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ad08966)
* fixed a bug in mpileup which causes segfaults
* bcftools: do not segfault when BCF contains errors
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0;
do {
mplp_aux_t *ma = (mplp_aux_t*)data;
int ret, skip = 0;
do {
- int has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
if (ret < 0) break;
ret = ma->iter? bam_iter_read(ma->fp, ma->iter, b) : bam_read1(ma->fp, b);
if (ret < 0) break;
+ has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0;
skip = 0;
if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
if (has_ref && ma->capQ_thres > 10) {
skip = 0;
if (has_ref && (ma->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, 1);
if (has_ref && ma->capQ_thres > 10) {
#endif
#ifndef PACKAGE_VERSION
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.11 (r851)"
+#define PACKAGE_VERSION "0.1.11-1 (r858)"
#endif
int bam_taf2baf(int argc, char *argv[]);
#endif
int bam_taf2baf(int argc, char *argv[]);
}
bgzf_read(bp->fp, b->str, b->l_str);
l = 12 + b->l_str;
}
bgzf_read(bp->fp, b->str, b->l_str);
l = 12 + b->l_str;
+ if (bcf_sync(b) < 0) return -2;
for (i = 0; i < b->n_gi; ++i) {
bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
l += b->gi[i].len * h->n_smpl;
for (i = 0; i < b->n_gi; ++i) {
bgzf_read(bp->fp, b->gi[i].data, b->gi[i].len * h->n_smpl);
l += b->gi[i].len * h->n_smpl;