {
+		q = dpcell[j]; s = curr; SET_INF(*s);
+		set_end_I(s->I, q, last);
+		end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
+		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+		++s; ++q;
+		for (i = 1; i != end; ++i, ++s, ++q) {
+			set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
+			set_I(s->I, q, last + i);
+			set_D(s->D, q, s - 1);
+		}
+		set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+		set_D(s->D, q, s - 1);
+		if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
+			set_end_I(s->I, q, last + i);
+		} else s->I = MINOR_INF;
+		s = curr; curr = last; last = s;
+	}
+	/* last row for part 1, use set_end_D() instead of set_D() */
+	if (j == len2 && b2 != len2 - 1) {
+		q = dpcell[j]; s = curr; SET_INF(*s);
+		set_end_I(s->I, q, last);
+		end = (j + b1 <= len1 + 1)? (j + b1 - 1) : len1;
+		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+		++s; ++q;
+		for (i = 1; i != end; ++i, ++s, ++q) {
+			set_M(s->M, q, last + i - 1, mat[seq1[i]]); /* this will change s->M ! */
+			set_I(s->I, q, last + i);
+			set_end_D(s->D, q, s - 1);
+		}
+		set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+		set_end_D(s->D, q, s - 1);
+		if (j + b1 - 1 > len1) { /* bug fixed, 040227 */
+			set_end_I(s->I, q, last + i);
+		} else s->I = MINOR_INF;
+		s = curr; curr = last; last = s;
+		++j;
+	}
+
+	/* core dynamic programming, part 2 */
+	for (; j <= len2 - b2 + 1; ++j) {
+		SET_INF(curr[j - b2]);
+		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+		end = j + b1 - 1;
+		for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i != end; ++i, ++s, ++q) {
+			set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+			set_I(s->I, q, last + i);
+			set_D(s->D, q, s - 1);
+		}
+		set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+		set_D(s->D, q, s - 1);
+		s->I = MINOR_INF;
+		s = curr; curr = last; last = s;
+	}
+
+	/* core dynamic programming, part 3 */
+	for (; j < len2; ++j) {
+		SET_INF(curr[j - b2]);
+		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+		for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
+			set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+			set_I(s->I, q, last + i);
+			set_D(s->D, q, s - 1);
+		}
+		set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
+		set_end_I(s->I, q, last + i);
+		set_D(s->D, q, s - 1);
+		s = curr; curr = last; last = s;
+	}
+	/* last row */
+	if (j == len2) {
+		SET_INF(curr[j - b2]);
+		mat = score_matrix + seq2[j] * N_MATRIX_ROW;
+		for (i = j - b2 + 1, q = dpcell[j] + i, s = curr + i; i < len1; ++i, ++s, ++q) {
+			set_M(s->M, q, last + i - 1, mat[seq1[i]]);
+			set_I(s->I, q, last + i);
+			set_end_D(s->D, q, s - 1);
+		}
+		set_M(s->M, q, last + len1 - 1, mat[seq1[i]]);
+		set_end_I(s->I, q, last + i);
+		set_end_D(s->D, q, s - 1);
+		s = curr; curr = last; last = s;
+	}
+
+	*_score = last[len1].M;
+	if (n_cigar) { /* backtrace */
+		path_t *p, *path = (path_t*)malloc(sizeof(path_t) * (len1 + len2 + 2));
+		i = len1; j = len2;
+		q = dpcell[j] + i;
+		s = last + len1;
+		max = s->M; type = q->Mt; ctype = FROM_M;
+		if (s->I > max) { max = s->I; type = q->It; ctype = FROM_I; }
+		if (s->D > max) { max = s->D; type = q->Dt; ctype = FROM_D; }
+
+		p = path;
+		p->ctype = ctype; p->i = i; p->j = j; /* bug fixed 040408 */
+		++p;
+		do {
+			switch (ctype) {
+			case FROM_M: --i; --j; break;
+			case FROM_I: --j; break;
+			case FROM_D: --i; break;
+			}
+			q = dpcell[j] + i;
+			ctype = type;
+			switch (type) {
+			case FROM_M: type = q->Mt; break;
+			case FROM_I: type = q->It; break;
+			case FROM_D: type = q->Dt; break;
+			}
+			p->ctype = ctype; p->i = i; p->j = j;
+			++p;
+		} while (i || j);
+		cigar = ka_path2cigar32(path, p - path - 1, n_cigar);
+		free(path);
+	}
+
+	/* free memory */
+	for (j = b2 + 1; j <= len2; ++j)
