X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bamtk.c;h=4de99d7482e5c35c7f682ad68a49a0bf3526afdf;hb=0993e913dc402cbb11783bf5d3f96eed1c437e06;hp=abb9015ab366a6d8dd6d7e256715f25bebd15869;hpb=8bee1f18418f068dc0d73ad6ec47084c2f830b32;p=samtools.git diff --git a/bamtk.c b/bamtk.c index abb9015..4de99d7 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,11 +9,12 @@ #endif #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.6-16 (r483)" +#define PACKAGE_VERSION "0.1.8-19 (r777)" #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 bam_sort(int argc, char *argv[]); @@ -22,9 +23,10 @@ int bam_mating(int argc, char *argv[]); 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 main_samview(int argc, char *argv[]); int main_import(int argc, char *argv[]); +int main_reheader(int argc, char *argv[]); int faidx_main(int argc, char *argv[]); int glf3_view_main(int argc, char *argv[]); @@ -78,17 +80,20 @@ static int usage() 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, " faidx index/extract FASTA\n"); #if _CURSES_LIB != 0 fprintf(stderr, " tview text alignment viewer\n"); #endif 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, "\n"); return 1; } @@ -106,9 +111,11 @@ int main(int argc, char *argv[]) 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], "index") == 0) return bam_index(argc-1, argv+1); + else if (strcmp(argv[1], "idxstats") == 0) return bam_idxstats(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); @@ -117,6 +124,7 @@ int main(int argc, char *argv[]) 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); #if _CURSES_LIB != 0 else if (strcmp(argv[1], "tview") == 0) return bam_tview_main(argc-1, argv+1); #endif