Class: HTS::Native::BamRecordHandle

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

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.create ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 237

static VALUE native_record_create(VALUE klass) { return wrap_record(bam_init1()); }

Instance Method Details

#aux_append(key, type, payload) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 504

static VALUE native_record_aux_append(VALUE self, VALUE key, VALUE type, VALUE payload) {
    StringValue(payload);
    return INT2NUM(bam_aux_append(get_record(self)->pointer, StringValueCStr(key), StringValueCStr(type)[0],
                                  RSTRING_LEN(payload), (uint8_t *)RSTRING_PTR(payload)));
}

#aux_delete(key) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 533

static VALUE native_record_aux_delete(VALUE self, VALUE key) {
    bam1_t *record = get_record(self)->pointer;
    uint8_t *aux = bam_aux_get(record, StringValueCStr(key));
    if (!aux) return Qfalse;
    if (bam_aux_del(record, aux) < 0) rb_raise(rb_eRuntimeError, "failed to delete AUX tag");
    return Qtrue;
}

#aux_entries ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 483

static VALUE native_record_aux_entries(VALUE self) {
    bam1_t *record = get_record(self)->pointer;
    uint8_t *aux = bam_aux_first(record);
    VALUE result = rb_ary_new();
    while (aux) {
        VALUE entry = aux_decode(aux, Qnil);
        rb_ary_unshift(entry, rb_str_new((char *)aux - 2, 2));
        rb_ary_push(result, entry);
        aux = bam_aux_next(record, aux);
    }
    return result;
}

#aux_get(key, requested) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 479

static VALUE native_record_aux_get(VALUE self, VALUE key, VALUE requested) {
    uint8_t *aux = bam_aux_get(get_record(self)->pointer, StringValueCStr(key));
    return aux ? aux_decode(aux, requested) : Qnil;
}

#aux_key?(key) ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'ext/htslib_native/native_bam.c', line 540

static VALUE native_record_aux_key(VALUE self, VALUE key) {
    return bam_aux_get(get_record(self)->pointer, StringValueCStr(key)) ? Qtrue : Qfalse;
}

#aux_update_array(key, type_value, array) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 509

static VALUE native_record_aux_update_array(VALUE self, VALUE key, VALUE type_value, VALUE array) {
    char type = StringValueCStr(type_value)[0];
    long count = RARRAY_LEN(array), i;
    size_t width;
    uint8_t *buffer;
    VALUE buffer_storage = 0;
    int result;
    switch (type) { case 'c': case 'C': width = 1; break; case 's': case 'S': width = 2; break; default: width = 4; }
    buffer = ALLOCV_N(uint8_t, buffer_storage, count * width + 1);
    for (i = 0; i < count; i++) {
        VALUE item = rb_ary_entry(array, i);
        if (type == 'c') { int8_t v = NUM2INT(item); memcpy(buffer + i, &v, 1); }
        else if (type == 'C') { uint8_t v = NUM2UINT(item); memcpy(buffer + i, &v, 1); }
        else if (type == 's') { int16_t v = NUM2INT(item); memcpy(buffer + i * 2, &v, 2); }
        else if (type == 'S') { uint16_t v = NUM2UINT(item); memcpy(buffer + i * 2, &v, 2); }
        else if (type == 'i') { int32_t v = NUM2INT(item); memcpy(buffer + i * 4, &v, 4); }
        else if (type == 'I') { uint32_t v = NUM2UINT(item); memcpy(buffer + i * 4, &v, 4); }
        else if (type == 'f') { float v = (float)NUM2DBL(item); memcpy(buffer + i * 4, &v, 4); }
        else { ALLOCV_END(buffer_storage); rb_raise(rb_eArgError, "invalid AUX array type"); }
    }
    result = bam_aux_update_array(get_record(self)->pointer, StringValueCStr(key), type, count, buffer);
    ALLOCV_END(buffer_storage);
    return INT2NUM(result);
}

#aux_update_float(key, value) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 498

static VALUE native_record_aux_update_float(VALUE self, VALUE key, VALUE value) {
    return INT2NUM(bam_aux_update_float(get_record(self)->pointer, StringValueCStr(key), NUM2DBL(value)));
}

#aux_update_int(key, value) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 495

static VALUE native_record_aux_update_int(VALUE self, VALUE key, VALUE value) {
    return INT2NUM(bam_aux_update_int(get_record(self)->pointer, StringValueCStr(key), NUM2LL(value)));
}

#aux_update_string(key, value) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 501

static VALUE native_record_aux_update_string(VALUE self, VALUE key, VALUE value) {
    return INT2NUM(bam_aux_update_str(get_record(self)->pointer, StringValueCStr(key), -1, StringValueCStr(value)));
}

