Class: HTS::Native::BcfRecordHandle

Inherits:
Object
  • Object
show all
Defined in:
ext/htslib_native/native_bcf.c

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.create ⇒ Object 



240
 
# File 'ext/htslib_native/native_bcf.c', line 240

static VALUE native_bcf_record_create(VALUE klass) { return wrap_bcf_record(bcf_init()); }

Instance Method Details

#alleles ⇒ Object 



259
 
# File 'ext/htslib_native/native_bcf.c', line 259

static VALUE native_bcf_record_alleles(VALUE self) { bcf1_t *r=get_bcf_record(self)->pointer; int i; VALUE a; check_bcf_unpack(r,BCF_UN_STR); a=rb_ary_new_capa(r->n_allele); for(i=0;i<r->n_allele;i++){if(!r->d.allele[i])raise_bcf_record_error("BCF allele is missing after unpack");rb_ary_push(a,rb_str_new_cstr(r->d.allele[i]));} return a; }

#core_get(field) ⇒ Object 



242
243
244
245
246
247
248
249
 
# File 'ext/htslib_native/native_bcf.c', line 242

static VALUE native_bcf_record_core_get(VALUE self,VALUE field) {
    bcf1_t *r=get_bcf_record(self)->pointer; ID id=SYM2ID(field);
    if(id==rb_intern("rid"))return INT2NUM(r->rid);
    if(id==rb_intern("pos"))return LL2NUM(r->pos);
    if(id==rb_intern("rlen"))return LL2NUM(r->rlen);
    if(id==rb_intern("qual"))return DBL2NUM(r->qual);
    rb_raise(rb_eArgError,"unknown BCF field");
}

#core_set(field, value) ⇒ Object 



250
251
252
253
254
255
256
 
# File 'ext/htslib_native/native_bcf.c', line 250

static VALUE native_bcf_record_core_set(VALUE self,VALUE field,VALUE value) {
    bcf1_t *r=get_bcf_record(self)->pointer; ID id=SYM2ID(field);
    if(id==rb_intern("rid"))r->rid=NUM2INT(value); else if(id==rb_intern("pos"))r->pos=NUM2LL(value);
    else if(id==rb_intern("qual"))r->qual=(float)NUM2DBL(value);
    else rb_raise(rb_eArgError,"unknown BCF field");
    return value;
}

#duplicate ⇒ Object 



241
 
# File 'ext/htslib_native/native_bcf.c', line 241

static VALUE native_bcf_record_duplicate(VALUE self) { return wrap_bcf_record(bcf_dup(get_bcf_record(self)->pointer)); }

#filter_ids ⇒ Object 



261
 
# File 'ext/htslib_native/native_bcf.c', line 261

static VALUE native_bcf_record_filter_ids(VALUE self) { bcf1_t *r=get_bcf_record(self)->pointer; int i; VALUE a; check_bcf_unpack(r,BCF_UN_FLT); a=rb_ary_new_capa(r->d.n_flt); for(i=0;i<r->d.n_flt;i++)rb_ary_push(a,INT2NUM(r->d.flt[i])); return a; }

#filter_names(header) ⇒ Object 



262
 
# File 'ext/htslib_native/native_bcf.c', line 262

static VALUE native_bcf_record_filter_names(VALUE self,VALUE header) { bcf1_t *r=get_bcf_record(self)->pointer; bcf_hdr_t *h=get_bcf_header(header)->pointer; int i; VALUE a; check_bcf_unpack(r,BCF_UN_FLT); a=rb_ary_new_capa(r->d.n_flt); for(i=0;i<r->d.n_flt;i++)rb_ary_push(a,rb_str_new_cstr(checked_bcf_id(h,r->d.flt[i]))); return a; }

#format_delete(header, key, type) ⇒ Object 



394
 
# File 'ext/htslib_native/native_bcf.c', line 394

static VALUE native_bcf_format_delete(VALUE self,VALUE header,VALUE key,VALUE type) {return INT2NUM(bcf_update_format(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,StringValueCStr(key),NULL,0,NUM2INT(type)));}

#format_fields(header) ⇒ Object 



278
 
# File 'ext/htslib_native/native_bcf.c', line 278

static VALUE native_bcf_record_format_fields(VALUE self,VALUE header) { return field_rows(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,1); }

