int bam_mpileup(int argc, char *argv[])
{
int c;
const char *file_list = NULL;
char **fn = NULL;
int nfiles = 0, use_orphan = 0, noref = 0;
mplp_conf_t mplp;
memset(&mplp, 0, sizeof(mplp_conf_t));
mplp.min_baseQ = 13;
mplp.capQ_thres = 0;
mplp.max_depth = 250; mplp.max_indel_depth = 250;
mplp.openQ = 40; mplp.extQ = 20; mplp.tandemQ = 100;
mplp.min_frac = 0.002; mplp.min_support = 1;
mplp.flag = MPLP_NO_ORPHAN | MPLP_REALN | MPLP_SMART_OVERLAPS;
mplp.argc = argc; mplp.argv = argv;
mplp.rflag_filter = BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP;
mplp.output_fname = NULL;
mplp.output_type = FT_VCF;
mplp.record_cmd_line = 1;
mplp.n_threads = 0;
mplp.bsmpl = bam_smpl_init();
static const struct option lopts[] =
{
{"rf", required_argument, NULL, 1}, // require flag
{"ff", required_argument, NULL, 2}, // filter flag
{"incl-flags", required_argument, NULL, 1},
{"excl-flags", required_argument, NULL, 2},
{"output", required_argument, NULL, 3},
{"open-prob", required_argument, NULL, 4},
{"ignore-RG", no_argument, NULL, 5},
{"ignore-rg", no_argument, NULL, 5},
{"gvcf", required_argument, NULL, 'g'},
{"no-reference", no_argument, NULL, 7},
{"no-version", no_argument, NULL, 8},
{"threads",required_argument,NULL,9},
{"illumina1.3+", no_argument, NULL, '6'},
{"count-orphans", no_argument, NULL, 'A'},
{"bam-list", required_argument, NULL, 'b'},
{"no-BAQ", no_argument, NULL, 'B'},
{"no-baq", no_argument, NULL, 'B'},
{"adjust-MQ", required_argument, NULL, 'C'},
{"adjust-mq", required_argument, NULL, 'C'},
{"max-depth", required_argument, NULL, 'd'},
{"redo-BAQ", no_argument, NULL, 'E'},
{"redo-baq", no_argument, NULL, 'E'},
{"fasta-ref", required_argument, NULL, 'f'},
{"read-groups", required_argument, NULL, 'G'},
{"region", required_argument, NULL, 'r'},
{"regions", required_argument, NULL, 'r'},
{"regions-file", required_argument, NULL, 'R'},
{"targets", required_argument, NULL, 't'},
{"targets-file", required_argument, NULL, 'T'},
{"min-MQ", required_argument, NULL, 'q'},
{"min-mq", required_argument, NULL, 'q'},
{"min-BQ", required_argument, NULL, 'Q'},
{"min-bq", required_argument, NULL, 'Q'},
{"ignore-overlaps", no_argument, NULL, 'x'},
{"output-type", required_argument, NULL, 'O'},
{"samples", required_argument, NULL, 's'},
{"samples-file", required_argument, NULL, 'S'},
{"annotate", required_argument, NULL, 'a'},
{"ext-prob", required_argument, NULL, 'e'},
{"gap-frac", required_argument, NULL, 'F'},
{"tandem-qual", required_argument, NULL, 'h'},
{"skip-indels", no_argument, NULL, 'I'},
{"max-idepth", required_argument, NULL, 'L'},
{"min-ireads ", required_argument, NULL, 'm'},
{"per-sample-mF", no_argument, NULL, 'p'},
{"per-sample-mf", no_argument, NULL, 'p'},
{"platforms", required_argument, NULL, 'P'},
{NULL, 0, NULL, 0}
};
while ((c = getopt_long(argc, argv, "Ag:f:r:R:q:Q:C:Bd:L:b:P:po:e:h:Im:F:EG:6O:xa:s:S:t:T:",lopts,NULL)) >= 0) {
switch (c) {
case 'x': mplp.flag &= ~MPLP_SMART_OVERLAPS; break;
case 1 :
mplp.rflag_require = bam_str2flag(optarg);
if ( mplp.rflag_require<0 ) { fprintf(stderr,"Could not parse --rf %s\n", optarg); return 1; }
break;
case 2 :
mplp.rflag_filter = bam_str2flag(optarg);
if ( mplp.rflag_filter<0 ) { fprintf(stderr,"Could not parse --ff %s\n", optarg); return 1; }
break;
case 3 : mplp.output_fname = optarg; break;
case 4 : mplp.openQ = atoi(optarg); break;
case 5 : bam_smpl_ignore_readgroups(mplp.bsmpl); break;
case 'g':
mplp.gvcf = gvcf_init(optarg);
if ( !mplp.gvcf ) error("Could not parse: --gvcf %s\n", optarg);
break;
case 'f':
mplp.fai = fai_load(optarg);
if (mplp.fai == NULL) return 1;
mplp.fai_fname = optarg;
break;
case 7 : noref = 1; break;
case 8 : mplp.record_cmd_line = 0; break;
case 9 : mplp.n_threads = strtol(optarg, 0, 0); break;
case 'd': mplp.max_depth = atoi(optarg); break;
case 'r': mplp.reg_fname = strdup(optarg); break;
case 'R': mplp.reg_fname = strdup(optarg); mplp.reg_is_file = 1; break;
case 't':
// In the original version the whole BAM was streamed which is inefficient
// with few BED intervals and big BAMs. Todo: devise a heuristic to determine
// best strategy, that is streaming or jumping.
