r283: prepare for fixing cross-ref aln

bntseq.c

@@ -288,21 +288,26 @@ int bwa_fa2pac(int argc, char *argv[])
 	return 0;
 }
 
+int bns_pos2rid(const bntseq_t *bns, int64_t pos_f)
+{
+	int left, mid, right;
+	if (pos_f >= bns->l_pac) return -1;
+	left = 0; mid = 0; right = bns->n_seqs;
+	while (left < right) { // binary search
+		mid = (left + right) >> 1;
+		if (pos_f >= bns->anns[mid].offset) {
+			if (mid == bns->n_seqs - 1) break;
+			if (pos_f < bns->anns[mid+1].offset) break; // bracketed
+			left = mid + 1;
+		} else right = mid;
+	}
+	return mid;
+}
+
 int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id)
 {
 	int left, mid, right, nn;
-	if (ref_id) {
-		left = 0; mid = 0; right = bns->n_seqs;
-		while (left < right) {
-			mid = (left + right) >> 1;
-			if (pos_f >= bns->anns[mid].offset) {
-				if (mid == bns->n_seqs - 1) break;
-				if (pos_f < bns->anns[mid+1].offset) break; // bracketed
-				left = mid + 1;
-			} else right = mid;
-		}
-		*ref_id = mid;
-	}
+	if (ref_id) *ref_id = bns_pos2rid(bns, pos_f);
 	left = 0; right = bns->n_holes; nn = 0;
 	while (left < right) {
 		mid = (left + right) >> 1;

bntseq.h

@@ -72,6 +72,7 @@ extern "C" {
 	bntseq_t *bns_restore_core(const char *ann_filename, const char* amb_filename, const char* pac_filename);
 	void bns_destroy(bntseq_t *bns);
 	int64_t bns_fasta2bntseq(gzFile fp_fa, const char *prefix, int for_only);
+	int bns_pos2rid(const bntseq_t *bns, int64_t pos_f);
 	int bns_cnt_ambi(const bntseq_t *bns, int64_t pos_f, int len, int *ref_id);
 	uint8_t *bns_get_seq(int64_t l_pac, const uint8_t *pac, int64_t beg, int64_t end, int64_t *len);
 

bwa.c

@@ -64,6 +64,10 @@ bseq1_t *bseq_read(int chunk_size, int *n_, void *ks1_, void *ks2_)
 	return seqs;
 }
 
+/*****************
+ * CIGAR related *
+ *****************/
+
 // Generate CIGAR when the alignment end points are known
 uint32_t *bwa_gen_cigar(const int8_t mat[25], int q, int r, int w_, int64_t l_pac, const uint8_t *pac, int l_query, uint8_t *query, int64_t rb, int64_t re, int *score, int *n_cigar)
 {

main.c

@@ -4,7 +4,7 @@
 #include "utils.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.6.2-r282-beta"
+#define PACKAGE_VERSION "0.6.2-r283-beta"
 #endif
 
 static int usage()