+#include <string.h>
+#include <assert.h>
+#include "kstring.h"
+#include "bam.h"
+
+static void replace_cigar(bam1_t *b, int n, uint32_t *cigar)
+{
+ if (n != b->core.n_cigar) {
+ int o = b->core.l_qname + b->core.n_cigar * 4;
+ if (b->data_len + (n - b->core.n_cigar) * 4 > b->m_data) {
+ b->m_data = b->data_len + (n - b->core.n_cigar) * 4;
+ kroundup32(b->m_data);
+ b->data = (uint8_t*)realloc(b->data, b->m_data);
+ }
+ memmove(b->data + b->core.l_qname + n * 4, b->data + o, b->data_len - o);
+ memcpy(b->data + b->core.l_qname, cigar, n * 4);
+ b->data_len += (n - b->core.n_cigar) * 4;
+ b->core.n_cigar = n;
+ } else memcpy(b->data + b->core.l_qname, cigar, n * 4);
+}
+
+#define write_cigar(_c, _n, _m, _v) do { \
+ if (_n == _m) { \
+ _m = _m? _m<<1 : 4; \
+ _c = (uint32_t*)realloc(_c, _m * 4); \
+ } \
+ _c[_n++] = (_v); \
+ } while (0)
+
+static void unpad_seq(bam1_t *b, kstring_t *s)
+{
+ int k, j, i;
+ uint32_t *cigar = bam1_cigar(b);
+ uint8_t *seq = bam1_seq(b);
+ ks_resize(s, b->core.l_qseq);
+ for (k = 0, s->l = 0, j = 0; k < b->core.n_cigar; ++k) {
+ int op, ol;
+ op = bam_cigar_op(cigar[k]);
+ ol = bam_cigar_oplen(cigar[k]);
+ assert(op == BAM_CMATCH || op == BAM_CDEL || op == BAM_CSOFT_CLIP);
+ if (op == BAM_CMATCH) {
+ for (i = 0; i < ol; ++i) s->s[s->l++] = bam1_seqi(seq, j);
+ ++j;
+ } else if (op == BAM_CSOFT_CLIP) {
+ j += ol;
+ } else {
+ for (i = 0; i < ol; ++i) s->s[s->l++] = 0;
+ }
+ }
+}
+
+int bam_pad2unpad(bamFile in, bamFile out)
+{
+ bam_header_t *h;
+ bam1_t *b;
+ kstring_t r, q;
+ uint32_t *cigar2 = 0;
+ int n2 = 0, m2 = 0, *posmap = 0;
+
+ h = bam_header_read(in);
+ bam_header_write(out, h);
+ b = bam_init1();
+ r.l = r.m = q.l = q.m = 0; r.s = q.s = 0;
+ while (bam_read1(in, b) >= 0) {
+ uint32_t *cigar = bam1_cigar(b);
+ n2 = 0;
+ if (b->core.pos == 0 && b->core.tid >= 0 && strcmp(bam1_qname(b), h->target_name[b->core.tid]) == 0) {
+ int i, k;
+ unpad_seq(b, &r);
+ 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
+ if (r.s[i]) ++k;
+ }
+ } else {
+ int i, k, op;
+ unpad_seq(b, &q);
+ if (bam_cigar_op(cigar[0]) == BAM_CSOFT_CLIP) write_cigar(cigar2, n2, m2, cigar[0]);
+ 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);
+ 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));
+ op = q.s[i]; k = 1;
+ } else ++k;
+ }
+ 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]);
+ 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;
+ for (i = k = 0; i < n2; ++i)
+ if (cigar2[i]) cigar2[k++] = cigar2[i];
+ n2 = k;
+ replace_cigar(b, n2, cigar2);
+ b->core.pos = posmap[b->core.pos];
+ }
+ bam_write1(out, b);
+ }
+ free(r.s); free(q.s); free(posmap);
+ bam_destroy1(b);
+ bam_header_destroy(h);
+ return 0;
+}
+
+int main_pad2unpad(int argc, char *argv[])
+{
+ bamFile in, out;
+ if (argc == 1) {
+ fprintf(stderr, "Usage: samtools pad2unpad <in.bam>\n");
+ return 1;
+ }
+ in = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+ out = bam_dopen(fileno(stdout), "w");
+ bam_pad2unpad(in, out);
+ bam_close(in); bam_close(out);
+ return 0;
+}