* wgsim-0.2.1

[samtools.git] / misc / wgsim.c

diff --git a/misc/wgsim.c b/misc/wgsim.c
index 1ae7572a6a6aff77b04acfea9f6fd194f3ee6f3e..46c9ff9bcda84686a124f37e6cf8de57915cbb54 100644 (file)
--- 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 "0.2.1"
 
 const uint8_t nst_nt4_table[256] = {
        4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4,  4, 4, 4, 4, 
@@ -352,14 +352,11 @@ 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) { \
@@ -372,7 +369,7 @@ void wgsim_core(FILE *fpout1, FILE *fpout2, FILE *fp_fa, int is_hap, uint64_t N,
                                                        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 +385,7 @@ 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 +421,9 @@ 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);
+                               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);
                                for (i = 0; i < s[j]; ++i)
                                        fputc("ACGTN"[(int)tmp_seq[j][i]], fpo[j]);
                                fprintf(fpo[j], "\n+\n%s\n", qstr);