Class: HTS::Native::PileupHandle

Inherits:

Object

• Object
• HTS::Native::PileupHandle

Defined in:

ext/htslib_native/native_bam.c

Class Method Summary

• .open(file_value, header_value, region_value, beg_value, end_value, max_value) ⇒ Object

Instance Method Summary

• #close ⇒ Object
• #next ⇒ Object
• #reset ⇒ Object

Class Method Details

.open(file_value, header_value, region_value, beg_value, end_value, max_value) ⇒ Object

# File 'ext/htslib_native/native_bam.c', line 856

static VALUE native_pileup_open(VALUE klass, VALUE file_value, VALUE header_value,
                                VALUE region_value, VALUE beg_value, VALUE end_value, VALUE max_value) {
    ruby_pileup_t *value;
    ruby_bam_file_t *file = get_file(file_value, 0);
    VALUE object;
    get_header(header_value);
    object = TypedData_Make_Struct(klass, ruby_pileup_t, &pileup_type, value);
    value->pileup = NULL;
    value->iterator = NULL;
    value->file = file_value;
    value->header = header_value;
    RB_OBJ_WRITE(object, &value->file, file_value);
    RB_OBJ_WRITE(object, &value->header, header_value);
    if (!NIL_P(region_value)) {
        if (!file->index) rb_raise(rb_eRuntimeError, "index file is required to use region pileup");
        if (NIL_P(beg_value) && NIL_P(end_value))
            value->iterator = sam_itr_querys(file->index, get_header(header_value)->pointer, StringValueCStr(region_value));
        else
            value->iterator = sam_itr_queryi(file->index,
                sam_hdr_name2tid(get_header(header_value)->pointer, StringValueCStr(region_value)),
                NUM2LL(beg_value), NUM2LL(end_value));
        if (!value->iterator) rb_raise(rb_eRuntimeError, "failed to query pileup region");
    }
    value->pileup = bam_plp_init(native_pileup_read, value);
    if (!value->pileup) rb_raise(rb_eNoMemError, "bam_plp_init failed");
    if (!NIL_P(max_value)) bam_plp_set_maxcnt(value->pileup, NUM2INT(max_value));
    return object;
}

Instance Method Details

#close ⇒ Object

# File 'ext/htslib_native/native_bam.c', line 933

static VALUE native_pileup_close(VALUE self) {
    ruby_pileup_t *value = get_pileup(self, 1);
    if (value->pileup) { bam_plp_destroy(value->pileup); value->pileup = NULL; }
    if (value->iterator) { hts_itr_destroy(value->iterator); value->iterator = NULL; }
    return Qnil;
}

#next ⇒ Object

# File 'ext/htslib_native/native_bam.c', line 913

static VALUE native_pileup_next(VALUE self) {
    ruby_pileup_t *value = get_pileup(self, 0);
    int tid = -1, count = 0;
    hts_pos_t position = -1;
    const bam_pileup1_t *entries = bam_plp64_auto(value->pileup, &tid, &position, &count);
    VALUE result;
    if (!entries) {
        if (count < 0) rb_raise(rb_eRuntimeError, "HTSlib pileup error");
        return Qnil;
    }
    result = rb_ary_new_capa(3);
    rb_ary_push(result, INT2NUM(tid));
    rb_ary_push(result, LL2NUM(position));
    rb_ary_push(result, pileup_rows(entries, count));
    return result;
}

#reset ⇒ Object

# File 'ext/htslib_native/native_bam.c', line 929

static VALUE native_pileup_reset(VALUE self) {
    bam_plp_reset(get_pileup(self, 0)->pileup);
    return Qnil;
}