* samtools-0.1.5-12 (r415)

 * FLAG now can be in HEX

diff --git a/bam.c b/bam.c
index 1ff4a5aba25028f4fccdd0735a9dcae594b6e9a8..33907f1a68ce1d998ad19e8387d5c9acfdb58939 100644 (file)
--- a/bam.c
+++ b/bam.c
@@ -236,7 +236,7 @@ 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;
@@ -244,7 +244,8 @@ char *bam_format1(const bam_header_t *header, const bam1_t *b)
        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);

diff --git a/bam.h b/bam.h
index 451b65aaf6131dc8e3c4ce1f41ffd5da541e761b..a33006d617093cc07a334de7cc74eeb37d880a63 100644 (file)
--- a/bam.h
+++ 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

diff --git a/bam_import.c b/bam_import.c
index c6fbafce979d93560d80265807833a8c9972dca0..2cadfcc6c73bd2f185616759d9ead6a75e543a14 100644 (file)
--- a/bam_import.c
+++ b/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) {

diff --git a/bamtk.c b/bamtk.c
index bbdf82c132dd64a82c0ee47353577b84698a5d29..5df14074cf4a13c219be0672ffa8b59477a38d90 100644 (file)
--- a/bamtk.c
+++ b/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[]);

diff --git a/sam.c b/sam.c
index 45cb05cf3dd6f8a04acfd4dd92c8d250835855a2..a3f2998687beb573186457837a844150e6245209 100644 (file)
--- a/sam.c
+++ b/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);

diff --git a/sam.h b/sam.h
index 86b757616e44b1e4de8ddd2da383534a805fe246..b8a0064cdec6472d366ae35fb4e0a276aa17c358 100644 (file)
--- a/sam.h
+++ b/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

diff --git a/sam_view.c b/sam_view.c
index 02aee3c034cbc668b51295039d92a6adb1e74d51..f253dbf7e65ecffd401a1dfcb854f93ed7463c71 100644 (file)
--- a/sam_view.c
+++ b/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");