#base_code(index) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 383

static VALUE native_record_base_code(VALUE self, VALUE index) {
    bam1_t *record = get_record(self)->pointer;
    long i = NUM2LONG(index);
    if (i < 0 || i >= record->core.l_qseq) return Qnil;
    return INT2NUM(bam_seqi(bam_get_seq(record), i));
}

#cigar=(text) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 331

static VALUE native_record_set_cigar(VALUE self, VALUE text) {
    bam1_t *record = get_record(self)->pointer;
    int result = bam_parse_cigar(StringValueCStr(text), NULL, record);
    if (result < 0) rb_raise(rb_eRuntimeError, "bam_parse_cigar failed: %d", result);
    native_record_update_bin(record);
    return text;
}

#cigar_values ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 323

static VALUE native_record_cigar_values(VALUE self) {
    bam1_t *record = get_record(self)->pointer;
    uint32_t *cigar = bam_get_cigar(record);
    VALUE result = rb_ary_new_capa(record->core.n_cigar);
    uint32_t i;
    for (i = 0; i < record->core.n_cigar; i++) rb_ary_push(result, UINT2NUM(cigar[i]));
    return result;
}

#core_get(field) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 292

static VALUE native_record_core_get(VALUE self, VALUE field) {
    bam1_core_t *core = &get_record(self)->pointer->core;
    ID id = SYM2ID(field);
    if (id == rb_intern("tid")) return INT2NUM(core->tid);
    if (id == rb_intern("mtid")) return INT2NUM(core->mtid);
    if (id == rb_intern("pos")) return LL2NUM(core->pos);
    if (id == rb_intern("mpos")) return LL2NUM(core->mpos);
    if (id == rb_intern("bin")) return UINT2NUM(core->bin);
    if (id == rb_intern("isize")) return LL2NUM(core->isize);
    if (id == rb_intern("mapq")) return UINT2NUM(core->qual);
    if (id == rb_intern("flag")) return UINT2NUM(core->flag);
    if (id == rb_intern("length")) return LL2NUM(core->l_qseq);
    rb_raise(rb_eArgError, "unknown BAM core field");
}

#core_set(field, new_value) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 306

static VALUE native_record_core_set(VALUE self, VALUE field, VALUE new_value) {
    bam1_t *record = get_record(self)->pointer;
    bam1_core_t *core = &record->core;
    ID id = SYM2ID(field);
    if (id == rb_intern("tid")) core->tid = NUM2INT(new_value);
    else if (id == rb_intern("mtid")) core->mtid = NUM2INT(new_value);
    else if (id == rb_intern("pos")) core->pos = NUM2LL(new_value);
    else if (id == rb_intern("mpos")) core->mpos = NUM2LL(new_value);
    else if (id == rb_intern("bin")) core->bin = NUM2UINT(new_value);
    else if (id == rb_intern("isize")) core->isize = NUM2LL(new_value);
    else if (id == rb_intern("mapq")) core->qual = NUM2UINT(new_value);
    else if (id == rb_intern("flag")) core->flag = NUM2UINT(new_value);
    else rb_raise(rb_eArgError, "unknown or read-only BAM core field");
    if (id == rb_intern("pos") || id == rb_intern("flag")) native_record_update_bin(record);
    return new_value;
}

#duplicate ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 238

static VALUE native_record_duplicate(VALUE self) { return wrap_record(bam_dup1(get_record(self)->pointer)); }

#endpos ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 322

static VALUE native_record_endpos(VALUE self) { return LL2NUM(bam_endpos(get_record(self)->pointer)); }

#format(header_value) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 395

static VALUE native_record_to_s(VALUE self, VALUE header_value) {
    kstring_t string = KS_INITIALIZE;
    int result = sam_format1(get_header(header_value)->pointer, get_record(self)->pointer, &string);
    VALUE value;
    if (result < 0) { free(string.s); rb_raise(rb_eRuntimeError, "failed to format BAM record"); }
    value = rb_str_new(string.s, string.l);
    free(string.s);
    return value;
}

#qlen ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 338

static VALUE native_record_qlen(VALUE self) {
    bam1_t *record = get_record(self)->pointer;
    return LL2NUM(bam_cigar2qlen(record->core.n_cigar, bam_get_cigar(record)));
}

#qname ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 283

static VALUE native_record_qname(VALUE self) { return rb_str_new_cstr(bam_get_qname(get_record(self)->pointer)); }

#qname=(name) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 284

static VALUE native_record_set_qname(VALUE self, VALUE name) {
    int result = bam_set_qname(get_record(self)->pointer, StringValueCStr(name));
    if (result < 0) rb_raise(rb_eRuntimeError, "bam_set_qname failed: %d", result);
    return name;
}

