* samtools-0.1.3-2 (r239)

 * fixed bugs in bam_aux.c (these functions nevered used by samtools)
 * removed bam_aux_init()/bam_aux_destroy()
 * added tagview for testing bam_aux

diff --git a/bam.h b/bam.h
index 76f3e0f99f783a1779df83fc4b1be7c88ec6aaf8..c0bde4b9374e742ddda46dcc9474e78d4a2c1d45 100644 (file)
--- a/bam.h
+++ b/bam.h
@@ -401,8 +401,8 @@ extern "C" {
          @abstract  Free the memory allocated for an alignment.
          @param  b  pointer to an alignment
         */
-#define bam_destroy1(b) do {                                                                                   \
-               if ((b)->hash) bam_aux_destroy(b); free((b)->data); free(b);    \
+#define bam_destroy1(b) do {                                           \
+               if ((b)->hash) free((b)->data); free(b);        \
        } while (0)
 
        /*!
@@ -600,11 +600,12 @@ extern "C" {
         */
        void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *begin, int *end);
 
-       int32_t bam_aux_geti(bam1_t *b, const char tag[2], int *err);
-       float bam_aux_getf(bam1_t *b, const char tag[2], int *err);
-       char bam_aux_getc(bam1_t *b, const char tag[2], int *err);
-       char *bam_aux_getZH(bam1_t *b, const char tag[2], int *err);
-       void bam_aux_destroy(bam1_t *b);
+       uint8_t *bam_aux_get(bam1_t *b, const char tag[2]);
+       int32_t bam_aux2i(const uint8_t *s);
+       float bam_aux2f(const uint8_t *s);
+       double bam_aux2d(const uint8_t *s);
+       char bam_aux2A(const uint8_t *s);
+       char *bam_aux2Z(const uint8_t *s);
 
        /*!  
          @abstract Calculate the rightmost coordinate of an alignment on the

diff --git a/bam_aux.c b/bam_aux.c
index 081f07bc367a57fe2bd139b4fd82ea73421b5d5d..f9be398f0e820d9b48b2002073039af1ebeb95d5 100644 (file)
--- a/bam_aux.c
+++ b/bam_aux.c
@@ -1,9 +1,27 @@
 #include <ctype.h>
 #include "bam.h"
 #include "khash.h"
-KHASH_MAP_INIT_INT(aux, uint8_t*)
 KHASH_MAP_INIT_STR(s, int)
 
+uint8_t *bam_aux_get(bam1_t *b, const char tag[2])
+{
+       uint8_t *s;
+       int y = tag[0]<<8 | tag[1];
+       s = bam1_aux(b);
+       while (s < b->data + b->data_len) {
+               int type, x = (int)s[0]<<8 | s[1];
+               s += 2;
+               if (x == y) return s;
+               type = toupper(*s); ++s;
+               if (type == 'C') ++s;
+               else if (type == 'S') s += 2;
+               else if (type == 'I' || type == 'F') s += 4;
+               else if (type == 'D') s += 8;
+               else if (type == 'Z' || type == 'H') { while (*s) putchar(*s++); ++s; }
+       }
+       return 0;
+}
+
 void bam_init_header_hash(bam_header_t *header)
 {
        if (header->hash == 0) {
@@ -71,90 +89,51 @@ void bam_parse_region(bam_header_t *header, const char *str, int *ref_id, int *b
        free(s);
 }
 
