X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=misc%2Fwgsim.c;h=7b5f095d910b06f3242419066ac8879b7cdb7454;hb=6ad0dc55ff3abf908a99935321ff8fa5efed4d88;hp=485dce1ac1da06cf4054c4d5a391871f929adb2a;hpb=bf2e331f1f15f89fd6dfc046333592fa76dec3d2;p=samtools.git

diff --git a/misc/wgsim.c b/misc/wgsim.c
index 485dce1..7b5f095 100644
--- a/misc/wgsim.c
+++ b/misc/wgsim.c
@@ -39,7 +39,7 @@
 #include <ctype.h>
 #include <string.h>
 
-#define PACKAGE_VERSION "0.2.2"
+#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, 
@@ -238,7 +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
@@ -304,7 +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) {
@@ -366,6 +366,7 @@ 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;				\
 					}													\