X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bamtk.c;h=8ba25811d2771e171fa08899015449618838f265;hp=79635d6bf1bca8bad00abdaa5f926b35a3fc59a0;hb=HEAD;hpb=f2f3968e11eead9ce5601b01890bc2339ff951e9 diff --git a/bamtk.c b/bamtk.c index 79635d6..8ba2581 100644 --- a/bamtk.c +++ b/bamtk.c @@ -8,12 +8,7 @@ #include "knetfile.h" #endif -#ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.12a (r862)" -#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[]); @@ -27,60 +22,24 @@ 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_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 \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 [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"); @@ -88,13 +47,21 @@ static int usage() 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; } @@ -110,7 +77,6 @@ int main(int argc, char *argv[]) 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); @@ -119,12 +85,19 @@ int main(int argc, char *argv[]) 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