+/* This program demonstrates how to generate pileup from multiple BAMs
+ * simutaneously, to achieve random access and to use the BED interface.
+ * To compile this program separately, you may:
+ *
+ * gcc -g -O2 -Wall -D_MAIN_BAM2BED bam2depth.c -L. -lbam -lz
+ */
+#include <stdlib.h>
+#include <string.h>
+#include <stdio.h>
+#include <unistd.h>
+#include "bam.h"
+
+typedef struct { // auxiliary data structure
+ bamFile fp; // the file handler
+ bam_iter_t iter; // NULL if a region not specified
+} aux_t;
+
+void *bed_read(const char *fn); // read a BED or position list file
+void bed_destroy(void *_h); // destroy the BED data structure
+int bed_overlap(const void *_h, const char *chr, int beg, int end); // test if chr:beg-end overlaps
+
+// This function reads a BAM alignment from one BAM file.
+static int read_bam(void *data, bam1_t *b)
+{
+ aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
+ return aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
+}
+
+#ifdef _MAIN_BAM2BED
+int main(int argc, char *argv[])
+#else
+int main_depth(int argc, char *argv[])
+#endif
+{
+ int i, n, tid, beg, end, pos, *n_plp;
+ const bam_pileup1_t **plp;
+ char *reg = 0; // specified region
+ void *bed = 0; // BED data structure
+ bam_header_t *h = 0; // BAM header of the 1st input
+ aux_t **data;
+ bam_mplp_t mplp;
+
+ // parse the command line
+ while ((n = getopt(argc, argv, "r:b:")) >= 0) {
+ switch (n) {
+ case 'r': reg = strdup(optarg); break; // parsing a region requires a BAM header
+ case 'b': bed = bed_read(optarg); break; // BED or position list file can be parsed now
+ }
+ }
+ if (optind == argc) {
+ fprintf(stderr, "Usage: bam2depth [-r reg] [-b in.bed] <in1.bam> [...]\n");
+ return 1;
+ }
+
+ // initialize the auxiliary data structures
+ n = argc - optind; // the number of BAMs on the command line
+ data = calloc(n, sizeof(void*));
+ beg = 0; end = 1<<30; tid = -1;
+ for (i = 0; i < n; ++i) {
+ bam_header_t *htmp;
+ data[i] = calloc(1, sizeof(aux_t));
+ data[i]->fp = bam_open(argv[optind+i], "r"); // open BAM
+ htmp = bam_header_read(data[i]->fp); // read the BAM header
+ if (i == 0) {
+ h = htmp; // keep the header for the 1st BAM
+ if (reg) bam_parse_region(h, reg, &tid, &beg, &end); // also parse the region
+ } else bam_header_destroy(htmp); // if not the 1st BAM, trash the header
+ if (tid >= 0) { // if a region is specified and parsed successfully
+ bam_index_t *idx = bam_index_load(argv[optind+i]); // load the index
+ data[i]->iter = bam_iter_query(idx, tid, beg, end); // set the iterator
+ bam_index_destroy(idx); // the index is not needed any more; phase out of the memory
+ }
+ }
+
+ // the core multi-pileup loop
+ mplp = bam_mplp_init(n, read_bam, (void**)data); // initialization
+ n_plp = calloc(n, sizeof(int)); // n_plp[i] is the number of covering reads from the i-th BAM
+ plp = calloc(n, sizeof(void*)); // plp[i] points to the array of covering reads internal in mplp
+ while (bam_mplp_auto(mplp, &tid, &pos, n_plp, plp) > 0) { // come to the next covered position
+ if (pos < beg || pos >= end) continue; // out of range; skip
+ if (bed && bed_overlap(bed, h->target_name[tid], pos, pos + 1) == 0) continue; // not in BED; skip
+ printf("%s\t%d", h->target_name[tid], pos+1);
+ for (i = 0; i < n; ++i) {
+ int j, m = 0;
+ const bam_pileup1_t *p = plp[i];
+ for (j = 0; j < n_plp[i]; ++j) // this loop counts #reads having deletions of refskip at tid:pos
+ if (p->is_del || p->is_refskip) ++m;
+ printf("\t%d", n_plp[i] - m);
+ }
+ putchar('\n');
+ }
+ free(n_plp); free(plp);
+ bam_mplp_destroy(mplp);
+
+ bam_header_destroy(h);
+ for (i = 0; i < n; ++i) {
+ bam_close(data[i]->fp);
+ if (data[i]->iter) bam_iter_destroy(data[i]->iter);
+ free(data[i]);
+ }
+ free(data); free(reg);
+ if (bed) bed_destroy(bed);
+ return 0;
+}