X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.c;h=5fac17df6ec27d7cbb04b5600c3ce54d5c06b354;hp=a65aed5d551053a50952e95d58a763a77fadd06e;hb=5075acdfc387c56ca8411cde3e419e867da9804d;hpb=e42445c748ed193f8d0a4277a844fa848f30c132

diff --git a/bam.c b/bam.c
index a65aed5..5fac17d 100644
--- a/bam.c
+++ b/bam.c
@@ -160,6 +160,19 @@ static void swap_endian_data(const bam1_core_t *c, int data_len, uint8_t *data)
 		else if (type == 'I' || type == 'F') { bam_swap_endian_4p(s); s += 4; }
 		else if (type == 'D') { bam_swap_endian_8p(s); s += 8; }
 		else if (type == 'Z' || type == 'H') { while (*s) ++s; ++s; }
+		else if (type == 'B') {
+			int32_t n, Bsize = bam_aux_type2size(*s);
+			memcpy(&n, s + 1, 4);
+			if (1 == Bsize) {
+			} else if (2 == Bsize) {
+				for (i = 0; i < n; i += 2)
+					bam_swap_endian_2p(s + 5 + i);
+			} else if (4 == Bsize) {
+				for (i = 0; i < n; i += 4)
+					bam_swap_endian_4p(s + 5 + i);
+			}
+			bam_swap_endian_4p(s+1); 
+		}
 	}
 }
 
@@ -289,6 +302,23 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
 		else if (type == 'f') { ksprintf(&str, "f:%g", *(float*)s); s += 4; }
 		else if (type == 'd') { ksprintf(&str, "d:%lg", *(double*)s); s += 8; }
 		else if (type == 'Z' || type == 'H') { kputc(type, &str); kputc(':', &str); while (*s) kputc(*s++, &str); ++s; }
+		else if (type == 'B') {
+			uint8_t sub_type = *(s++);
+			int32_t n;
+			memcpy(&n, s, 4);
+			s += 4; // no point to the start of the array
+			kputc(type, &str); kputc(':', &str); kputc(sub_type, &str); // write the typing
+			for (i = 0; i < n; ++i) {
+				kputc(',', &str);
+				if ('c' == sub_type || 'c' == sub_type) { kputw(*(int8_t*)s, &str); ++s; }
+				else if ('C' == sub_type) { kputw(*(uint8_t*)s, &str); ++s; }
+				else if ('s' == sub_type) { kputw(*(int16_t*)s, &str); s += 2; }
+				else if ('S' == sub_type) { kputw(*(uint16_t*)s, &str); s += 2; }
+				else if ('i' == sub_type) { kputw(*(int32_t*)s, &str); s += 4; }
+				else if ('I' == sub_type) { kputuw(*(uint32_t*)s, &str); s += 4; }
+				else if ('f' == sub_type) { ksprintf(&str, "%g", *(float*)s); s += 4; }
+			}
+		}
 	}
 	return str.s;
 }