bamtk.c

/*  bamtk.c -- main samtools command front-end.

    Copyright (C) 2008-2015 Genome Research Ltd.

    Author: Heng Li <lh3@sanger.ac.uk>

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.  */

#include <stdio.h>
#include <unistd.h>
#include <fcntl.h>
#include <stdarg.h>
#include <string.h>
#include <errno.h>
#include "htslib/hts.h"
#include "samtools.h"
#include "version.h"

int bam_taf2baf(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[]);
int bam_tview_main(int argc, char *argv[]);
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 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 main_pad2unpad(int argc, char *argv[]);
int main_bedcov(int argc, char *argv[]);
int main_bamshuf(int argc, char *argv[]);
int main_stats(int argc, char *argv[]);
int main_flags(int argc, char *argv[]);
int main_split(int argc, char *argv[]);

int faidx_main(int argc, char *argv[]);
int dict_main(int argc, char *argv[]);

const char *samtools_version()
{
    return SAMTOOLS_VERSION;
}

void print_error(const char *format, ...)
{
    va_list args;
    va_start(args, format);
    fprintf(stderr, "samtools: ");
    vfprintf(stderr, format, args);
    fprintf(stderr, "\n");
    va_end(args);
}

void print_error_errno(const char *format, ...)
{
    int err = errno;
    va_list args;
    va_start(args, format);
    fprintf(stderr, "samtools: ");
    vfprintf(stderr, format, args);
    fprintf(stderr, ": %s\n", strerror(err));
    va_end(args);
}

static void usage(FILE *fp)
{
    /* Please improve the grouping */

    fprintf(fp,
"\n"
"Program: samtools (Tools for alignments in the SAM format)\n"
"Version: %s (using htslib %s)\n\n", samtools_version(), hts_version());
    fprintf(fp,
"Usage:   samtools <command> [options]\n\n"
"Commands:\n"
"  -- indexing\n"
"         dict        create a sequence dictionary file\n"
"         faidx       index/extract FASTA\n"
"         index       index alignment\n"
"  -- editing\n"
"         calmd       recalculate MD/NM tags and '=' bases\n"
"         fixmate     fix mate information\n"
"         reheader    replace BAM header\n"
"         rmdup       remove PCR duplicates\n"
"         targetcut   cut fosmid regions (for fosmid pool only)\n"
"  -- file operations\n"
"         bamshuf     shuffle and group alignments by name\n"
"         cat         concatenate BAMs\n"
"         merge       merge sorted alignments\n"
"         mpileup     multi-way pileup\n"
"         sort        sort alignment file\n"
"         split       splits a file by read group\n"
"         bam2fq      converts a BAM to a FASTQ\n"
"  -- stats\n"
"         bedcov      read depth per BED region\n"
"         depth       compute the depth\n"
"         flagstat    simple stats\n"
"         idxstats    BAM index stats\n"
"         phase       phase heterozygotes\n"
"         stats       generate stats (former bamcheck)\n"
"  -- viewing\n"
"         flags       explain BAM flags\n"
"         tview       text alignment viewer\n"
"         view        SAM<->BAM<->CRAM conversion\n"
//"         depad       convert padded BAM to unpadded BAM\n" // not stable
"\n");
#ifdef _WIN32
    fprintf(fp,
"\n"
"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
}

int main(int argc, char *argv[])
{
#ifdef _WIN32
    setmode(fileno(stdout), O_BINARY);
    setmode(fileno(stdin),  O_BINARY);
#endif
    if (argc < 2) { usage(stderr); return 1; }

    if (strcmp(argv[1], "help") == 0 || strcmp(argv[1], "--help") == 0) {
        if (argc == 2) { usage(stdout); return 0; }

        // Otherwise change "samtools help COMMAND [...]" to "samtools COMMAND";
        // main_xyz() functions by convention display the subcommand's usage
        // when invoked without any arguments.
        argv++;
        argc = 2;
    }

    int ret = 0;
    if (strcmp(argv[1], "view") == 0)           ret = main_samview(argc-1, argv+1);
    else if (strcmp(argv[1], "import") == 0)    ret = main_import(argc-1, argv+1);
    else if (strcmp(argv[1], "mpileup") == 0)   ret = bam_mpileup(argc-1, argv+1);
    else if (strcmp(argv[1], "merge") == 0)     ret = bam_merge(argc-1, argv+1);
    else if (strcmp(argv[1], "sort") == 0)      ret = bam_sort(argc-1, argv+1);
    else if (strcmp(argv[1], "index") == 0)     ret = bam_index(argc-1, argv+1);
    else if (strcmp(argv[1], "idxstats") == 0)  ret = bam_idxstats(argc-1, argv+1);
    else if (strcmp(argv[1], "faidx") == 0)     ret = faidx_main(argc-1, argv+1);
    else if (strcmp(argv[1], "dict") == 0)      ret = dict_main(argc-1, argv+1);
    else if (strcmp(argv[1], "fixmate") == 0)   ret = bam_mating(argc-1, argv+1);
    else if (strcmp(argv[1], "rmdup") == 0)     ret = bam_rmdup(argc-1, argv+1);
    else if (strcmp(argv[1], "flagstat") == 0)  ret = bam_flagstat(argc-1, argv+1);
    else if (strcmp(argv[1], "calmd") == 0)     ret = bam_fillmd(argc-1, argv+1);
    else if (strcmp(argv[1], "fillmd") == 0)    ret = bam_fillmd(argc-1, argv+1);
    else if (strcmp(argv[1], "reheader") == 0)  ret = main_reheader(argc-1, argv+1);
    else if (strcmp(argv[1], "cat") == 0)       ret = main_cat(argc-1, argv+1);
    else if (strcmp(argv[1], "targetcut") == 0) ret = main_cut_target(argc-1, argv+1);
    else if (strcmp(argv[1], "phase") == 0)     ret = main_phase(argc-1, argv+1);
    else if (strcmp(argv[1], "depth") == 0)     ret = main_depth(argc-1, argv+1);
    else if (strcmp(argv[1], "bam2fq") == 0)    ret = main_bam2fq(argc-1, argv+1);
    else if (strcmp(argv[1], "pad2unpad") == 0) ret = main_pad2unpad(argc-1, argv+1);
    else if (strcmp(argv[1], "depad") == 0)     ret = main_pad2unpad(argc-1, argv+1);
    else if (strcmp(argv[1], "bedcov") == 0)    ret = main_bedcov(argc-1, argv+1);
    else if (strcmp(argv[1], "bamshuf") == 0)   ret = main_bamshuf(argc-1, argv+1);
    else if (strcmp(argv[1], "stats") == 0)     ret = main_stats(argc-1, argv+1);
    else if (strcmp(argv[1], "flags") == 0)     ret = main_flags(argc-1, argv+1);
    else if (strcmp(argv[1], "split") == 0)     ret = main_split(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)   ret = bam_tview_main(argc-1, argv+1);
#endif
    else if (strcmp(argv[1], "--version") == 0) {
        printf(
"samtools %s\n"
"Using htslib %s\n"
"Copyright (C) 2015 Genome Research Ltd.\n",
               samtools_version(), hts_version());
    }
    else if (strcmp(argv[1], "--version-only") == 0) {
        printf("%s+htslib-%s\n", samtools_version(), hts_version());
    }
    else {
        fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
        return 1;
    }
    return ret;
}