Class: HTS::Native::BamFileHandle

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

Class Method Summary collapse

Instance Method Summary collapse

Class Method Details

.build_index(path, index, shift, threads) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 607

static VALUE native_bam_build_index(VALUE klass, VALUE path, VALUE index, VALUE shift, VALUE threads) {
    return INT2NUM(sam_index_build3(StringValueCStr(path), NIL_P(index) ? NULL : StringValueCStr(index),
                                    NUM2INT(shift), NUM2INT(threads)));
}

.open(path_value, mode_value) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 517

static VALUE native_bam_open(VALUE klass, VALUE path_value, VALUE mode_value) {
    ruby_bam_file_t *value;
    VALUE object = TypedData_Make_Struct(klass, ruby_bam_file_t, &bam_file_type, value);
    value->index = NULL;
    value->active_io = 0;
    value->path = rb_str_dup(StringValue(path_value));
    RB_OBJ_WRITE(object, &value->path, value->path);
    value->file = hts_open(StringValueCStr(value->path), StringValueCStr(mode_value));
    if (!value->file) rb_syserr_fail_str(ENOENT, path_value);
    return object;
}

Instance Method Details

#close ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 528

static VALUE native_bam_close(VALUE self) {
    ruby_bam_file_t *value = get_file(self, 1);
    if (value->active_io) rb_raise(rb_eIOError, "cannot close BAM during active I/O");
    if (value->index) { hts_idx_destroy(value->index); value->index = NULL; }
    if (value->file) { hts_close(value->file); value->file = NULL; }
    return Qnil;
}

#closed? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'ext/htslib_native/native_bam.c', line 535

static VALUE native_bam_closed(VALUE self) { return get_file(self, 1)->file ? Qfalse : Qtrue; }

#file_format ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 567

static VALUE native_bam_format(VALUE self) {
    const htsFormat *format = hts_get_format(get_file(self, 0)->file);
    if (!format) return Qnil;
    switch (format->format) {
    case sam: return rb_str_new_cstr("sam");
    case bam: return rb_str_new_cstr("bam");
    case cram: return rb_str_new_cstr("cram");
    case vcf: return rb_str_new_cstr("vcf");
    case bcf: return rb_str_new_cstr("bcf");
    default: return rb_str_new_cstr("unknown_format");
    }
}

#file_format_version ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 579

static VALUE native_bam_format_version(VALUE self) {
    const htsFormat *format = hts_get_format(get_file(self, 0)->file);
    if (!format) return Qnil;
    if (format->version.minor == -1) return rb_sprintf("%d", format->version.major);
    return rb_sprintf("%d.%d", format->version.major, format->version.minor);
}

#index_loaded? ⇒ Boolean

Returns:

  • (Boolean) 


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# File 'ext/htslib_native/native_bam.c', line 606

static VALUE native_bam_index_loaded(VALUE self) { return get_file(self, 0)->index ? Qtrue : Qfalse; }

#load_index(index_value) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 598

static VALUE native_bam_load_index(VALUE self, VALUE index_value) {
    ruby_bam_file_t *value = get_file(self, 0);
    if (value->index) { hts_idx_destroy(value->index); value->index = NULL; }
    value->index = NIL_P(index_value)
        ? sam_index_load3(value->file, StringValueCStr(value->path), NULL, HTS_IDX_SAVE_REMOTE)
        : sam_index_load2(value->file, StringValueCStr(value->path), StringValueCStr(index_value));
    return value->index ? Qtrue : Qfalse;
}

#query_interval(tid, beg, end) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 611

static VALUE native_bam_query_interval(VALUE self, VALUE tid, VALUE beg, VALUE end) {
    ruby_bam_file_t *file = get_file(self, 0);
    if (!file->index) rb_raise(rb_eRuntimeError, "index file is required");
    return wrap_iterator(self, sam_itr_queryi(file->index, NUM2INT(tid), NUM2LL(beg), NUM2LL(end)));
}

#query_region(header, region) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 616

static VALUE native_bam_query_region(VALUE self, VALUE header, VALUE region) {
    ruby_bam_file_t *file = get_file(self, 0);
    if (!file->index) rb_raise(rb_eRuntimeError, "index file is required");
    return wrap_iterator(self, sam_itr_querys(file->index, get_header(header)->pointer, StringValueCStr(region)));
}

#read(header, record) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 553

static VALUE native_bam_read(VALUE self, VALUE header, VALUE record) {
    ruby_bam_file_t *file=get_file(self,0); bam_io_args_t args={file->file,get_header(header)->pointer,get_record(record)->pointer,NULL,0};
    bam_io_begin(file); rb_thread_call_without_gvl(bam_read_without_gvl,&args,RUBY_UBF_IO,NULL); file->active_io=0; return INT2NUM(args.result);
}

#read_header ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 544

static VALUE native_bam_read_header(VALUE self) {
    ruby_bam_file_t *file=get_file(self,0); bam_header_read_args_t args={file->file,NULL};
    bam_io_begin(file); rb_thread_call_without_gvl(bam_read_header_without_gvl,&args,RUBY_UBF_IO,NULL); file->active_io=0;
    return wrap_header(args.result);
}

#seek(offset) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 585

static VALUE native_bam_seek(VALUE self, VALUE offset) {
    htsFile *file = get_file(self, 0)->file;
    int64_t position = NUM2LL(offset);
    if (file->is_cram) return LL2NUM(cram_seek(file->fp.cram, position, SEEK_SET));
    if (file->is_bgzf) return LL2NUM(bgzf_seek(file->fp.bgzf, position, SEEK_SET));
    return LL2NUM(hseek(file->fp.hfile, position, SEEK_SET));
}

#set_fai(path) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 561

static VALUE native_bam_set_fai(VALUE self, VALUE path) {
    return INT2NUM(hts_set_fai_filename(get_file(self, 0)->file, StringValueCStr(path)));
}

#set_threads(count) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 564

static VALUE native_bam_set_threads(VALUE self, VALUE count) {
    return INT2NUM(hts_set_threads(get_file(self, 0)->file, NUM2INT(count)));
}

#tell ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 592

static VALUE native_bam_tell(VALUE self) {
    htsFile *file = get_file(self, 0)->file;
    if (file->is_cram) return Qnil;
    if (file->is_bgzf) return LL2NUM(bgzf_tell(file->fp.bgzf));
    return LL2NUM(htell(file->fp.hfile));
}

#write(header, record) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 557

static VALUE native_bam_write(VALUE self, VALUE header, VALUE record) {
    ruby_bam_file_t *file=get_file(self,0); bam_io_args_t args={file->file,get_header(header)->pointer,get_record(record)->pointer,NULL,0};
    bam_io_begin(file); rb_thread_call_without_gvl(bam_write_without_gvl,&args,RUBY_UBF_IO,NULL); file->active_io=0; return INT2NUM(args.result);
}

#write_header(header) ⇒ Object 



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# File 'ext/htslib_native/native_bam.c', line 549

static VALUE native_bam_write_header(VALUE self, VALUE header) {
    ruby_bam_file_t *file=get_file(self,0); bam_io_args_t args={file->file,get_header(header)->pointer,NULL,NULL,0};
    bam_io_begin(file); rb_thread_call_without_gvl(bam_write_header_without_gvl,&args,RUBY_UBF_IO,NULL); file->active_io=0; return INT2NUM(args.result);
}