#include "knetfile.h"
#endif
-#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.8 (r613)"
-#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[]);
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 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()
{
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, " 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");
#if _CURSES_LIB != 0
fprintf(stderr, " tview text alignment viewer\n");
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");
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");
+#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;
}
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);
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);
+ 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);
+ 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
projects / samtools.git / blobdiff