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added calls and description for bam_calnh.
author
Henry Amrhein
<hamrhein@caltech.edu>
Fri, 21 Dec 2012 20:36:17 +0000
(12:36 -0800)
committer
Henry Amrhein
<hamrhein@caltech.edu>
Fri, 21 Dec 2012 20:36:17 +0000
(12:36 -0800)
bamtk.c
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diff --git
a/bamtk.c
b/bamtk.c
index 8ba25811d2771e171fa08899015449618838f265..52b12df86edb655f21e9d73d1325a0c505f20eb7 100644
(file)
--- a/
bamtk.c
+++ b/
bamtk.c
@@
-19,6
+19,7
@@
int bam_rmdup(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
int bam_fillmd(int argc, char *argv[]);
int bam_idxstats(int argc, char *argv[]);
int bam_flagstat(int argc, char *argv[]);
int bam_fillmd(int argc, char *argv[]);
int bam_idxstats(int argc, char *argv[]);
+int bam_calnh(int argc, char **argv);
int main_samview(int argc, char *argv[]);
int main_import(int argc, char *argv[]);
int main_reheader(int argc, char *argv[]);
int main_samview(int argc, char *argv[]);
int main_import(int argc, char *argv[]);
int main_reheader(int argc, char *argv[]);
@@
-55,6
+56,7
@@
static int usage()
fprintf(stderr, " cat concatenate BAMs\n");
fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
fprintf(stderr, " phase phase heterozygotes\n");
fprintf(stderr, " cat concatenate BAMs\n");
fprintf(stderr, " targetcut cut fosmid regions (for fosmid pool only)\n");
fprintf(stderr, " phase phase heterozygotes\n");
+ fprintf(stderr, " calnh calculate NH tags\n");
fprintf(stderr, "\n");
#ifdef _WIN32
fprintf(stderr, "\
fprintf(stderr, "\n");
#ifdef _WIN32
fprintf(stderr, "\
@@
-98,6
+100,7
@@
int main(int argc, char *argv[])
fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;
}
fprintf(stderr, "[main] The `pileup' command has been removed. Please use `mpileup' instead.\n");
return 1;
}
+ else if (strcmp(argv[1], "calnh") == 0) return bam_calnh(argc-1, argv+1);
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif
#if _CURSES_LIB != 0
else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1);
#endif