+		dpcell[j] += j - b2;
+	for (j = 0; j <= len2; ++j)
+		free(dpcell[j]);
+	free(dpcell);
+	free(curr); free(last);
+
+	return cigar;
+}
+
+typedef struct {
+	int M, I, D;
+} score_aux_t;
+
+#define MINUS_INF -0x40000000
+
+// matrix: len2 rows and len1 columns
+int ka_global_score(const uint8_t *_seq1, int len1, const uint8_t *_seq2, int len2, const ka_param2_t *ap)
+{
+	
+#define __score_aux(_p, _q0, _sc, _io, _ie, _do, _de) {					\
+		int t1, t2;														\
+		score_aux_t *_q;												\
+		_q = _q0;														\
+		_p->M = _q->M >= _q->I? _q->M : _q->I;							\
+		_p->M = _p->M >= _q->D? _p->M : _q->D;							\
+		_p->M += (_sc);													\
+		++_q;      t1 = _q->M - _io - _ie; t2 = _q->I - _ie; _p->I = t1 >= t2? t1 : t2; \
+		_q = _p-1; t1 = _q->M - _do - _de; t2 = _q->D - _de; _p->D = t1 >= t2? t1 : t2; \
+	}
+
+	int i, j, bw, scmat_size = ap->row, *scmat = ap->matrix, ret;
+	const uint8_t *seq1, *seq2;
+	score_aux_t *curr, *last, *swap;
+	bw = abs(len1 - len2) + ap->band_width;
+	i = len1 > len2? len1 : len2;
+	if (bw > i + 1) bw = i + 1;
+	seq1 = _seq1 - 1; seq2 = _seq2 - 1;
+	curr = calloc(len1 + 2, sizeof(score_aux_t));
+	last = calloc(len1 + 2, sizeof(score_aux_t));
+	{ // the zero-th row
+		int x, end = len1;
+		score_aux_t *p;
+		j = 0;
+		x = j + bw; end = len1 < x? len1 : x; // band end
+		p = curr;
+		p->M = 0; p->I = p->D = MINUS_INF;
+		for (i = 1, p = &curr[1]; i <= end; ++i, ++p)
+			p->M = p->I = MINUS_INF, p->D = -(ap->edo + ap->ede * i);
+		p->M = p->I = p->D = MINUS_INF;
+		swap = curr; curr = last; last = swap;
+	}
+	for (j = 1; j < len2; ++j) {
+		int x, beg = 0, end = len1, *scrow, col_end;
+		score_aux_t *p;
+		x = j - bw; beg =    0 > x?    0 : x; // band start
+		x = j + bw; end = len1 < x? len1 : x; // band end
+		if (beg == 0) { // from zero-th column
+			p = curr;
+			p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j);
+			++beg; // then beg = 1
+		}
+		scrow = scmat + seq2[j] * scmat_size;
+		if (end == len1) col_end = 1, --end;
+		else col_end = 0;
+		for (i = beg, p = &curr[beg]; i <= end; ++i, ++p)
+			__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->ido, ap->ide);
+		if (col_end) {
+			__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->ido, ap->ide);
+			++p;
+		}
+		p->M = p->I = p->D = MINUS_INF;
+//		for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n');
+		swap = curr; curr = last; last = swap;
+	}
+	{ // the last row
+		int x, beg = 0, *scrow;
+		score_aux_t *p;
+		j = len2;
+		x = j - bw; beg = 0 > x?    0 : x; // band start
+		if (beg == 0) { // from zero-th column
+			p = curr;
+			p->M = p->D = MINUS_INF; p->I = -(ap->eio + ap->eie * j);
+			++beg; // then beg = 1
+		}
+		scrow = scmat + seq2[j] * scmat_size;
+		for (i = beg, p = &curr[beg]; i < len1; ++i, ++p)
+			__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->iio, ap->iie, ap->edo, ap->ede);
+		__score_aux(p, &last[i-1], scrow[(int)seq1[i]], ap->eio, ap->eie, ap->edo, ap->ede);
+//		for (i = 0; i <= len1; ++i) printf("(%d,%d,%d) ", curr[i].M, curr[i].I, curr[i].D); putchar('\n');
+	}
+	ret = curr[len1].M >= curr[len1].I? curr[len1].M : curr[len1].I;
+	ret = ret >= curr[len1].D? ret : curr[len1].D;
+	free(curr); free(last);
+	return ret;
+}
+
+#ifdef _MAIN
+int main(int argc, char *argv[])
+{
+//	int len1 = 35, len2 = 35;
+//	uint8_t *seq1 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\0\1";
+//	uint8_t *seq2 = (uint8_t*)"\0\0\3\3\2\0\0\0\1\0\2\1\2\1\3\2\3\3\3\0\2\3\2\1\1\3\3\3\2\3\3\1\0\1\0";
+	int len1 = 4, len2 = 4;
+	uint8_t *seq1 = (uint8_t*)"\1\0\0\1";
+	uint8_t *seq2 = (uint8_t*)"\1\0\1\0";
+	int sc;
+//	ka_global_core(seq1, 2, seq2, 1, &ka_param_qual, &sc, 0);
+	sc = ka_global_score(seq1, len1, seq2, len2, &ka_param2_qual);
+	printf("%d\n", sc);
+	return 0;
+}
+#endif