X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam.c;h=0055e8427667dd95151ea1a1bef5dd14e74e15f1;hp=ee7642b3434248c9b44ef918435f150f101cae00;hb=aa08abe5f0b84ee0dd3491f00fe357d661c08e0c;hpb=317f5e8dd22cc9e1e5e05fbcaeb3b9aca7447351

diff --git a/bam.c b/bam.c
index ee7642b..0055e84 100644
--- a/bam.c
+++ b/bam.c
@@ -7,7 +7,7 @@
 #include "kstring.h"
 #include "sam_header.h"
 
-int bam_is_be = 0;
+int bam_is_be = 0, bam_verbose = 2;
 char *bam_flag2char_table = "pPuUrR12sfd\0\0\0\0\0";
 
 /**************************
@@ -32,7 +32,7 @@ int32_t bam_cigar2qlen(const bam1_core_t *c, const uint32_t *cigar)
 	int32_t l = 0;
 	for (k = 0; k < c->n_cigar; ++k) {
 		int op = cigar[k] & BAM_CIGAR_MASK;
-		if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP)
+		if (op == BAM_CMATCH || op == BAM_CINS || op == BAM_CSOFT_CLIP || op == BAM_CEQUAL || op == BAM_CDIFF)
 			l += cigar[k] >> BAM_CIGAR_SHIFT;
 	}
 	return l;
@@ -70,6 +70,7 @@ bam_header_t *bam_header_read(bamFile fp)
 {
 	bam_header_t *header;
 	char buf[4];
+	int magic_len;
 	int32_t i = 1, name_len;
 	// check EOF
 	i = bgzf_check_EOF(fp);
@@ -78,11 +79,11 @@ bam_header_t *bam_header_read(bamFile fp)
 		// with ESPIPE.  Suppress the error message in this case.
 		if (errno != ESPIPE) perror("[bam_header_read] bgzf_check_EOF");
 	}
-	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent.\n");
+	else if (i == 0) fprintf(stderr, "[bam_header_read] EOF marker is absent. The input is probably truncated.\n");
 	// read "BAM1"
-	if (bam_read(fp, buf, 4) != 4) return 0;
-	if (strncmp(buf, "BAM\001", 4)) {
-		fprintf(stderr, "[bam_header_read] wrong header\n");
+	magic_len = bam_read(fp, buf, 4);
+	if (magic_len != 4 || strncmp(buf, "BAM\001", 4) != 0) {
+		fprintf(stderr, "[bam_header_read] invalid BAM binary header (this is not a BAM file).\n");
 		return 0;
 	}
 	header = bam_header_init();
@@ -140,6 +141,7 @@ int bam_header_write(bamFile fp, const bam_header_t *header)
 			bam_write(fp, &x, 4);
 		} else bam_write(fp, &header->target_len[i], 4);
 	}
+	bgzf_flush(fp);
 	return 0;
 }
 
@@ -158,6 +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); 
+		}
 	}
 }
 
@@ -207,6 +222,7 @@ inline int bam_write1_core(bamFile fp, const bam1_core_t *c, int data_len, uint8
 	x[5] = c->mtid;
 	x[6] = c->mpos;
 	x[7] = c->isize;
+	bgzf_flush_try(fp, 4 + block_len);
 	if (bam_is_be) {
 		for (i = 0; i < 8; ++i) bam_swap_endian_4p(x + i);
 		y = block_len;
@@ -232,8 +248,8 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
 	kstring_t str;
 	str.l = str.m = 0; str.s = 0;
 
