static void flanks_sam_open()
{
if(!futil_path_has_extension(sam_path, ".bam") &&
!futil_path_has_extension(sam_path, ".sam"))
{
cmd_print_usage("Mapped flanks is not .sam or .bam file: %s", sam_path);
}
bool isbam = futil_path_has_extension(sam_path, ".bam");
samfh = sam_open(sam_path, isbam ? "rb" : "rs");
if(samfh == NULL) die("Cannot open SAM/BAM %s", sam_path);
// Load BAM header
bam_header = sam_hdr_read(samfh);
bamentry = bam_init1();
}
// reqtype: v=>vcf, z=>compressed vcf, b=>bcf, bu=>uncompressed bcf
int vcf_misc_get_outtype(const char *reqtype, const char *path)
{
int mode = -1;
if(reqtype) {
const char *ot = reqtype;
if(!strcmp(ot,"vcf") || !strcmp(ot,"uvcf") || !strcmp(ot,"v")) mode = 0;
else if(!strcmp(ot,"vcfgz") || !strcmp(ot,"z")) mode = 1;
else if(!strcmp(ot,"ubcf") || !strcmp(ot,"u")) mode = 2;
else if(!strcmp(ot,"bcf") || !strcmp(ot,"b")) mode = 3;
else die("Unkown output type: %s", ot);
}
else if(path) {
if( futil_path_has_extension(path,".vcf")) mode = 0;
else if(futil_path_has_extension(path,".vcfgz")) mode = 1;
else if(futil_path_has_extension(path,".vcf.gz")) mode = 1;
else if(futil_path_has_extension(path,".ubcf")) mode = 2;
else if(futil_path_has_extension(path,".bcf")) mode = 3;
}
// default to uncompressed VCF
return mode < 0 ? 0 : mode;
}
// returns -1 if we cannot calc
int64_t seq_est_seq_bases(seq_file_t **files, size_t nfiles)
{
size_t i;
int64_t est_num_bases = 0;
for(i = 0; i < nfiles; i++) {
if(strcmp(files[i]->path,"-") != 0) {
off_t fsize = futil_get_file_size(files[i]->path);
if(fsize < 0) warn("Cannot get file size: %s", files[i]->path);
else {
if(seq_is_fastq(files[i]) || seq_is_sam(files[i])) fsize /= 2;
if(futil_path_has_extension(files[i]->path,".gz")) fsize *= 4;
est_num_bases += fsize;
}
}
else return -1;
}
return est_num_bases;
}