if ( optarg[0]=='^' ) optarg++;
else mplp.bed_logic = 1;
mplp.bed = regidx_init(NULL,regidx_parse_reg,NULL,0,NULL);
mplp.bed_itr = regitr_init(mplp.bed);
if ( regidx_insert_list(mplp.bed,optarg,',') !=0 )
{
fprintf(stderr,"Could not parse the targets: %s\n", optarg);
exit(EXIT_FAILURE);
}
break;
case 'T':
if ( optarg[0]=='^' ) optarg++;
else mplp.bed_logic = 1;
mplp.bed = regidx_init(optarg,NULL,NULL,0,NULL);
if (!mplp.bed) { fprintf(stderr, "bcftools mpileup: Could not read file \"%s\"", optarg); return 1; }
break;
case 'P': mplp.pl_list = strdup(optarg); break;
case 'p': mplp.flag |= MPLP_PER_SAMPLE; break;
case 'B': mplp.flag &= ~MPLP_REALN; break;
case 'I': mplp.flag |= MPLP_NO_INDEL; break;
case 'E': mplp.flag |= MPLP_REDO_BAQ; break;
case '6': mplp.flag |= MPLP_ILLUMINA13; break;
case 's': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,0)<0 ) error("Could not read samples: %s\n",optarg); break;
case 'S': if ( bam_smpl_add_samples(mplp.bsmpl,optarg,1)<0 ) error("Could not read samples: %s\n",optarg); break;
case 'O':
switch (optarg[0]) {
case 'b': mplp.output_type = FT_BCF_GZ; break;
case 'u': mplp.output_type = FT_BCF; break;
case 'z': mplp.output_type = FT_VCF_GZ; break;
case 'v': mplp.output_type = FT_VCF; break;
default: error("[error] The option \"-O\" changed meaning when mpileup moved to bcftools. Did you mean: \"bcftools mpileup --output-type\" or \"samtools mpileup --output-BP\"?\n");
}
break;
case 'C': mplp.capQ_thres = atoi(optarg); break;
case 'q': mplp.min_mq = atoi(optarg); break;
case 'Q': mplp.min_baseQ = atoi(optarg); break;
case 'b': file_list = optarg; break;
case 'o': {
char *end;
long value = strtol(optarg, &end, 10);
// Distinguish between -o INT and -o FILE (a bit of a hack!)
