Make repeated seeks possible

Repeated seeks with implicitly created region list wouldn't initialize
all internal structures to the original clean state, as demonstrated by
the issue #1362, resolved by this commit

synced_bcf_reader.c

@@ -838,6 +838,7 @@ static void bcf_sr_seek_start(bcf_srs_t *readers)
     for (i=0; i<reg->nseqs; i++)
         reg->regs[i].creg = -1;
     reg->iseq = 0;
+    reg->prev_seq = -1;
 }
 
 
@@ -851,8 +852,18 @@ int bcf_sr_seek(bcf_srs_t *readers, const char *seq, hts_pos_t pos)
         bcf_sr_seek_start(readers);
         return 0;
     }
-    bcf_sr_regions_overlap(readers->regions, seq, pos, pos);
+
     int i, nret = 0;
+
+    // Need to position both the readers and the regions. The latter is a bit of a mess
+    // because we can have in memory or external regions. The safe way is:
+    //  - reset all regions as if they were not read from at all (bcf_sr_seek_start)
+    //  - find the requested iseq (stored in the seq_hash)
+    //  - position regions to the requested position (bcf_sr_regions_overlap)
+    bcf_sr_seek_start(readers);
+    if ( khash_str2int_get(readers->regions->seq_hash, seq, &i)>=0 ) readers->regions->iseq = i;
+    bcf_sr_regions_overlap(readers->regions, seq, pos, pos);
+
     for (i=0; i<readers->nreaders; i++)
     {
         nret += _reader_seek(&readers->readers[i],seq,pos,MAX_CSI_COOR-1);