* samtools-0.1.2-10

[samtools.git] / bamtk.c

diff --git a/bamtk.c b/bamtk.c
index dd9aa26871b31b0e64fd3ca15e7015558318a72d..9ebaac6b4ccff5582f4c77a746265b036b9026b6 100644 (file)
--- a/bamtk.c
+++ b/bamtk.c
@@ -3,7 +3,7 @@
 #include "bam.h"
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.1-19"
+#define PACKAGE_VERSION "0.1.2-10"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);
@@ -14,6 +14,7 @@ int bam_sort(int argc, char *argv[]);
 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 faidx_main(int argc, char *argv[]);
 int glf_view_main(int argc, char *argv[]);
@@ -64,6 +65,7 @@ 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 (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 +96,7 @@ static int usage()
        fprintf(stderr, "         fixmate     fix mate information\n");
        fprintf(stderr, "         rmdup       remove PCR duplicates\n");
        fprintf(stderr, "         glfview     print GLFv2 file\n");
+       fprintf(stderr, "         flagstat    simple stats\n");
        fprintf(stderr, "\n");
        return 1;
 }
@@ -111,6 +114,7 @@ int main(int argc, char *argv[])
        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 glf_view_main(argc-1, argv+1);
+       else if (strcmp(argv[1], "flagstat") == 0) return bam_flagstat(argc-1, argv+1);
 #ifndef _NO_CURSES
        else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
 #endif