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Imported Upstream version 0.1.14
[samtools.git]
/
bamtk.c
diff --git
a/bamtk.c
b/bamtk.c
index 082767c8d6bf0a29be8f1b73101b8a7c43e29a08..5309d5ece3040e1413d9c2617d6efd1f5e0dfd67 100644
(file)
--- a/
bamtk.c
+++ b/
bamtk.c
@@
-8,10
+8,6
@@
#include "knetfile.h"
#endif
#include "knetfile.h"
#endif
-#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.9 (r783)"
-#endif
-
int bam_taf2baf(int argc, char *argv[]);
int bam_pileup(int argc, char *argv[]);
int bam_mpileup(int argc, char *argv[]);
int bam_taf2baf(int argc, char *argv[]);
int bam_pileup(int argc, char *argv[]);
int bam_mpileup(int argc, char *argv[]);
@@
-27,6
+23,9
@@
int bam_idxstats(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[]);
+int main_cut_target(int argc, char *argv[]);
+int main_phase(int argc, char *argv[]);
+int main_cat(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
int glf3_view_main(int argc, char *argv[]);
int faidx_main(int argc, char *argv[]);
int glf3_view_main(int argc, char *argv[]);
@@
-75,7
+74,7
@@
static int usage()
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
{
fprintf(stderr, "\n");
fprintf(stderr, "Program: samtools (Tools for alignments in the SAM format)\n");
- fprintf(stderr, "Version: %s\n\n",
PACKAGE
_VERSION);
+ fprintf(stderr, "Version: %s\n\n",
BAM
_VERSION);
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, "Usage: samtools <command> [options]\n\n");
fprintf(stderr, "Command: view SAM<->BAM conversion\n");
fprintf(stderr, " sort sort alignment file\n");
@@
-94,7
+93,16
@@
static int usage()
fprintf(stderr, " merge merge sorted alignments\n");
fprintf(stderr, " rmdup remove PCR duplicates\n");
fprintf(stderr, " reheader replace BAM header\n");
fprintf(stderr, " merge merge sorted alignments\n");
fprintf(stderr, " rmdup remove PCR duplicates\n");
fprintf(stderr, " reheader replace BAM header\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, "\n");
fprintf(stderr, "\n");
+#ifdef _WIN32
+ fprintf(stderr, "\
+Note: The Windows version of SAMtools is mainly designed for read-only\n\
+ operations, such as viewing the alignments and generating the pileup.\n\
+ Binary files generated by the Windows version may be buggy.\n\n");
+#endif
return 1;
}
return 1;
}
@@
-125,6
+133,9
@@
int main(int argc, char *argv[])
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);
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);
+ else if (strcmp(argv[1], "cat") == 0) return main_cat(argc-1, argv+1);
+ 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);
#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