BOOL CDKnownProcesses::DestroyWindow()
{
// TODO: Add your specialized code here and/or call the base class
SavePosition();
CListColumnPositions list_columns(_T("KnownProcess_List"), &m_lKnownProcesses);
list_columns.SavePositions();
return CDialog::DestroyWindow();
}
void CDKnownProcesses::RestorePosition()
{
WINDOWPLACEMENT wpl;
UINT dw = 0;
if (g_pReestr->GetBinaryValue(_T("KnownPosition"), (DWORD) &wpl, sizeof(wpl)))
SetWindowPlacement(&wpl);
CListColumnPositions list_columns(_T("KnownProcess_List"), &m_lKnownProcesses);
list_columns.RestorePositions();
}
int main_vcfquery(int argc, char *argv[])
{
int c, collapse = 0;
args_t *args = (args_t*) calloc(1,sizeof(args_t));
args->argc = argc; args->argv = argv;
int regions_is_file = 0, targets_is_file = 0;
static struct option loptions[] =
{
{"help",0,0,'h'},
{"list-samples",0,0,'l'},
{"include",1,0,'i'},
{"exclude",1,0,'e'},
{"format",1,0,'f'},
{"output-file",1,0,'o'},
{"regions",1,0,'r'},
{"regions-file",1,0,'R'},
{"targets",1,0,'t'},
{"targets-file",1,0,'T'},
{"annots",1,0,'a'},
{"samples",1,0,'s'},
{"samples-file",1,0,'S'},
{"print-header",0,0,'H'},
{"collapse",1,0,'c'},
{"vcf-list",1,0,'v'},
{"allow-undef-tags",0,0,'u'},
{0,0,0,0}
};
while ((c = getopt_long(argc, argv, "hlr:R:f:a:s:S:Ht:T:c:v:i:e:o:u",loptions,NULL)) >= 0) {
switch (c) {
case 'o': args->fn_out = optarg; break;
case 'f': args->format_str = strdup(optarg); break;
case 'H': args->print_header = 1; break;
case 'v': args->vcf_list = optarg; break;
case 'c':
if ( !strcmp(optarg,"snps") ) collapse |= COLLAPSE_SNPS;
else if ( !strcmp(optarg,"indels") ) collapse |= COLLAPSE_INDELS;
else if ( !strcmp(optarg,"both") ) collapse |= COLLAPSE_SNPS | COLLAPSE_INDELS;
else if ( !strcmp(optarg,"any") ) collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"all") ) collapse |= COLLAPSE_ANY;
else if ( !strcmp(optarg,"some") ) collapse |= COLLAPSE_SOME;
else error("The --collapse string \"%s\" not recognised.\n", optarg);
break;
case 'a':
{
kstring_t str = {0,0,0};
kputs("%CHROM\t%POS\t%MASK\t%REF\t%ALT\t%", &str);
char *p = optarg;
while ( *p )
{
if ( *p==',' )
kputs("\t%", &str);
else
kputc(*p, &str);
p++;
}
kputc('\n', &str);
args->format_str = str.s;
break;
}
case 'e': args->filter_str = optarg; args->filter_logic |= FLT_EXCLUDE; break;
case 'i': args->filter_str = optarg; args->filter_logic |= FLT_INCLUDE; break;
case 'r': args->regions_list = optarg; break;
case 'R': args->regions_list = optarg; regions_is_file = 1; break;
case 't': args->targets_list = optarg; break;
case 'T': args->targets_list = optarg; targets_is_file = 1; break;
case 'l': args->list_columns = 1; break;
case 'u': args->allow_undef_tags = 1; break;
case 's': args->sample_list = optarg; break;
case 'S': args->sample_list = optarg; args->sample_is_file = 1; break;
case 'h':
case '?': usage();
default: error("Unknown argument: %s\n", optarg);
}
}
char *fname = NULL;
if ( optind>=argc )
{
if ( !isatty(fileno((FILE *)stdin)) ) fname = "-";
}
else fname = argv[optind];
if ( args->list_columns )
{
if ( !fname ) error("Missing the VCF file name\n");
args->files = bcf_sr_init();
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
list_columns(args);
bcf_sr_destroy(args->files);
free(args);
return 0;
}
if ( !args->format_str ) usage();
args->out = args->fn_out ? fopen(args->fn_out, "w") : stdout;
if ( !args->out ) error("%s: %s\n", args->fn_out,strerror(errno));
if ( !args->vcf_list )
{
if ( !fname ) usage();
args->files = bcf_sr_init();
args->files->collapse = collapse;
if ( optind+1 < argc ) args->files->require_index = 1;
if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list, targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
while ( fname )
{
if ( !bcf_sr_add_reader(args->files, fname) ) error("Failed to open %s: %s\n", fname,bcf_sr_strerror(args->files->errnum));
fname = ++optind < argc ? argv[optind] : NULL;
}
init_data(args);
query_vcf(args);
free(args->format_str);
destroy_data(args);
bcf_sr_destroy(args->files);
fclose(args->out);
free(args);
return 0;
}
// multiple VCFs
int i, k, nfiles, prev_nsamples = 0;
char **fnames, **prev_samples = NULL;
fnames = hts_readlist(args->vcf_list, 1, &nfiles);
if ( !nfiles ) error("No files in %s?\n", args->vcf_list);
for (i=0; i<nfiles; i++)
{
args->files = bcf_sr_init();
args->files->collapse = collapse;
if ( args->regions_list && bcf_sr_set_regions(args->files, args->regions_list, regions_is_file)<0 )
error("Failed to read the regions: %s\n", args->regions_list);
if ( optind < argc ) args->files->require_index = 1;
if ( args->targets_list )
{
if ( bcf_sr_set_targets(args->files, args->targets_list,targets_is_file, 0)<0 )
error("Failed to read the targets: %s\n", args->targets_list);
}
if ( !bcf_sr_add_reader(args->files, fnames[i]) ) error("Failed to open %s: %s\n", fnames[i],bcf_sr_strerror(args->files->errnum));
for (k=optind; k<argc; k++)
if ( !bcf_sr_add_reader(args->files, argv[k]) ) error("Failed to open %s: %s\n", argv[k],bcf_sr_strerror(args->files->errnum));
init_data(args);
if ( i==0 )
prev_samples = copy_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header));
else
{
args->print_header = 0;
if ( compare_header(args->header, args->files->readers[0].header->samples, bcf_hdr_nsamples(args->files->readers[0].header), prev_samples, prev_nsamples) )
error("Different samples in %s and %s\n", fnames[i-1],fnames[i]);
}
query_vcf(args);
destroy_data(args);
bcf_sr_destroy(args->files);
}
fclose(args->out);
destroy_list(fnames, nfiles);
destroy_list(prev_samples, prev_nsamples);
free(args->format_str);
free(args);
return 0;
}
