X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;ds=sidebyside;f=misc%2Fwgsim.c;h=7b5f095d910b06f3242419066ac8879b7cdb7454;hb=6ad0dc55ff3abf908a99935321ff8fa5efed4d88;hp=1ae7572a6a6aff77b04acfea9f6fd194f3ee6f3e;hpb=115b2e9f98151f208207aae6286acd12adf019de;p=samtools.git

diff --git a/misc/wgsim.c b/misc/wgsim.c
index 1ae7572..7b5f095 100644
--- a/misc/wgsim.c
+++ b/misc/wgsim.c
@@ -39,7 +39,7 @@
 #include <ctype.h>
 #include <string.h>
 
-#define PACKAGE_VERSION "0.2.0"
+#define PACKAGE_VERSION "0.2.3"
 
 const uint8_t nst_nt4_table[256] = {
 	4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
@@ -173,6 +173,7 @@ static double MUT_RATE = 0.001;
 static double INDEL_FRAC = 0.1;
 static double INDEL_EXTEND = 0.3;
 static int IS_SOLID = 0;
+static int SHOW_MM_INFO = 1;
 
 void maq_mut_diref(const seq_t *seq, int is_hap, mutseq_t *hap1, mutseq_t *hap2)
 {
@@ -237,7 +238,7 @@ void maq_print_mutref(const char *name, const seq_t *seq, mutseq_t *hap1, mutseq
 		c[0] = nst_nt4_table[(int)seq->s[i]];
 		c[1] = hap1->s[i]; c[2] = hap2->s[i];
 		if (c[0] >= 4) continue;
-		if ((c[1] & mutmsk) != NOCHANGE || (c[1] & mutmsk) != NOCHANGE) {
+		if ((c[1] & mutmsk) != NOCHANGE || (c[2] & mutmsk) != NOCHANGE) {
 			printf("%s\t%d\t", name, i+1);
 			if (c[1] == c[2]) { // hom
 				if ((c[1]&mutmsk) == SUBSTITUTE) { // substitution
@@ -303,7 +304,7 @@ void wgsim_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int is_hap, uint64_t N,
 	tmp_seq[1] = (uint8_t*)calloc(l+2, 1);
 	size[0] = size_l; size[1] = size_r;
 
-	Q = (int)(-10.0 * log(ERR_RATE) / log(10.0) + 0.499) + 33;
+	Q = (ERR_RATE == 0.0)? 'I' : (int)(-10.0 * log(ERR_RATE) / log(10.0) + 0.499) + 33;
 
 	tot_len = n_ref = 0;
 	while ((l = seq_read_fasta(fp_fa, &seq, name, 0)) >= 0) {
@@ -352,14 +353,11 @@ void wgsim_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int is_hap, uint64_t N,
 			n_sub[0] = n_sub[1] = n_indel[0] = n_indel[1] = n_err[0] = n_err[1] = 0;
 
 #define __gen_read(x, start, iter) do {									\
-				for (i = (start), k = 0, ext_coor[x] = -1; i >= 0 && i < seq.l && k < s[x]; iter) {	\
+				for (i = (start), k = 0, ext_coor[x] = -10; i >= 0 && i < seq.l && k < s[x]; iter) {	\
 					int c = target[i], mut_type = c & mutmsk;			\
 					if (ext_coor[x] < 0) {								\
+						if (mut_type != NOCHANGE && mut_type != SUBSTITUTE) continue; \
 						ext_coor[x] = i;								\
-						if (mut_type != NOCHANGE && mut_type != SUBSTITUTE) { \
-							ext_coor[x] = -1;							\
-							break;										\
-						}												\
 					}													\
 					if (mut_type == DELETE) ++n_indel[x];				\
 					else if (mut_type == NOCHANGE || mut_type == SUBSTITUTE) { \
@@ -368,11 +366,12 @@ void wgsim_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int is_hap, uint64_t N,
 					} else {											\
 						int n, ins;										\
 						++n_indel[x];									\
+						tmp_seq[x][k++] = c & 0xf;						\
 						for (n = mut_type>>12, ins = c>>4; n > 0 && k < s[x]; --n, ins >>= 2) \
 							tmp_seq[x][k++] = ins & 0x3;				\
 					}													\
 				}														\
-				if (k != s[x]) ext_coor[x] = -1;						\
+				if (k != s[x]) ext_coor[x] = -10;						\
 			} while (0)
 
