* samtools-0.1.3-9 (r256)

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 1dac729ab27bbd18d670f813161de0558db3197c..ff82825c29abc4f578561a1e0032a60f23e00f65 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.2-24"
+#define PACKAGE_VERSION "0.1.3-9 (r256)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -15,6 +15,7 @@ int bam_tview_main(int argc, char *argv[]);
 int bam_mating(int argc, char *argv[]);
 int bam_rmdup(int argc, char *argv[]);
 int bam_flagstat(int argc, char *argv[]);
+int bam_fillmd(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
 int glf3_view_main(int argc, char *argv[]);
@@ -51,6 +52,10 @@ int bam_view(int argc, char *argv[])
        fp = strcmp(argv[optind], "-")? bam_open(argv[optind], "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;
+       }
        if (is_bam) {
                assert(fpout = bam_dopen(fileno(stdout), "w"));
                bam_header_write(fpout, header);
@@ -82,7 +87,10 @@ int bam_view(int argc, char *argv[])
                for (i = optind + 1; i < argc; ++i) {
                        int tid, beg, end;
                        bam_parse_region(header, argv[i], &tid, &beg, &end);
-                       if (tid < 0) return 0;
+                       if (tid < 0) {
+                               fprintf(stderr, "[bam_view] fail to get the reference name. Abort!\n");
+                               return 1;
+                       }
                        if (is_bam) bam_fetch(fp, idx, tid, beg, end, fpout, view_auxb);
                        else bam_fetch(fp, idx, tid, beg, end, header, view_aux);
                }
@@ -94,6 +102,46 @@ 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");
@@ -112,8 +160,9 @@ static int usage()
        fprintf(stderr, "         index       index alignment\n");
        fprintf(stderr, "         fixmate     fix mate information\n");
        fprintf(stderr, "         rmdup       remove PCR duplicates\n");
-       fprintf(stderr, "         glfview     print GLFv2 file\n");
+       fprintf(stderr, "         glfview     print GLFv3 file\n");
        fprintf(stderr, "         flagstat    simple stats\n");
+       fprintf(stderr, "         fillmd      fill the MD tag and change identical base to =\n");
        fprintf(stderr, "\n");
        return 1;
 }
@@ -132,6 +181,8 @@ 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);
+       else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
 #ifndef _NO_CURSES
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif