r280: tolerate a freebayes weirdo; not assert fail

lh3 · Mar 23, 2016 · 479f2fe · 479f2fe
1 parent c7f8b56
commit 479f2fe
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/atomic.c b/atomic.c
@@ -163,8 +163,9 @@ void bcf_atomize(const bcf_hdr_t *h, bcf1_t *b, bcf_atom_v *a)
 						bcf_add_atom(a, b->rid, b->pos + x + j, 1, i, 1, &b->d.allele[0][x+j], 1, &b->d.allele[i][y+j]);
 				x += l, y += l;
 			} else if (*p == 'I') {
-				assert(x > 0 && y > 0);
-				bcf_add_atom(a, b->rid, b->pos + x - 1, 1, i, 1, &b->d.allele[0][x-1], l+1, &b->d.allele[i][y-1]);
+				if (x == 0 || y == 0)
+					fprintf(stderr, "[W::%s] invalid insertion (%d,%d) at %s:%d\n", __func__, x, y, h->id[BCF_DT_CTG][b->rid].key, b->pos + 1);
+				else bcf_add_atom(a, b->rid, b->pos + x - 1, 1, i, 1, &b->d.allele[0][x-1], l+1, &b->d.allele[i][y-1]);
 				y += l;
 			} else if (*p == 'D') {
 				assert(x > 0 && y > 0);

diff --git a/main.c b/main.c
@@ -3,7 +3,7 @@
 #include <string.h>
 #include <ctype.h>
 
-#define BGT_VERSION "1.0-r279-dirty"
+#define BGT_VERSION "1.0-r280-dirty"
 
 int main_import(int argc, char *argv[]);
 int main_view(int argc, char *argv[]);