-	ksprintf(&str, "%s\t", bam1_qname(b));
-	if (of == BAM_OFDEC) ksprintf(&str, "%d\t", c->flag);
+	kputsn(bam1_qname(b), c->l_qname-1, &str); kputc('\t', &str);
+	if (of == BAM_OFDEC) { kputw(c->flag, &str); kputc('\t', &str); }
 	else if (of == BAM_OFHEX) ksprintf(&str, "0x%x\t", c->flag);
 	else { // BAM_OFSTR
 		for (i = 0; i < 16; ++i)
@@ -241,41 +257,68 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
 				kputc(bam_flag2char_table[i], &str);
 		kputc('\t', &str);
 	}
-	if (c->tid < 0) kputs("*\t", &str);
-	else ksprintf(&str, "%s\t", header->target_name[c->tid]);
-	ksprintf(&str, "%d\t%d\t", c->pos + 1, c->qual);
+	if (c->tid < 0) kputsn("*\t", 2, &str);
+	else {
+		if (header) kputs(header->target_name[c->tid] , &str);
+		else kputw(c->tid, &str);
+		kputc('\t', &str);
+	}
+	kputw(c->pos + 1, &str); kputc('\t', &str); kputw(c->qual, &str); kputc('\t', &str);
 	if (c->n_cigar == 0) kputc('*', &str);
 	else {
-		for (i = 0; i < c->n_cigar; ++i)
-			ksprintf(&str, "%d%c", bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, "MIDNSHP"[bam1_cigar(b)[i]&BAM_CIGAR_MASK]);
+		for (i = 0; i < c->n_cigar; ++i) {
+			kputw(bam1_cigar(b)[i]>>BAM_CIGAR_SHIFT, &str);
+			kputc("MIDNSHP=X"[bam1_cigar(b)[i]&BAM_CIGAR_MASK], &str);
+		}
 	}
 	kputc('\t', &str);
-	if (c->mtid < 0) kputs("*\t", &str);
-	else if (c->mtid == c->tid) kputs("=\t", &str);
-	else ksprintf(&str, "%s\t", header->target_name[c->mtid]);
-	ksprintf(&str, "%d\t%d\t", c->mpos + 1, c->isize);
+	if (c->mtid < 0) kputsn("*\t", 2, &str);
+	else if (c->mtid == c->tid) kputsn("=\t", 2, &str);
+	else {
+		if (header) kputs(header->target_name[c->mtid], &str);
+		else kputw(c->mtid, &str);
+		kputc('\t', &str);
+	}
+	kputw(c->mpos + 1, &str); kputc('\t', &str); kputw(c->isize, &str); kputc('\t', &str);
 	if (c->l_qseq) {
 		for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
 		kputc('\t', &str);
 		if (t[0] == 0xff) kputc('*', &str);
 		else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
-	} else ksprintf(&str, "*\t*");
+	} else kputsn("*\t*", 3, &str);
 	s = bam1_aux(b);
 	while (s < b->data + b->data_len) {
 		uint8_t type, key[2];
 		key[0] = s[0]; key[1] = s[1];
 		s += 2; type = *s; ++s;
-		ksprintf(&str, "\t%c%c:", key[0], key[1]);
-		if (type == 'A') { ksprintf(&str, "A:%c", *s); ++s; }
-		else if (type == 'C') { ksprintf(&str, "i:%u", *s); ++s; }
-		else if (type == 'c') { ksprintf(&str, "i:%d", *s); ++s; }
-		else if (type == 'S') { ksprintf(&str, "i:%u", *(uint16_t*)s); s += 2; }
-		else if (type == 's') { ksprintf(&str, "i:%d", *(int16_t*)s); s += 2; }
-		else if (type == 'I') { ksprintf(&str, "i:%u", *(uint32_t*)s); s += 4; }
-		else if (type == 'i') { ksprintf(&str, "i:%d", *(int32_t*)s); s += 4; }
+		kputc('\t', &str); kputsn((char*)key, 2, &str); kputc(':', &str);
+		if (type == 'A') { kputsn("A:", 2, &str); kputc(*s, &str); ++s; }
+		else if (type == 'C') { kputsn("i:", 2, &str); kputw(*s, &str); ++s; }
+		else if (type == 'c') { kputsn("i:", 2, &str); kputw(*(int8_t*)s, &str); ++s; }
+		else if (type == 'S') { kputsn("i:", 2, &str); kputw(*(uint16_t*)s, &str); s += 2; }
+		else if (type == 's') { kputsn("i:", 2, &str); kputw(*(int16_t*)s, &str); s += 2; }
+		else if (type == 'I') { kputsn("i:", 2, &str); kputuw(*(uint32_t*)s, &str); s += 4; }
+		else if (type == 'i') { kputsn("i:", 2, &str); kputw(*(int32_t*)s, &str); s += 4; }
 		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') { ksprintf(&str, "%c:", type); while (*s) kputc(*s++, &str); ++s; }
+		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;
 }
@@ -288,10 +331,26 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
 void bam_view1(const bam_header_t *header, const bam1_t *b)
 {
 	char *s = bam_format1(header, b);
-	printf("%s\n", s);
+	puts(s);
 	free(s);
 }
 
+int bam_validate1(const bam_header_t *header, const bam1_t *b)
+{
+	char *s;
+
+	if (b->core.tid < -1 || b->core.mtid < -1) return 0;
+	if (header && (b->core.tid >= header->n_targets || b->core.mtid >= header->n_targets)) return 0;
+
+	if (b->data_len < b->core.l_qname) return 0;
+	s = memchr(bam1_qname(b), '\0', b->core.l_qname);
+	if (s != &bam1_qname(b)[b->core.l_qname-1]) return 0;
+
+	// FIXME: Other fields could also be checked, especially the auxiliary data
+
+	return 1;
+}
+
 // FIXME: we should also check the LB tag associated with each alignment
 const char *bam_get_library(bam_header_t *h, const bam1_t *b)
 {