#qualities ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 364

static VALUE native_record_qualities(VALUE self) {
    bam1_t *record = get_record(self)->pointer;
    uint8_t *qualities = bam_get_qual(record);
    hts_pos_t i, length = record->core.l_qseq;
    VALUE result = rb_ary_new_capa(length);
    for (i = 0; i < length; i++) rb_ary_push(result, UINT2NUM(qualities[i]));
    return result;
}

#quality_at(index) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 389

static VALUE native_record_quality_at(VALUE self, VALUE index) {
    bam1_t *record = get_record(self)->pointer;
    long i = NUM2LONG(index);
    if (i < 0 || i >= record->core.l_qseq) return Qnil;
    return UINT2NUM(bam_get_qual(record)[i]);
}

#quality_string ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 372

static VALUE native_record_quality_string(VALUE self) {
    bam1_t *record = get_record(self)->pointer;
    uint8_t *qualities = bam_get_qual(record);
    hts_pos_t i, length = record->core.l_qseq;
    VALUE result;
    if (length == 0) return rb_str_new("", 0);
    if (qualities[0] == 255) return rb_str_new("*", 1);
    result = rb_str_new(NULL, length);
    for (i = 0; i < length; i++) RSTRING_PTR(result)[i] = (char)(qualities[i] + 33);
    return result;
}

#replace(qname, flag, tid, pos, mapq, cigar_value, mtid, mpos, isize, sequence, qualities) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 239

static VALUE native_record_replace(VALUE self, VALUE qname, VALUE flag, VALUE tid, VALUE pos,
                                   VALUE mapq, VALUE cigar_value, VALUE mtid, VALUE mpos,
                                   VALUE isize, VALUE sequence, VALUE qualities) {
    bam1_t *record = get_record(self)->pointer;
    long cigar_count, i;
    uint32_t *cigar = NULL;
    VALUE cigar_storage = 0;
    const char *quality_data = NULL;
    int result;

    StringValue(qname);
    StringValue(sequence);
    if (memchr(RSTRING_PTR(qname), '\0', RSTRING_LEN(qname))) {
        rb_raise(rb_eArgError, "qname must not contain NUL bytes");
    }
    Check_Type(cigar_value, T_ARRAY);
    cigar_count = RARRAY_LEN(cigar_value);
    if (cigar_count > 0) {
        cigar = ALLOCV_N(uint32_t, cigar_storage, cigar_count);
        for (i = 0; i < cigar_count; i++) cigar[i] = NUM2UINT(rb_ary_entry(cigar_value, i));
    }
    if (!NIL_P(qualities)) {
        StringValue(qualities);
        if (RSTRING_LEN(qualities) != RSTRING_LEN(sequence)) {
            ALLOCV_END(cigar_storage);
            rb_raise(rb_eArgError, "qualities length must match sequence length");
        }
        quality_data = RSTRING_PTR(qualities);
    }

    errno = 0;
    result = bam_set1(record,
                      (size_t)RSTRING_LEN(qname), RSTRING_PTR(qname),
                      NUM2UINT(flag), NUM2INT(tid), NUM2LL(pos), NUM2UINT(mapq),
                      (size_t)cigar_count, cigar,
                      NUM2INT(mtid), NUM2LL(mpos), NUM2LL(isize),
                      (size_t)RSTRING_LEN(sequence), RSTRING_PTR(sequence), quality_data, 0);
    ALLOCV_END(cigar_storage);
    if (result < 0) {
        if (errno) rb_sys_fail("bam_set1");
        rb_raise(rb_eRuntimeError, "bam_set1 failed: %d", result);
    }
    return self;
}

#rlen ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 342

static VALUE native_record_rlen(VALUE self) {
    bam1_t *record = get_record(self)->pointer;
    return LL2NUM(bam_cigar2rlen(record->core.n_cigar, bam_get_cigar(record)));
}

#sequence ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 346

static VALUE native_record_sequence(VALUE self) {
    static const char table[] = "=ACMGRSVTWYHKDBN";
    bam1_t *record = get_record(self)->pointer;
    uint8_t *packed = bam_get_seq(record);
    hts_pos_t i, length = record->core.l_qseq;
    VALUE result = rb_str_new(NULL, length);
    char *out = RSTRING_PTR(result);
    for (i = 0; i < length; i++) out[i] = table[bam_seqi(packed, i)];
    return result;
}

#sequence_codes ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 356

static VALUE native_record_sequence_codes(VALUE self) {
    bam1_t *record = get_record(self)->pointer;
    uint8_t *packed = bam_get_seq(record);
    hts_pos_t i, length = record->core.l_qseq;
    VALUE result = rb_ary_new_capa(length);
    for (i = 0; i < length; i++) rb_ary_push(result, INT2NUM(bam_seqi(packed, i)));
    return result;
}