* samtools-0.1.5-12 (r415)

 * FLAG now can be in HEX

bam.c

@@ -236,15 +236,16 @@ int bam_write1(bamFile fp, const bam1_t *b)
 	return bam_write1_core(fp, &b->core, b->data_len, b->data);
 }
 
-char *bam_format1(const bam_header_t *header, const bam1_t *b)
+char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int is_hex)
 {
 	uint8_t *s = bam1_seq(b), *t = bam1_qual(b);
 	int i;
 	const bam1_core_t *c = &b->core;
 	kstring_t str;
 	str.l = str.m = 0; str.s = 0;
 
-	ksprintf(&str, "%s\t%d\t", bam1_qname(b), c->flag);
+	if (is_hex) ksprintf(&str, "%s\t0x%x\t", bam1_qname(b), c->flag);
+	else ksprintf(&str, "%s\t%d\t", bam1_qname(b), c->flag);
 	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);
@@ -282,6 +283,11 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
 	return str.s;
 }
 
+char *bam_format1(const bam_header_t *header, const bam1_t *b)
+{
+	return bam_format1_core(header, b, 0);
+}
+
 void bam_view1(const bam_header_t *header, const bam1_t *b)
 {
 	char *s = bam_format1(header, b);

bam.h

@@ -431,6 +431,8 @@ extern "C" {
 	 */
 	char *bam_format1(const bam_header_t *header, const bam1_t *b);
 
+	char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int is_hex);
+
 	/*! @typedef
 	  @abstract Structure for one alignment covering the pileup position.
 	  @field  b      pointer to the alignment

bam_import.c

@@ -297,7 +297,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 		doff += c->l_qname;
 	}
 	{ // flag, tid, pos, qual
-		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->flag = atoi(str->s);
+		long flag;
+		char *s;
+		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
+		flag = strtol((char*)str->s, &s, 0);
+		c->flag = flag;
 		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1; c->tid = bam_get_tid(header, str->s);
 		if (c->tid < 0 && strcmp(str->s, "*")) {
 			if (header->n_targets == 0) {

bamtk.c

@@ -4,7 +4,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-11 (r408)"
+#define PACKAGE_VERSION "0.1.5-12 (r415)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);

sam.c

@@ -3,6 +3,7 @@
 
 #define TYPE_BAM  1
 #define TYPE_READ 2
+#define TYPE_HEX  4
 
 bam_header_t *bam_header_dup(const bam_header_t *h0)
 {
@@ -75,6 +76,7 @@ samfile_t *samopen(const char *fn, const char *mode, const void *aux)
 			// open file
 			fp->x.tamw = strcmp(fn, "-")? fopen(fn, "w") : stdout;
 			if (fp->x.tamr == 0) goto open_err_ret;
+			if (strstr(mode, "x")) fp->type |= TYPE_HEX;
 			// write header
 			if (strstr(mode, "h")) {
 				int i;
@@ -126,7 +128,7 @@ int samwrite(samfile_t *fp, const bam1_t *b)
 	if (fp == 0 || (fp->type & TYPE_READ)) return -1; // not open for writing
 	if (fp->type & TYPE_BAM) return bam_write1(fp->x.bam, b);
 	else {
-		char *s = bam_format1(fp->header, b);
+		char *s = bam_format1_core(fp->header, b, fp->type & TYPE_HEX);
 		int l = strlen(s);
 		fputs(s, fp->x.tamw); fputc('\n', fp->x.tamw);
 		free(s);

sam.h

@@ -15,7 +15,7 @@
 
 /*! @typedef
   @abstract SAM/BAM file handler
-  @field  type    type of the handler; bit 1 for BAM and bit 2 for reading
+  @field  type    type of the handler; bit 1 for BAM, 2 for reading and bit 3 for is_hex
   @field  bam   BAM file handler; valid if (type&1) == 1
   @field  tamr  SAM file handler for reading; valid if type == 2
   @field  tamw  SAM file handler for writing; valid if type == 0
@@ -41,11 +41,11 @@ extern "C" {
 	  @param fn SAM/BAM file name; "-" is recognized as stdin (for
 	  reading) or stdout (for writing).
 
-	  @param mode open mode /[rw](b?)(u?)(h?)/: 'r' for reading, 'w' for
-	  writing, 'b' for BAM I/O, 'u' for uncompressed BAM output and 'h'
-	  for outputing header in SAM. If 'b' present, it must immediately
-	  follow 'r' or 'w'. Valid modes are "r", "w", "wh", "rb", "wb" and
-	  "wbu" exclusively.
+	  @param mode open mode /[rw](b?)(u?)(h?)(x?)/: 'r' for reading, 'w'
+	  for writing, 'b' for BAM I/O, 'u' for uncompressed BAM output, 'h'
+	  for outputing header in SAM and 'x' for HEX flag. If 'b' present,
+	  it must immediately follow 'r' or 'w'. Valid modes are "r", "w",
+	  "wh", "wx", "whx", "rb", "wb" and "wbu" exclusively.
 
 	  @param aux auxiliary data; if mode[0]=='w', aux points to
 	  bam_header_t; if strcmp(mode, "rb")!=0 and @SQ header lines in SAM

sam_view.c

@@ -35,13 +35,13 @@ static int usage(void);
 
 int main_samview(int argc, char *argv[])
 {
-	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0;
+	int c, is_header = 0, is_header_only = 0, is_bamin = 1, ret = 0, is_uncompressed = 0, is_bamout = 0, is_hex = 0;
 	samfile_t *in = 0, *out = 0;
 	char in_mode[5], out_mode[5], *fn_out = 0, *fn_list = 0;
 
 	/* parse command-line options */
 	strcpy(in_mode, "r"); strcpy(out_mode, "w");
-	while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:")) >= 0) {
+	while ((c = getopt(argc, argv, "Sbt:hHo:q:f:F:ul:r:x")) >= 0) {
 		switch (c) {
 		case 'S': is_bamin = 0; break;
 		case 'b': is_bamout = 1; break;
@@ -55,6 +55,7 @@ int main_samview(int argc, char *argv[])
 		case 'u': is_uncompressed = 1; break;
 		case 'l': g_library = strdup(optarg); break;
 		case 'r': g_rg = strdup(optarg); break;
+		case 'x': is_hex = 1; break;
 		default: return usage();
 		}
 	}
@@ -64,6 +65,7 @@ int main_samview(int argc, char *argv[])
 	if (is_bamin) strcat(in_mode, "b");
 	if (is_header) strcat(out_mode, "h");
 	if (is_uncompressed) strcat(out_mode, "u");
+	if (is_hex && !is_bamout) strcat(out_mode, "x");
 	if (argc == optind) return usage();
 
 	// open file handlers
@@ -123,6 +125,7 @@ static int usage()
 	fprintf(stderr, "         -H       print header only (no alignments)\n");
 	fprintf(stderr, "         -S       input is SAM\n");
 	fprintf(stderr, "         -u       uncompressed BAM output (force -b)\n");
+	fprintf(stderr, "         -x       output FLAG in HEX (samtools-C specific)\n");
 	fprintf(stderr, "         -t FILE  list of reference names and lengths (force -S) [null]\n");
 	fprintf(stderr, "         -o FILE  output file name [stdout]\n");
 	fprintf(stderr, "         -f INT   required flag, 0 for unset [0]\n");