 			if (!IS_SOLID) {
@@ -388,6 +387,7 @@ void wgsim_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int is_hap, uint64_t N,
 				} else { // FF pair
 					__gen_read(0, pos, ++i);
 					__gen_read(1, pos + d - 1 - s[1], ++i);
+					++ext_coor[0]; ++ext_coor[1];
 				}
 				// change to color sequence: (0,1,2,3) -> (A,C,G,T)
 				for (j = 0; j < 2; ++j) {
@@ -423,8 +423,15 @@ void wgsim_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int is_hap, uint64_t N,
 			for (j = 0; j < 2; ++j) {
 				for (i = 0; i < s[j]; ++i) qstr[i] = Q;
 				qstr[i] = 0;
-				fprintf(fpo[j], "@%s_%u_%u_%d:%d:%d_%llx/%d\n", name, ext_coor[0]+1, ext_coor[1]+1,
-						n_err[j], n_sub[j], n_indel[j], (long long)ii, j==0? is_flip+1 : 2-is_flip);
+				if (SHOW_MM_INFO) {
+					fprintf(fpo[j], "@%s_%u_%u_%d:%d:%d_%d:%d:%d_%llx/%d\n", name, ext_coor[0]+1, ext_coor[1]+1,
+							n_err[0], n_sub[0], n_indel[0], n_err[1], n_sub[1], n_indel[1],
+							(long long)ii, j==0? is_flip+1 : 2-is_flip);
+				} else {
+					fprintf(fpo[j], "@%s_%u_%u_%llx/%d %d:%d:%d_%d:%d:%d\n", name, ext_coor[0]+1, ext_coor[1]+1,
+							(long long)ii, j==0? is_flip+1 : 2-is_flip,
+							n_err[0], n_sub[0], n_indel[0], n_err[1], n_sub[1], n_indel[1]);
+				}
 				for (i = 0; i < s[j]; ++i)
 					fputc("ACGTN"[(int)tmp_seq[j][i]], fpo[j]);
 				fprintf(fpo[j], "\n+\n%s\n", qstr);
@@ -453,6 +460,7 @@ static int simu_usage()
 	fprintf(stderr, "         -R FLOAT      fraction of indels [%.2f]\n", INDEL_FRAC);
 	fprintf(stderr, "         -X FLOAT      probability an indel is extended [%.2f]\n", INDEL_EXTEND);
 	fprintf(stderr, "         -c            generate reads in color space (SOLiD reads)\n");
+	fprintf(stderr, "         -C            show mismatch info in comment rather than read name\n");
 	fprintf(stderr, "         -h            haplotype mode\n");
 	fprintf(stderr, "\n");
 	fprintf(stderr, "Note: For SOLiD reads, the first read is F3 and the second is R3.\n\n");
@@ -467,7 +475,7 @@ int main(int argc, char *argv[])
 
 	N = 1000000; dist = 500; std_dev = 50;
 	size_l = size_r = 70;
-	while ((c = getopt(argc, argv, "e:d:s:N:1:2:r:R:hX:c")) >= 0) {
+	while ((c = getopt(argc, argv, "e:d:s:N:1:2:r:R:hX:cC")) >= 0) {
 		switch (c) {
 		case 'd': dist = atoi(optarg); break;
 		case 's': std_dev = atoi(optarg); break;
@@ -479,6 +487,7 @@ int main(int argc, char *argv[])
 		case 'R': INDEL_FRAC = atof(optarg); break;
 		case 'X': INDEL_EXTEND = atof(optarg); break;
 		case 'c': IS_SOLID = 1; break;
+		case 'C': SHOW_MM_INFO = 0; break;
 		case 'h': is_hap = 1; break;
 		}
 	}