--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyPRADA_1.2/tools/bwa-0.5.7-mh/cs2nt.c	Thu Feb 20 00:44:58 2014 -0500
@@ -0,0 +1,191 @@
+#include <string.h>
+#include <stdint.h>
+#include <stdlib.h>
+#include "bwtaln.h"
+#include "stdaln.h"
+
+/*
+  Here is a delicate example. ref_nt=ATTAAC(RBRBG), read_cs=RBBOG. If we
+  decode as ATTGAC(RBGOG), there are one color change and one nt change;
+  if we decode as ATTAAC(RBRBG), there are two color changes.
+
+  In DP, if color quality is smaller than COLOR_MM, we will use COLOR_MM
+  as the penalty; otherwise, we will use color quality as the
+  penalty. This means we always prefer two consistent color changes over
+  a nt change, but if a color has high quality, we may prefer one nt
+  change.
+
+  In the above example, the penalties of the two types of decoding are
+  q(B)+25 and q(B)+q(O), respectively. If q(O)>25, we prefer the first;
+  otherwise the second. Note that no matter what we choose, the fourth
+  base will get a low nt quality.
+ */
+
+#define COLOR_MM 19
+#define NUCL_MM  25
+
+static const int nst_ntnt2cs_table[] = { 4, 0, 0, 1, 0, 2, 3, 4, 0, 3, 2, 4, 1, 4, 4, 4 };
+
+/*
+  {A,C,G,T,N} -> {0,1,2,3,4}
+  nt_ref[0..size]: nucleotide reference: 0/1/2/3/4
+  cs_read[0..size-1]: color read+qual sequence: base<<6|qual; qual==63 for N
+  nt_read[0..size]: nucleotide read sequence: 0/1/2/3 (returned)
+  btarray[0..4*size]: backtrack array (working space)
+ */
+void cs2nt_DP(int size, const uint8_t *nt_ref, const uint8_t *cs_read, uint8_t *nt_read, uint8_t *btarray)
+{
+	int h[8], curr, last;
+	int x, y, xmin, hmin, k;
+
+	// h[0..3] and h[4..7] are the current and last best score array, depending on curr and last
+
+	// recursion: initial value
+	if (nt_ref[0] >= 4) memset(h, 0, sizeof(int) << 2);
+	else {
+		for (x = 0; x != 4; ++x) h[x] = NUCL_MM;
+		h[nt_ref[0]] = 0;
+	}
+	// recursion: main loop
+	curr = 1; last = 0;
+	for (k = 1; k <= size; ++k) {
+		for (x = 0; x != 4; ++x) {
+			int min = 0x7fffffff, ymin = 0;
+			for (y = 0; y != 4; ++y) {
+				int s = h[last<<2|y];
+				if ((cs_read[k-1]&0x3f) != 63 && cs_read[k-1]>>6 != nst_ntnt2cs_table[1<<x|1<<y])
+					s += ((cs_read[k-1]&0x3f) < COLOR_MM)? COLOR_MM : (cs_read[k-1]&0x3f); // color mismatch
+				if (nt_ref[k] < 4 && nt_ref[k] != x) s += NUCL_MM; // nt mismatch
+				if (s < min) {
+					min = s; ymin = y;
+				}
+			}
+			h[curr<<2|x] = min; btarray[k<<2|x] = ymin;
+		}
+		last = curr; curr = 1 - curr; // swap
+	}
+	// back trace
+	hmin = 0x7fffffff; xmin = 0;
+	for (x = 0; x != 4; ++x) {
+		if (h[last<<2|x] < hmin) {
+			hmin = h[last<<2|x]; xmin = x;
+		}
+	}
+	nt_read[size] = xmin;
+	for (k = size - 1; k >= 0; --k)
+		nt_read[k] = btarray[(k+1)<<2 | nt_read[k+1]];
+}
+/*
+  nt_read[0..size]: nucleotide read sequence: 0/1/2/3
+  cs_read[0..size-1]: color read+qual sequence: base<<6|qual; qual==63 for N
+  tarray[0..size*2-1]: temporary array
+ */
+uint8_t *cs2nt_nt_qual(int size, const uint8_t *nt_read, const uint8_t *cs_read, uint8_t *tarray)
+{
+	int k, c1, c2;
+	uint8_t *t2array = tarray + size;
+	// get the color sequence of nt_read
+	c1 = nt_read[0];
