Fix missing declaration for getopt on Mac OS X

[samtools.git] / padding.c

diff --git a/padding.c b/padding.c
index ad68728b28761d114c99ef0ebcbad339102d99b9..033a7916237f94314bcf9661880a3fcde4604156 100644 (file)
--- a/padding.c
+++ b/padding.c
@@ -38,14 +38,15 @@ static void unpad_seq(bam1_t *b, kstring_t *s)
                op = bam_cigar_op(cigar[k]);
                ol = bam_cigar_oplen(cigar[k]);
                if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
-                       for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
-                       ++j;
+                       for (i = 0; i < ol; ++i, ++j) s->s[s->l++] = bam1_seqi(seq, j);
                } else if (op == BAM_CSOFT_CLIP) {
                        j += ol;
-               } else if (op == BAM_CDEL) {
+               } else if (op == BAM_CHARD_CLIP) {
+                       /* do nothing */
+               } else if (op == BAM_CDEL || op == BAM_CPAD) {
                        for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
                 } else {
-                       fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
+                       fprintf(stderr, "[depad] ERROR: Didn't expect CIGAR op %c in read %s\n", BAM_CIGAR_STR[op], bam1_qname(b));
                         assert(-1);
                }
        }
@@ -56,11 +57,12 @@ int bam_pad2unpad(bamFile in, bamFile out)
        bam_header_t *h;
        bam1_t *b;
        kstring_t r, q;
-        int r_tid = -1;
+       int r_tid = -1;
        uint32_t *cigar2 = 0;
        int n2 = 0, m2 = 0, *posmap = 0;
 
        h = bam_header_read(in);
+       /* TODO - The reference sequence lengths in the BAM + SAM headers should be updated */
        bam_header_write(out, h);
        b = bam_init1();
        r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
@@ -74,11 +76,15 @@ int bam_pad2unpad(bamFile in, bamFile out)
                        */
                        r_tid = b->core.tid;
                        unpad_seq(b, &r);
+                       if (h->target_len[r_tid] != r.l) {
+                               fprintf(stderr, "[depad] ERROR: (Padded) length of %s is %i in BAM header, but %ld in embedded reference\n", bam1_qname(b), h->target_len[r_tid], r.l);
+                               return -1;
+                       }
                        write_cigar(cigar2, n2, m2, bam_cigar_gen(b->core.l_qseq, BAM_CMATCH));
                        replace_cigar(b, n2, cigar2);
                        posmap = realloc(posmap, r.m * sizeof(int));
                        for (i = k = 0; i < r.l; ++i) {
-                               posmap[i] = k; // note that a read should NOT start at a padding
+                               posmap[i] = k;
                                if (r.s[i]) ++k;
                        }
                } else if (b->core.n_cigar > 0) {
@@ -92,8 +98,19 @@ int bam_pad2unpad(bamFile in, bamFile out)
                        }
                        unpad_seq(b, &q);
                        if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+                       if (bam_cigar_op(cigar[0]) == BAM_CHARD_CLIP) {
+                               write_cigar(cigar2, n2, m2, cigar[0]);
+                               if (b->core.n_cigar > 2 && bam_cigar_op(cigar[1]) == BAM_CSOFT_CLIP) {
+                                       write_cigar(cigar2, n2, m2, cigar[1]);
+                               }
+                       }
+                       /* Include any pads if starts with an insert */
+                       for (k = 0; k+1 < b->core.pos && !r.s[b->core.pos - k - 1]; ++k);
+                       if (k) write_cigar(cigar2, n2, m2, bam_cigar_gen(k, BAM_CPAD));
+                       /* Determine CIGAR operator for each base in the aligned read */
                        for (i = 0, k = b->core.pos; i < q.l; ++i, ++k)
                                q.s[i] = q.s[i]? (r.s[k]? BAM_CMATCH : BAM_CINS) : (r.s[k]? BAM_CDEL : BAM_CPAD);
+                       /* Count consecutive CIGAR operators to turn into a CIGAR string */
                        for (i = k = 1, op = q.s[0]; i < q.l; ++i) {
                                if (op != q.s[i]) {
                                        write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
@@ -102,6 +119,13 @@ int bam_pad2unpad(bamFile in, bamFile out)
                        }
                        write_cigar(cigar2, n2, m2, bam_cigar_gen(k, op));
                        if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+                        if (bam_cigar_op(cigar[b->core.n_cigar-1]) == BAM_CHARD_CLIP) {
+                               if (b->core.n_cigar > 2 && bam_cigar_op(cigar[b->core.n_cigar-2]) == BAM_CSOFT_CLIP) {
+                                       write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-2]);
+                               }
+                               write_cigar(cigar2, n2, m2, cigar[b->core.n_cigar-1]);
+                       }
+                       /* Remove redundant P operators between M operators, e.g. 5M2P10M -> 15M */
                        for (i = 2; i < n2; ++i)
                                if (bam_cigar_op(cigar2[i]) == BAM_CMATCH && bam_cigar_op(cigar2[i-1]) == BAM_CPAD && bam_cigar_op(cigar2[i-2]) == BAM_CMATCH)
                                        cigar2[i] += cigar2[i-2], cigar2[i-2] = cigar2[i-1] = 0;