make pileup work with CIGAR with I/D at the beginning or in the end

diff --git a/bam_pileup.c b/bam_pileup.c
index d9a75da013eecf772336bf5a03ef9baa4851b41d..3c41a169127fcc5d3977df3e8febd944b7ced77e 100644 (file)
--- a/bam_pileup.c
+++ b/bam_pileup.c
@@ -73,18 +73,28 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
                                p->qpos = y + (pos - x);
                                if (x == pos && is_restart) p->is_head = 1;
                                if (x + l - 1 == pos) { // come to the end of a match
-                                       if (k < c->n_cigar - 1) { // there are additional operation(s)
+                                       int has_next_match = 0;
+                                       unsigned i;
+                                       for (i = k + 1; i < c->n_cigar; ++i) {
+                                               uint32_t cigar = bam1_cigar(b)[i];
+                                               int opi = cigar&BAM_CIGAR_MASK;
+                                               if (opi == BAM_CMATCH) {
+                                                       has_next_match = 1;
+                                                       break;
+                                               } else if (opi == BAM_CSOFT_CLIP || opi == BAM_CREF_SKIP || opi == BAM_CHARD_CLIP) break;
+                                       }
+                                       if (!has_next_match) p->is_tail = 1;
+                                       if (k < c->n_cigar - 1 && has_next_match) { // there are additional operation(s)
                                                uint32_t cigar = bam1_cigar(b)[k+1]; // next CIGAR
                                                int op_next = cigar&BAM_CIGAR_MASK; // next CIGAR operation
                                                if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
                                                else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
-                                               if (op_next == BAM_CDEL || op_next == BAM_CINS) {
-                                                       if (k + 2 < c->n_cigar) op_next = bam1_cigar(b)[k+2]&BAM_CIGAR_MASK;
-                                                       else p->is_tail = 1;
+                                               else if (op_next == BAM_CPAD && k + 2 < c->n_cigar) { // no working for adjacent padding
+                                                       cigar = bam1_cigar(b)[k+2]; op_next = cigar&BAM_CIGAR_MASK;
+                                                       if (op_next == BAM_CDEL) p->indel = -(int32_t)(cigar>>BAM_CIGAR_SHIFT); // del
+                                                       else if (op_next == BAM_CINS) p->indel = cigar>>BAM_CIGAR_SHIFT; // ins
                                                }
-                                               if (op_next == BAM_CSOFT_CLIP || op_next == BAM_CREF_SKIP || op_next == BAM_CHARD_CLIP)
-                                                       p->is_tail = 1; // tail
-                                       } else p->is_tail = 1; // this is the last operation; set tail
+                                       }
                                }
                        }
                        x += l; y += l;
@@ -96,7 +106,8 @@ static inline int resolve_cigar(bam_pileup1_t *p, uint32_t pos)
                        x += l;
                } else if (op == BAM_CREF_SKIP) x += l;
                else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
-               is_restart = (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
+               if (is_restart) is_restart ^= (op == BAM_CMATCH);
+               else is_restart ^= (op == BAM_CREF_SKIP || op == BAM_CSOFT_CLIP || op == BAM_CHARD_CLIP);
                if (x > pos) {
                        if (op == BAM_CREF_SKIP) ret = 0; // then do not put it into pileup at all
                        break;

diff --git a/examples/toy.fa b/examples/toy.fa
new file mode 100644 (file)
index 0000000..38312c1
--- /dev/null
+++ b/examples/toy.fa
@@ -0,0 +1,2 @@
+>ref
+AGCATGTTAGATAAGATAGCTGTGCTAGTAGGCAGTCAGCGCCAT

diff --git a/examples/toy.sam b/examples/toy.sam
new file mode 100644 (file)
index 0000000..baf7388
--- /dev/null
+++ b/examples/toy.sam
@@ -0,0 +1,7 @@
+@SQ    SN:ref  LN:45
+r001   163     ref     7       30      8M2I4M1D3M      =       37      39      TTAGATAAAGGATACTG       *
+r002   0       ref     9       30      1S2I6M1P1I4M2I  *       0       0       AAAAGATAAGGATAAA        *
+r003   0       ref     9       30      5H6M    *       0       0       AGCTAA  *
+r004   0       ref     16      30      6M14N1I5M       *       0       0       ATAGCTCTCAGC    *
+r003   16      ref     29      30      6H5M    *       0       0       TAGGC   *
+r001   83      ref     37      30      9M      =       7       -39     CAGCGCCAT       *
\ No newline at end of file