+	for (k = 1; k <= size; ++k) {
+		c2 = nt_read[k]; // in principle, there is no 'N' in nt_read[]; just in case
+		tarray[k-1] = (c1 >= 4 || c2 >= 4)? 4 : nst_ntnt2cs_table[1<<c1 | 1<<c2];
+		c1 = c2;
+	}
+	for (k = 1; k != size; ++k) {
+		int q = 0;
+		if (tarray[k-1] == cs_read[k-1]>>6 && tarray[k] == cs_read[k]>>6) {
+			q = (int)(cs_read[k-1]&0x3f) + (int)(cs_read[k]&0x3f) + 10;
+		} else if (tarray[k-1] == cs_read[k-1]>>6) {
+			q = (int)(cs_read[k-1]&0x3f) - (int)(cs_read[k]&0x3f);
+		} else if (tarray[k] == cs_read[k]>>6) {
+			q = (int)(cs_read[k]&0x3f) - (int)(cs_read[k-1]&0x3f);
+		} // else, q = 0
+		if (q < 0) q = 0;
+		if (q > 60) q = 60;
+		t2array[k] = nt_read[k]<<6 | q;
+		if ((cs_read[k-1]&0x3f) == 63 || (cs_read[k]&0x3f) == 63) t2array[k] = 0;
+	}
+	return t2array + 1; // of size-2
+}
+
+// this function will be called when p->seq has been reversed by refine_gapped()
+void bwa_cs2nt_core(bwa_seq_t *p, bwtint_t l_pac, ubyte_t *pac)
+{
+	uint8_t *ta, *nt_read, *btarray, *tarray, *nt_ref, *cs_read, *new_nt_read;
+	int i, len;
+	uint8_t *seq;
+
+	// set temporary arrays
+	if (p->type == BWA_TYPE_NO_MATCH) return;
+	len = p->len + p->n_gapo + p->n_gape + 100; // leave enough space
+	ta = (uint8_t*)malloc(len * 7);
+	nt_ref = ta;
+	cs_read = nt_ref + len;
+	nt_read = cs_read + len;
+	btarray = nt_read + len;
+	tarray = nt_read + len;
+
+#define __gen_csbase(_cs, _i, _seq) do {							\
+		int q = p->qual[p->strand? p->len - 1 - (_i) : (_i)] - 33;	\
+		if (q > 60) q = 60;											\
+		if (_seq[_i] > 3) q = 63;									\
+		(_cs) = _seq[_i]<<6 | q;									\
+	} while (0)
+
+	// generate len, nt_ref[] and cs_read
+	seq = p->strand? p->rseq : p->seq;
+	nt_ref[0] = p->pos? bns_pac(pac, p->pos-1) : 4;
+	if (p->cigar == 0) { // no gap or clipping
+		len = p->len;
+		for (i = 0; i < p->len; ++i) {
+			__gen_csbase(cs_read[i], i, seq);
+			nt_ref[i+1] = bns_pac(pac, p->pos + i);
+		}
+	} else {
+		int k, z;
+		bwtint_t x, y;
+		x = p->pos; y = 0;
+		for (k = z = 0; k < p->n_cigar; ++k) {
+			int l = __cigar_len(p->cigar[k]);
+			if (__cigar_op(p->cigar[k]) == FROM_M) {
+				for (i = 0; i < l; ++i, ++x, ++y) {
+					__gen_csbase(cs_read[z], y, seq);
+					nt_ref[z+1] = bns_pac(pac, x);
+					++z;
+				}
+			} else if (__cigar_op(p->cigar[k]) == FROM_I) {
+				for (i = 0; i < l; ++i, ++y) {
+					__gen_csbase(cs_read[z], y, seq);
+					nt_ref[z+1] = 4;
+					++z;
+				}
+			} else if (__cigar_op(p->cigar[k]) == FROM_S) y += l;
+			else x += l;
+		}
+		len = z;
+	}
+
+	cs2nt_DP(len, nt_ref, cs_read, nt_read, btarray);
+	new_nt_read = cs2nt_nt_qual(len, nt_read, cs_read, tarray);
+
+	// update p
+	p->len = p->full_len = len - 1;
+	for (i = 0; i < p->len; ++i) {
+		if ((new_nt_read[i]&0x3f) == 63) {
+			p->qual[i] = 33; seq[i] = 4;
+		} else {
+			p->qual[i] = (new_nt_read[i]&0x3f) + 33;
+			seq[i] = new_nt_read[i]>>6;
+		}
+	}
+	p->qual[p->len] = seq[p->len] = 0;
+	if (p->strand) {
+		memcpy(p->seq, seq, p->len);
+		seq_reverse(p->len, p->seq, 1);
+		seq_reverse(p->len, p->qual, 0);
+	} else {
+		memcpy(p->rseq, seq, p->len);
+		seq_reverse(p->len, p->rseq, 1);
+	}
+	free(ta);
+}