--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/examples/chk_indel.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,83 @@
+/* To compile, copy this file to the samtools source code directory and compile with:
+     gcc -g -O2 -Wall chk_indel_rg.c -o chk_indel_rg -Wall -I. -L. -lbam -lz
+*/
+
+#include <string.h>
+#include "bam.h"
+
+typedef struct {
+	long cnt[4]; // short:ins, short:del, long:ins, long:del
+} rgcnt_t;
+
+#include "khash.h"
+KHASH_MAP_INIT_STR(rgcnt, rgcnt_t)
+
+#define MAX_LEN 127
+#define Q_THRES 10
+#define L_THRES 6 // short: <=L_THRES; otherwise long
+
+int main(int argc, char *argv[])
+{
+	bamFile fp;
+	bam1_t *b;
+	int i, x;
+	khash_t(rgcnt) *h;
+	khint_t k;
+
+	if (argc == 1) {
+		fprintf(stderr, "Usage: chk_indel_rg <in.bam>\n\n");
+		fprintf(stderr, "Output: filename, RG, #ins-in-short-homopolymer, #del-in-short, #ins-in-long, #del-in-long\n");
+		return 1;
+	}
+
+	h = kh_init(rgcnt);
+	fp = bam_open(argv[1], "r");
+	bam_header_destroy(bam_header_read(fp)); // we do not need the header
+	b = bam_init1();
+
+	while (bam_read1(fp, b) >= 0) {
+		if (b->core.n_cigar >= 3 && b->core.qual >= Q_THRES) {
+			const uint8_t *seq;
+			const uint32_t *cigar = bam1_cigar(b);
+			char *rg;
+			for (i = 0; i < b->core.n_cigar; ++i) // check if there are 1bp indels
+				if (bam_cigar_oplen(cigar[i]) == 1 && (bam_cigar_op(cigar[i]) == BAM_CDEL || bam_cigar_op(cigar[i]) == BAM_CINS))
+					break;
+			if (i == b->core.n_cigar) continue; // no 1bp ins or del
+			if ((rg = (char*)bam_aux_get(b, "RG")) == 0) continue; // no RG tag
+			seq = bam1_seq(b);
+			for (i = x = 0; i < b->core.n_cigar; ++i) {
+				int op = bam_cigar_op(cigar[i]);
+				if (bam_cigar_oplen(cigar[i]) == 1 && (op == BAM_CDEL || op == BAM_CINS)) {
+					int c, j, hrun, which;
+					c = bam1_seqi(seq, x);
+					for (j = x + 1, hrun = 0; j < b->core.l_qseq; ++j, ++hrun) // calculate the hompolymer run length
+						if (bam1_seqi(seq, j) != c) break;
+					k = kh_get(rgcnt, h, rg + 1);
+					if (k == kh_end(h)) { // absent
+						char *key = strdup(rg + 1);
+						k = kh_put(rgcnt, h, key, &c);
+						memset(&kh_val(h, k), 0, sizeof(rgcnt_t));
+					}
+					which = (hrun <= L_THRES? 0 : 1)<<1 | (op == BAM_CINS? 0 : 1);
+					++kh_val(h, k).cnt[which];
+				}
+				if (bam_cigar_type(op)&1) ++x;
+			}
+		}
+	}
+
+	for (k = 0; k != kh_end(h); ++k) {
+		if (!kh_exist(h, k)) continue;
+		printf("%s\t%s", argv[1], kh_key(h, k));
+		for (i = 0; i < 4; ++i)
+			printf("\t%ld", kh_val(h, k).cnt[i]);
+		putchar('\n');
+		free((char*)kh_key(h, k));
+	}
+
+	bam_destroy1(b);
+	bam_close(fp);
+	kh_destroy(rgcnt, h);
+	return 0;
+}