if (*end == '\0') mplp.openQ = value;
else mplp.output_fname = optarg;
}
break;
case 'e': mplp.extQ = atoi(optarg); break;
case 'h': mplp.tandemQ = atoi(optarg); break;
case 'A': use_orphan = 1; break;
case 'F': mplp.min_frac = atof(optarg); break;
case 'm': mplp.min_support = atoi(optarg); break;
case 'L': mplp.max_indel_depth = atoi(optarg); break;
case 'G': bam_smpl_add_readgroups(mplp.bsmpl, optarg, 1); break;
case 'a':
if (optarg[0]=='?') {
list_annotations(stderr);
return 1;
}
mplp.fmt_flag |= parse_format_flag(optarg);
break;
default:
fprintf(stderr,"Invalid option: '%c'\n", c);
return 1;
}
}
if ( mplp.gvcf && !(mplp.fmt_flag&B2B_FMT_DP) )
{
fprintf(stderr,"[warning] The -t DP option is required with --gvcf, switching on.\n");
mplp.fmt_flag |= B2B_FMT_DP;
}
if ( mplp.flag&(MPLP_BCF|MPLP_VCF|MPLP_NO_COMP) )
{
if ( mplp.flag&MPLP_VCF )
{
if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_VCF;
else mplp.output_type = FT_VCF_GZ;
}
else if ( mplp.flag&MPLP_BCF )
{
if ( mplp.flag&MPLP_NO_COMP ) mplp.output_type = FT_BCF;
else mplp.output_type = FT_BCF_GZ;
}
}
if ( !(mplp.flag&MPLP_REALN) && mplp.flag&MPLP_REDO_BAQ )
{
fprintf(stderr,"Error: The -B option cannot be combined with -E\n");
return 1;
}
if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
if (argc == 1)
{
print_usage(stderr, &mplp);
return 1;
}
if (!mplp.fai && !noref) {
fprintf(stderr,"Error: mpileup requires the --fasta-ref option by default; use --no-reference to run without a fasta reference\n");
return 1;
}
int ret,i;
if (file_list)
{
if ( read_file_list(file_list,&nfiles,&fn) ) return 1;
mplp.files = fn;
mplp.nfiles = nfiles;
}
else
{
mplp.nfiles = argc - optind;
mplp.files = (char**) malloc(mplp.nfiles*sizeof(char*));
for (i=0; i<mplp.nfiles; i++) mplp.files[i] = strdup(argv[optind+i]);
}
ret = mpileup(&mplp);
for (i=0; i<mplp.nfiles; i++) free(mplp.files[i]);
free(mplp.files);
free(mplp.reg_fname); free(mplp.pl_list);
if (mplp.fai) fai_destroy(mplp.fai);
if (mplp.bed) regidx_destroy(mplp.bed);
if (mplp.bed_itr) regitr_destroy(mplp.bed_itr);
if (mplp.reg) regidx_destroy(mplp.reg);
bam_smpl_destroy(mplp.bsmpl);
return ret;
}
int main(int argc, char *argv[])
{
int first,i;
char* f;
group_t* group;
int sh_override = -1;
int list_packages = 0;
for (i=1; i<argc && *argv[i] == '-'; i++)
{
for (f=argv[i]+1; *f; f++)
switch (*f)
{
case 'v':
debugging = 1;
silent = 0;
break;
case 's':
debugging = 0;
silent = 1;
break;
case 'c':
sh_override = 1;
break;
case 'b':
sh_override = 0;
break;
case 'f':
main_package_filename = argv[++i];
break;
case 'l':
list_packages = 1;
break;
default:
fprintf(stderr, "usepackage: unrecognised flag '%c'\n", *f);
exit(1);
}
}
if (!list_packages && (i >= argc))
{
fprintf(stderr, "\n%s %s, %s\n", PACKAGE_NAME, PACKAGE_VERSION, COPYRIGHT);
fprintf(stderr, "Bug reports and comments to: %s\n", PACKAGE_BUGREPORT);
fprintf(stderr, "Discussion/announcement list: %s\n\n", MAILING_LIST);
fprintf(stderr, "usage: use [-vs] [-f <file>] <package> [<package>...]\n");
fprintf(stderr, " use -l\n\n");
fprintf(stderr, " -v : verbose\n");
fprintf(stderr, " -s : silence match warnings\n");
fprintf(stderr, " -f : use <file> as main packages file\n");
fprintf(stderr, " -l : list available packages\n\n");
exit(1);
}
DEBUG(stderr, "%s\n", PACKAGE_NAME);
DEBUG(stderr, "Version: %s\n", PACKAGE_VERSION);
DEBUG(stderr, "%s\n", COPYRIGHT);
uname(&the_host_info);
DEBUG(stderr, "host: %s\n", the_host_info.nodename);
DEBUG(stderr, "operating system: %s %s\n", the_host_info.sysname,
the_host_info.release);
DEBUG(stderr, "architecture: %s\n", the_host_info.machine);
the_shell = get_user_shell();
DEBUG(stderr, "shell: %s\n", the_shell);
if (sh_override != -1)
csh_user = sh_override;
else
csh_user = ((!strcmp(the_shell, "csh")) || (!strcmp(the_shell, "tcsh")));
the_environment = new_list();
the_scripts = new_list();
if (get_packages(&the_packages, &the_groups, &the_annotations))
{
fprintf(stderr, "usepackage: couldn't load package information.\n");
exit(2);
}
if (list_packages)
{
fprintf(stderr, "\nusepackage %s, %s\n\n", VERSION, COPYRIGHT);
fprintf(stderr, "Available packages are:\n\n");
list_annotations();
fprintf(stderr, "\nAvailable groups are:\n\n");
list_groups();
fprintf(stderr, "\n");
exit(0);
}
for (first = i, i = argc - 1 ; i >= first ; i--)
{
if (group = get_group(argv[i]))
use_group(group);
else
use_package(argv[i]);
}
print_env();
print_scripts();
return(0);
}