#format_get(header_value, key_value, type_value, raw_value) ⇒ Object 



356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
 
# File 'ext/htslib_native/native_bcf.c', line 356

static VALUE native_bcf_format_get(VALUE self,VALUE header_value,VALUE key_value,VALUE type_value,VALUE raw_value) {
    bcf_hdr_t*h=get_bcf_header(header_value)->pointer;bcf1_t*r=get_bcf_record(self)->pointer;int type=NUM2INT(type_value),cap=0,count;void*dst=NULL;
    if(type==BCF_HT_STR){
        char **strings=NULL;
        int sample_count=bcf_hdr_nsamples(h);
        bcf_string_result_t result;
        count=bcf_get_format_string(h,r,StringValueCStr(key_value),&strings,&cap);
        if(count<0){const char *key=StringValueCStr(key_value);free(strings);if(count==-3)return Qnil;raise_bcf_field_read_error("FormatReadError",key,count);}
        result.strings=strings;result.sample_count=sample_count;
        return rb_ensure(bcf_string_result_to_ruby,(VALUE)(uintptr_t)&result,
                         bcf_string_result_free,(VALUE)(uintptr_t)&result);
    }
    count=bcf_get_format_values(h,r,StringValueCStr(key_value),&dst,&cap,type);if(count<0){const char *key=StringValueCStr(key_value);free(dst);if(count==-3)return Qnil;raise_bcf_field_read_error("FormatReadError",key,count);}
    bcf_format_result_t result={dst,count,type,raw_value};
    return rb_ensure(bcf_format_result_to_ruby,(VALUE)(uintptr_t)&result,
                     bcf_value_result_free,(VALUE)(uintptr_t)&result);
}

#format_record(header) ⇒ Object 



263
 
# File 'ext/htslib_native/native_bcf.c', line 263

static VALUE native_bcf_record_to_s(VALUE self,VALUE header) { kstring_t s=KS_INITIALIZE; VALUE v; if(vcf_format(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,&s)<0){free(s.s);rb_raise(rb_eRuntimeError,"failed to format BCF record");}v=rb_str_new(s.s,s.l);free(s.s);return v; }

#format_update(header, key, type_value, values) ⇒ Object 



373
374
375
376
377
378
 
# File 'ext/htslib_native/native_bcf.c', line 373

static VALUE native_bcf_format_update(VALUE self,VALUE header,VALUE key,VALUE type_value,VALUE values) {
    bcf_hdr_t*h=get_bcf_header(header)->pointer;bcf1_t*r=get_bcf_record(self)->pointer;int type=NUM2INT(type_value),n,i,result;VALUE storage=0;
    if(type==BCF_HT_INT){int32_t*p;n=RARRAY_LEN(values);p=ALLOCV_N(int32_t,storage,n?n:1);for(i=0;i<n;i++)p[i]=NUM2INT(rb_ary_entry(values,i));result=bcf_update_format_int32(h,r,StringValueCStr(key),p,n);ALLOCV_END(storage);}
    else if(type==BCF_HT_REAL){float*p;n=RARRAY_LEN(values);p=ALLOCV_N(float,storage,n?n:1);for(i=0;i<n;i++)p[i]=(float)NUM2DBL(rb_ary_entry(values,i));result=bcf_update_format_float(h,r,StringValueCStr(key),p,n);ALLOCV_END(storage);}
    else {int i;char**strings;n=RARRAY_LEN(values);strings=ALLOCV_N(char*,storage,n?n:1);for(i=0;i<n;i++){VALUE string=rb_ary_entry(values,i);strings[i]=StringValueCStr(string);}result=bcf_update_format_string(h,r,StringValueCStr(key),(const char**)strings,n);ALLOCV_END(storage);}return INT2NUM(result);
}

#format_update_float_words(header, key, values) ⇒ Object 



379
380
381
382
383
384
385
386
387
388
389
390
391
392
 
# File 'ext/htslib_native/native_bcf.c', line 379

static VALUE native_bcf_format_update_float_words(VALUE self,VALUE header,VALUE key,VALUE values) {
    bcf_hdr_t *h=get_bcf_header(header)->pointer;
    bcf1_t *r=get_bcf_record(self)->pointer;
    int n=RARRAY_LEN(values),i,result;
    VALUE storage=0;
    float *floats=ALLOCV_N(float,storage,n?n:1);
    for(i=0;i<n;i++){
        uint32_t word=NUM2UINT(rb_ary_entry(values,i));
        memcpy(&floats[i],&word,sizeof(word));
    }
    result=bcf_update_format_float(h,r,StringValueCStr(key),floats,n);
    ALLOCV_END(storage);
    return INT2NUM(result);
}

#genotype_update(header, values) ⇒ Object 



393
 
# File 'ext/htslib_native/native_bcf.c', line 393

static VALUE native_bcf_genotype_update(VALUE self,VALUE header,VALUE values) {VALUE storage=0;int32_t*p;int n=RARRAY_LEN(values),i;p=ALLOCV_N(int32_t,storage,n?n:1);for(i=0;i<n;i++)p[i]=NUM2INT(rb_ary_entry(values,i));int result=bcf_update_genotypes(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,p,n);ALLOCV_END(storage);return INT2NUM(result);}

