--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/bam2depth.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,143 @@
+/* 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 -o bam2depth -D_MAIN_BAM2DEPTH 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
+	int min_mapQ, min_len; // mapQ filter; length filter
+} 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) // read level filters better go here to avoid pileup
+{
+	aux_t *aux = (aux_t*)data; // data in fact is a pointer to an auxiliary structure
+	int ret = aux->iter? bam_iter_read(aux->fp, aux->iter, b) : bam_read1(aux->fp, b);
+	if (!(b->core.flag&BAM_FUNMAP)) {
+		if ((int)b->core.qual < aux->min_mapQ) b->core.flag |= BAM_FUNMAP;
+		else if (aux->min_len && bam_cigar2qlen(&b->core, bam1_cigar(b)) < aux->min_len) b->core.flag |= BAM_FUNMAP;
+	}
+	return ret;
+}
+
+int read_file_list(const char *file_list,int *n,char **argv[]);
+
+#ifdef _MAIN_BAM2DEPTH
+int main(int argc, char *argv[])
+#else
+int main_depth(int argc, char *argv[])
+#endif
+{
+	int i, n, tid, beg, end, pos, *n_plp, baseQ = 0, mapQ = 0, min_len = 0, nfiles;
+	const bam_pileup1_t **plp;
+	char *reg = 0; // specified region
+	void *bed = 0; // BED data structure
+    char *file_list = NULL, **fn = NULL;
+	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:q:Q:l:f:")) >= 0) {
+		switch (n) {
+			case 'l': min_len = atoi(optarg); break; // minimum query length
+			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
+			case 'q': baseQ = atoi(optarg); break;   // base quality threshold
+			case 'Q': mapQ = atoi(optarg); break;    // mapping quality threshold
+			case 'f': file_list = optarg; break;
+		}
+	}
+	if (optind == argc && !file_list) {
+        fprintf(stderr, "\n");
+        fprintf(stderr, "Usage: samtools depth [options] in1.bam [in2.bam [...]]\n");
+        fprintf(stderr, "Options:\n");
+        fprintf(stderr, "   -b <bed>            list of positions or regions\n");
+        fprintf(stderr, "   -f <list>           list of input BAM filenames, one per line [null]\n");
+        fprintf(stderr, "   -l <int>            minQLen\n");
+        fprintf(stderr, "   -q <int>            base quality threshold\n");
+        fprintf(stderr, "   -Q <int>            mapping quality threshold\n");
+        fprintf(stderr, "   -r <chr:from-to>    region\n");
+        fprintf(stderr, "\n");
+		return 1;
+	}
+
+	// initialize the auxiliary data structures
+    if (file_list) 
+    {
+        if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
+        n = nfiles;
+        argv = fn;
+        optind = 0;
+    }
+    else
+        n = argc - optind; // the number of BAMs on the command line
+	data = calloc(n, sizeof(void*)); // data[i] for the i-th input
+	beg = 0; end = 1<<30; tid = -1;  // set the default region
+	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
+		data[i]->min_mapQ = mapQ;                    // set the mapQ filter
+		data[i]->min_len  = min_len;                 // set the qlen filter
+		htmp = bam_header_read(data[i]->fp);         // read the BAM header
+		if (i == 0) {
+			h = htmp; // keep the header of 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
+		fputs(h->target_name[tid], stdout); printf("\t%d", pos+1); // a customized printf() would be faster
+		for (i = 0; i < n; ++i) { // base level filters have to go here
+			int j, m = 0;
+			for (j = 0; j < n_plp[i]; ++j) {
+				const bam_pileup1_t *p = plp[i] + j; // DON'T modfity plp[][] unless you really know
+				if (p->is_del || p->is_refskip) ++m; // having dels or refskips at tid:pos
+				else if (bam1_qual(p->b)[p->qpos] < baseQ) ++m; // low base quality
+			}
+			printf("\t%d", n_plp[i] - m); // this the depth to output
+		}
+		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);
+    if ( file_list )
+    {
+        for (i=0; i<n; i++) free(fn[i]);
+        free(fn);
+    }
+	return 0;
+}