Imported Upstream version 0.1.18

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index 5886570a88f9fbdc43e6442f1f76df7f9e100243..8ba25811d2771e171fa08899015449618838f265 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -9,7 +9,6 @@
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
-int bam_pileup(int argc, char *argv[]);
 int bam_mpileup(int argc, char *argv[]);
 int bam_merge(int argc, char *argv[]);
 int bam_index(int argc, char *argv[]);
@@ -27,49 +26,9 @@ int main_cut_target(int argc, char *argv[]);
 int main_phase(int argc, char *argv[]);
 int main_cat(int argc, char *argv[]);
 int main_depth(int argc, char *argv[]);
+int main_bam2fq(int argc, char *argv[]);
 
 int faidx_main(int argc, char *argv[]);
-int glf3_view_main(int argc, char *argv[]);
-
-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()
 {
@@ -79,7 +38,6 @@ static int usage()
        fprintf(stderr, "Usage:   samtools <command> [options]\n\n");
        fprintf(stderr, "Command: view        SAM<->BAM conversion\n");
        fprintf(stderr, "         sort        sort alignment file\n");
-       fprintf(stderr, "         pileup      generate pileup output\n");
        fprintf(stderr, "         mpileup     multi-way pileup\n");
        fprintf(stderr, "         depth       compute the depth\n");
        fprintf(stderr, "         faidx       index/extract FASTA\n");
@@ -89,7 +47,6 @@ static int usage()
        fprintf(stderr, "         index       index alignment\n");
        fprintf(stderr, "         idxstats    BAM index stats (r595 or later)\n");
        fprintf(stderr, "         fixmate     fix mate information\n");
-       fprintf(stderr, "         glfview     print GLFv3 file\n");
        fprintf(stderr, "         flagstat    simple stats\n");
        fprintf(stderr, "         calmd       recalculate MD/NM tags and '=' bases\n");
        fprintf(stderr, "         merge       merge sorted alignments\n");
@@ -120,7 +77,6 @@ int main(int argc, char *argv[])
        if (argc < 2) return usage();
        if (strcmp(argv[1], "view") == 0) return main_samview(argc-1, argv+1);
        else if (strcmp(argv[1], "import") == 0) return main_import(argc-1, argv+1);
-       else if (strcmp(argv[1], "pileup") == 0) return bam_pileup(argc-1, argv+1);
        else if (strcmp(argv[1], "mpileup") == 0) return bam_mpileup(argc-1, argv+1);
        else if (strcmp(argv[1], "merge") == 0) return bam_merge(argc-1, argv+1);
        else if (strcmp(argv[1], "sort") == 0) return bam_sort(argc-1, argv+1);
@@ -129,9 +85,7 @@ int main(int argc, char *argv[])
        else if (strcmp(argv[1], "faidx") == 0) return faidx_main(argc-1, argv+1);
        else if (strcmp(argv[1], "fixmate") == 0) return bam_mating(argc-1, argv+1);
        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], "calmd") == 0) return bam_fillmd(argc-1, argv+1);
        else if (strcmp(argv[1], "fillmd") == 0) return bam_fillmd(argc-1, argv+1);
        else if (strcmp(argv[1], "reheader") == 0) return main_reheader(argc-1, argv+1);
@@ -139,6 +93,11 @@ int main(int argc, char *argv[])
        else if (strcmp(argv[1], "targetcut") == 0) return main_cut_target(argc-1, argv+1);
        else if (strcmp(argv[1], "phase") == 0) return main_phase(argc-1, argv+1);
        else if (strcmp(argv[1], "depth") == 0) return main_depth(argc-1, argv+1);
+       else if (strcmp(argv[1], "bam2fq") == 0) return main_bam2fq(argc-1, argv+1);
+       else if (strcmp(argv[1], "pileup") == 0) {
+               fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
+               return 1;
+       }
 #if _CURSES_LIB != 0
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif