--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/sample.c	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,107 @@
+#include <stdlib.h>
+#include <string.h>
+#include "sample.h"
+#include "khash.h"
+KHASH_MAP_INIT_STR(sm, int)
+
+bam_sample_t *bam_smpl_init(void)
+{
+	bam_sample_t *s;
+	s = calloc(1, sizeof(bam_sample_t));
+	s->rg2smid = kh_init(sm);
+	s->sm2id = kh_init(sm);
+	return s;
+}
+
+void bam_smpl_destroy(bam_sample_t *sm)
+{
+	int i;
+	khint_t k;
+	khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+	if (sm == 0) return;
+	for (i = 0; i < sm->n; ++i) free(sm->smpl[i]);
+	free(sm->smpl);
+	for (k = kh_begin(rg2smid); k != kh_end(rg2smid); ++k)
+		if (kh_exist(rg2smid, k)) free((char*)kh_key(rg2smid, k));
+	kh_destroy(sm, sm->rg2smid);
+	kh_destroy(sm, sm->sm2id);
+	free(sm);
+}
+
+static void add_pair(bam_sample_t *sm, khash_t(sm) *sm2id, const char *key, const char *val)
+{
+	khint_t k_rg, k_sm;
+	int ret;
+	khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+	k_rg = kh_get(sm, rg2smid, key);
+	if (k_rg != kh_end(rg2smid)) return; // duplicated @RG-ID
+	k_rg = kh_put(sm, rg2smid, strdup(key), &ret);
+	k_sm = kh_get(sm, sm2id, val);
+	if (k_sm == kh_end(sm2id)) { // absent
+		if (sm->n == sm->m) {
+			sm->m = sm->m? sm->m<<1 : 1;
+			sm->smpl = realloc(sm->smpl, sizeof(void*) * sm->m);
+		}
+		sm->smpl[sm->n] = strdup(val);
+		k_sm = kh_put(sm, sm2id, sm->smpl[sm->n], &ret);
+		kh_val(sm2id, k_sm) = sm->n++;
+	}
+	kh_val(rg2smid, k_rg) = kh_val(sm2id, k_sm);
+}
+
+int bam_smpl_add(bam_sample_t *sm, const char *fn, const char *txt)
+{
+	const char *p = txt, *q, *r;
+	kstring_t buf, first_sm;
+	int n = 0;
+	khash_t(sm) *sm2id = (khash_t(sm)*)sm->sm2id;
+	if (txt == 0) {
+		add_pair(sm, sm2id, fn, fn);
+		return 0;
+	}
+	memset(&buf, 0, sizeof(kstring_t));
+    memset(&first_sm, 0, sizeof(kstring_t));
+	while ((q = strstr(p, "@RG")) != 0) {
+		p = q + 3;
+		r = q = 0;
+		if ((q = strstr(p, "\tID:")) != 0) q += 4;
+		if ((r = strstr(p, "\tSM:")) != 0) r += 4;
+		if (r && q) {
+			char *u, *v;
+			int oq, or;
+			for (u = (char*)q; *u && *u != '\t' && *u != '\n'; ++u);
+			for (v = (char*)r; *v && *v != '\t' && *v != '\n'; ++v);
+			oq = *u; or = *v; *u = *v = '\0';
+			buf.l = 0; kputs(fn, &buf); kputc('/', &buf); kputs(q, &buf);
+			add_pair(sm, sm2id, buf.s, r);
+            if ( !first_sm.s )
+                kputs(r,&first_sm); 
+			*u = oq; *v = or;
+		} else break;
+		p = q > r? q : r;
+		++n;
+	}
+	if (n == 0) add_pair(sm, sm2id, fn, fn);
+    // If there is only one RG tag present in the header and reads are not annotated, don't refuse to work but
+    //  use the tag instead.
+    else if ( n==1 && first_sm.s )
+        add_pair(sm,sm2id,fn,first_sm.s);
+    if ( first_sm.s )
+        free(first_sm.s);
+
+//	add_pair(sm, sm2id, fn, fn);
+	free(buf.s);
+	return 0;
+}
+
+int bam_smpl_rg2smid(const bam_sample_t *sm, const char *fn, const char *rg, kstring_t *str)
+{
+	khint_t k;
+	khash_t(sm) *rg2smid = (khash_t(sm)*)sm->rg2smid;
+	if (rg) {
+		str->l = 0;
+		kputs(fn, str); kputc('/', str); kputs(rg, str);
+		k = kh_get(sm, rg2smid, str->s);
+	} else k = kh_get(sm, rg2smid, fn);
+	return k == kh_end(rg2smid)? -1 : kh_val(rg2smid, k);
+}