-void bam_aux_init(bam1_t *b)
-{
-       khash_t(aux) *h;
-       uint8_t *s;
-       if (b->hash == 0) {
-               h = kh_init(aux);
-               b->hash = h;
-       } else {
-               h = (khash_t(aux)*)b->hash;
-               kh_clear(aux, h);
-       }
-       s = bam1_aux(b);
-       while (s < b->data + b->data_len) {
-               uint32_t x = (uint32_t)s[0]<<8 | s[1];
-               int ret, type;
-               khint_t k;
-               s += 2; type = toupper(*s); ++s;
-               k = kh_put(aux, h, x, &ret);
-               kh_value(h, k) = s;
-               if (type == 'C') ++s;
-               else if (type == 'S') s += 2;
-               else if (type == 'I') s += 4;
-               else if (type == 'F') s += 4;
-               else if (type == 'Z') { while (*s) putchar(*s++); ++s; }
-       }
-}
-void bam_aux_destroy(bam1_t *b)
-{
-       khash_t(aux) *h = (khash_t(aux)*)b->hash;
-       kh_destroy(aux, h);
-       b->hash = 0;
-}
-static uint8_t *bam_aux_get_core(bam1_t *b, const char tag[2])
-{
-       uint32_t x = (uint32_t)tag[0]<<8 | tag[1];
-       khint_t k;
-       khash_t(aux) *h;
-       if (b->hash == 0) bam_aux_init(b);
-       h = (khash_t(aux)*)b->hash;
-       k = kh_get(aux, h, x);
-       if (k == kh_end(h)) return 0;
-       return kh_value(h, k);
-}
-int32_t bam_aux_geti(bam1_t *b, const char tag[2], int *err)
+int32_t bam_aux2i(const uint8_t *s)
 {
        int type;
-       uint8_t *s = bam_aux_get_core(b, tag);
-       *err = 0;
-       if (s == 0) { *err = -1; return 0; }
+       if (s == 0) return 0;
        type = *s++;
        if (type == 'c') return (int32_t)*(int8_t*)s;
        else if (type == 'C') return (int32_t)*(uint8_t*)s;
        else if (type == 's') return (int32_t)*(int16_t*)s;
        else if (type == 'S') return (int32_t)*(uint16_t*)s;
        else if (type == 'i' || type == 'I') return *(int32_t*)s;
-       else { *err = -2; return 0; }
+       else return 0;
 }
-float bam_aux_getf(bam1_t *b, const char tag[2], int *err)
+
+float bam_aux2f(const uint8_t *s)
 {
        int type;
-       uint8_t *s = bam_aux_get_core(b, tag);
-       *err = 0;
        type = *s++;
-       if (s == 0) { *err = -1; return 0; }
+       if (s == 0) return 0.0;
        if (type == 'f') return *(float*)s;
-       else { *err = -2; return 0; }
+       else return 0.0;
 }
-char bam_aux_getc(bam1_t *b, const char tag[2], int *err)
+
+double bam_aux2d(const uint8_t *s)
 {
        int type;
-       uint8_t *s = bam_aux_get_core(b, tag);
-       *err = 0;
        type = *s++;
-       if (s == 0) { *err = -1; return 0; }
-       if (type == 'c') return *(char*)s;
-       else { *err = -2; return 0; }
+       if (s == 0) return 0.0;
+       if (type == 'd') return *(double*)s;
+       else return 0.0;
 }
-char *bam_aux_getZH(bam1_t *b, const char tag[2], int *err)
+
+char bam_aux2A(const uint8_t *s)
+{
+       int type;
+       type = *s++;
+       if (s == 0) return 0;
+       if (type == 'A') return *(char*)s;
+       else return 0;
+}
+
+char *bam_aux2Z(const uint8_t *s)
 {
        int type;
-       uint8_t *s = bam_aux_get_core(b, tag);
-       *err = 0;
        type = *s++;
-       if (s == 0) { *err = -1; return 0; }
+       if (s == 0) return 0;
        if (type == 'Z' || type == 'H') return (char*)s;
-       else { *err = -2; return 0; }
+       else return 0;
 }

diff --git a/bamtk.c b/bamtk.c
index a19abc44c57c3961c273688949c559bda3e9bc0a..f12f9003bdb858c0d031ff4de87a437b47e29342 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.3-1"
+#define PACKAGE_VERSION "0.1.3-2"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -101,6 +101,46 @@ int bam_view(int argc, char *argv[])
        return 0;
 }
 
+int bam_tagview(int argc, char *argv[])
+{
+       bamFile fp;
+       bam_header_t *header;
+       bam1_t *b;
+       char tag[2];
+       int ret;
+       if (argc < 3) {
+               fprintf(stderr, "Usage: samtools tagview <in.bam> <tag>\n");
+               return 1;
+       }
+       fp = strcmp(argv[1], "-")? bam_open(argv[1], "r") : bam_dopen(fileno(stdin), "r");
+       assert(fp);
+       header = bam_header_read(fp);
+       if (header == 0) {
+               fprintf(stderr, "[bam_view] fail to read the BAM header. Abort!\n");
+               return 1;
+       }
+       tag[0] = argv[2][0]; tag[1] = argv[2][1];
+       b = (bam1_t*)calloc(1, sizeof(bam1_t));
+       while ((ret = bam_read1(fp, b)) >= 0) {
+               uint8_t *d = bam_aux_get(b, tag);
+               if (d) {
+                       printf("%s\t%d\t", bam1_qname(b), b->core.flag);
+                       if (d[0] == 'Z' || d[0] == 'H') printf("%s\n", bam_aux2Z(d));
+                       else if (d[0] == 'f') printf("%f\n", bam_aux2f(d));
+                       else if (d[0] == 'd') printf("%lf\n", bam_aux2d(d));
+                       else if (d[0] == 'A') printf("%c\n", bam_aux2A(d));
+                       else if (d[0] == 'c' || d[0] == 's' || d[0] == 'i') printf("%d\n", bam_aux2i(d));
+                       else if (d[0] == 'C' || d[0] == 'S' || d[0] == 'I') printf("%u\n", bam_aux2i(d));
+                       else printf("\n");
+               }
+       }
+       if (ret < -1) fprintf(stderr, "[bam_view] truncated file? Continue anyway. (%d)\n", ret);
+       free(b->data); free(b);
+       bam_header_destroy(header);
+       bam_close(fp);
+       return 0;
+}
+
 static int usage()
 {
        fprintf(stderr, "\n");
@@ -139,6 +179,7 @@ int main(int argc, char *argv[])
        else if (strcmp(argv[1], "rmdup") == 0) return bam_rmdup(argc-1, argv+1);
        else if (strcmp(argv[1], "glfview") == 0) return glf3_view_main(argc-1, argv+1);
        else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
+       else if (strcmp(argv[1], "tagview") == 0) return bam_tagview(argc-1, argv+1);
 #ifndef _NO_CURSES
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif