Use hts_pos_t in tweak_overlap_quality() and related functions

While not strictly necessary (the positions in question are
relative to that of read 'b') it makes data types consistent
and reduces the possibility of accidental overflow.

Also adds a check that the position in the sequence is valid
before trying to use it for array look-ups.

Author: daviesrob

sam.c

@@ -4015,9 +4015,9 @@ void bam_plp_destructor(bam_plp_t plp,
  *  Returns BAM_CMATCH, -1 when there is no more cigar to process or the requested position is not covered,
  *  or -2 on error.
  */
-static inline int cigar_iref2iseq_set(uint32_t **cigar, uint32_t *cigar_max, int *icig, int *iseq, hts_pos_t *iref)
+static inline int cigar_iref2iseq_set(uint32_t **cigar, uint32_t *cigar_max, hts_pos_t *icig, hts_pos_t *iseq, hts_pos_t *iref)
 {
-    int pos = *iref;
+    hts_pos_t pos = *iref;
     if ( pos < 0 ) return -1;
     *icig = 0;
     *iseq = 0;
@@ -4050,7 +4050,7 @@ static inline int cigar_iref2iseq_set(uint32_t **cigar, uint32_t *cigar_max, int
     *iseq = -1;
     return -1;
 }
-static inline int cigar_iref2iseq_next(uint32_t **cigar, uint32_t *cigar_max, int *icig, int *iseq, hts_pos_t *iref)
+static inline int cigar_iref2iseq_next(uint32_t **cigar, uint32_t *cigar_max, hts_pos_t *icig, hts_pos_t *iseq, hts_pos_t *iref)
 {
     while ( *cigar < cigar_max )
     {
@@ -4079,8 +4079,8 @@ static int tweak_overlap_quality(bam1_t *a, bam1_t *b)
 {
     uint32_t *a_cigar = bam_get_cigar(a), *a_cigar_max = a_cigar + a->core.n_cigar;
     uint32_t *b_cigar = bam_get_cigar(b), *b_cigar_max = b_cigar + b->core.n_cigar;
-    int a_icig = 0, a_iseq = 0;
-    int b_icig = 0, b_iseq = 0;
+    hts_pos_t a_icig = 0, a_iseq = 0;
+    hts_pos_t b_icig = 0, b_iseq = 0;
     uint8_t *a_qual = bam_get_qual(a), *b_qual = bam_get_qual(b);
     uint8_t *a_seq  = bam_get_seq(a), *b_seq = bam_get_seq(b);
 
@@ -4114,6 +4114,9 @@ static int tweak_overlap_quality(bam1_t *a, bam1_t *b)
         iref++;
         if ( a_iref+a->core.pos != b_iref+b->core.pos ) continue;   // only CMATCH positions, don't know what to do with indels
 
+        if (a_iseq > a->core.l_qseq || b_iseq > b->core.l_qseq)
+            return -1;  // Fell off end of sequence, bad CIGAR?
+
         if ( bam_seqi(a_seq,a_iseq) == bam_seqi(b_seq,b_iseq) )
         {
             #if DBG