#id ⇒ Object 



257
 
# File 'ext/htslib_native/native_bcf.c', line 257

static VALUE native_bcf_record_id(VALUE self) { bcf1_t *r=get_bcf_record(self)->pointer; check_bcf_unpack(r,BCF_UN_STR); if(!r->d.id)raise_bcf_record_error("BCF record ID is missing after unpack"); return rb_str_new_cstr(r->d.id); }

#info_fields(header) ⇒ Object 



277
 
# File 'ext/htslib_native/native_bcf.c', line 277

static VALUE native_bcf_record_info_fields(VALUE self,VALUE header) { return field_rows(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,0); }

#info_get(header, key, type) ⇒ Object 



324
 
# File 'ext/htslib_native/native_bcf.c', line 324

static VALUE native_bcf_info_get(VALUE self,VALUE header,VALUE key,VALUE type) { return info_get(self,header,key,type); }

#info_present?(header, key, type) ⇒ Boolean

Returns:

  • (Boolean) 


325
 
# File 'ext/htslib_native/native_bcf.c', line 325

static VALUE native_bcf_info_present(VALUE self,VALUE header,VALUE key,VALUE type) { return NIL_P(info_get(self,header,key,type))?Qfalse:Qtrue; }

#info_update(header, key, type_value, values) ⇒ Object 



326
327
328
329
330
331
332
333
334
335
336
 
# File 'ext/htslib_native/native_bcf.c', line 326

static VALUE native_bcf_info_update(VALUE self,VALUE header,VALUE key,VALUE type_value,VALUE values) {
    bcf_hdr_t*h=get_bcf_header(header)->pointer;bcf1_t*r=get_bcf_record(self)->pointer;int type=NUM2INT(type_value),n,i,result;void*data=NULL;VALUE storage=0;
    if(type!=BCF_HT_FLAG && (NIL_P(values) || values==Qfalse)){
        return INT2NUM(bcf_update_info(h,r,StringValueCStr(key),NULL,0,type));
    }
    if(type==BCF_HT_INT){int32_t*p;n=RARRAY_LEN(values);p=ALLOCV_N(int32_t,storage,n?n:1);for(i=0;i<n;i++)p[i]=NUM2INT(rb_ary_entry(values,i));data=p;result=bcf_update_info(h,r,StringValueCStr(key),data,n,type);ALLOCV_END(storage);}
    else if(type==BCF_HT_REAL){float*p;n=RARRAY_LEN(values);p=ALLOCV_N(float,storage,n?n:1);for(i=0;i<n;i++)p[i]=(float)NUM2DBL(rb_ary_entry(values,i));data=p;result=bcf_update_info(h,r,StringValueCStr(key),data,n,type);ALLOCV_END(storage);}
    else if(type==BCF_HT_STR){result=bcf_update_info(h,r,StringValueCStr(key),StringValueCStr(values),1,type);}
    else { n=RTEST(values)?1:0; result=bcf_update_info(h,r,StringValueCStr(key),NULL,n,type); }
    return INT2NUM(result);
}

#max_unpack=(level) ⇒ Object 



264
 
# File 'ext/htslib_native/native_bcf.c', line 264

static VALUE native_bcf_record_set_unpack(VALUE self,VALUE level){get_bcf_record(self)->pointer->max_unpack=NUM2INT(level);return level;}

#set_alleles(header, value) ⇒ Object 



260
 
# File 'ext/htslib_native/native_bcf.c', line 260

static VALUE native_bcf_record_set_alleles(VALUE self,VALUE header,VALUE value) { return INT2NUM(bcf_update_alleles_str(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,StringValueCStr(value))); }

#set_id(header, id) ⇒ Object 



258
 
# File 'ext/htslib_native/native_bcf.c', line 258

static VALUE native_bcf_record_set_id(VALUE self,VALUE header,VALUE id) { return INT2NUM(bcf_update_id(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,StringValueCStr(id))); }

#subset(header, map) ⇒ Object 



265
 
# File 'ext/htslib_native/native_bcf.c', line 265

static VALUE native_bcf_record_subset(VALUE self,VALUE header,VALUE map){VALUE storage=0;int count=RARRAY_LEN(map),i,*imap=ALLOCV_N(int,storage,count?count:1);for(i=0;i<count;i++)imap[i]=NUM2INT(rb_ary_entry(map,i));int result=bcf_subset(get_bcf_header(header)->pointer,get_bcf_record(self)->pointer,count,imap);ALLOCV_END(storage);return INT2NUM(result);}