.. seq:module:: bio.vcf

:seq:mod:`bio.vcf`
------------------

Source code: `bio/vcf.seq <https://github.com/seq-lang/seq/blob/master/stdlib/bio/vcf.seq>`_

.. seq:data:: BCF_UN_STR



.. seq:data:: BCF_UN_FLT



.. seq:data:: BCF_UN_INFO



.. seq:data:: BCF_UN_SHR



.. seq:data:: BCF_UN_FMT



.. seq:data:: BCF_UN_IND



.. seq:data:: BCF_UN_ALL



.. seq:data:: BCF_HL_FLT



.. seq:data:: BCF_HL_INFO



.. seq:data:: BCF_HL_FMT



.. seq:data:: BCF_HL_CTG



.. seq:data:: BCF_HL_STR



.. seq:data:: BCF_HL_GEN



.. seq:data:: BCF_HT_FLAG



.. seq:data:: BCF_HT_INT



.. seq:data:: BCF_HT_REAL



.. seq:data:: BCF_HT_STR



.. seq:data:: BCF_VL_FIXED



.. seq:data:: BCF_VL_VAR



.. seq:data:: BCF_VL_A



.. seq:data:: BCF_VL_G



.. seq:data:: BCF_VL_R



.. seq:data:: BCF_DT_ID



.. seq:data:: BCF_DT_CTG



.. seq:data:: BCF_DT_SAMPLE



.. seq:data:: BCF_BT_NULL



.. seq:data:: BCF_BT_INT8



.. seq:data:: BCF_BT_INT16



.. seq:data:: BCF_BT_INT32



.. seq:data:: BCF_BT_FLOAT



.. seq:data:: BCF_BT_CHAR



.. seq:data:: BCF_AUX_NONE



.. seq:data:: INT8_MIN



.. seq:data:: INT16_MIN



.. seq:data:: INT32_MIN



.. seq:data:: bcf_int8_vector_end



.. seq:data:: bcf_int16_vector_end



.. seq:data:: bcf_int32_vector_end



.. seq:data:: bcf_str_vector_end



.. seq:data:: bcf_int8_missing



.. seq:data:: bcf_int16_missing



.. seq:data:: bcf_int32_missing



.. seq:data:: bcf_float_missing



.. seq:data:: bcf_float_vector_end



.. seq:data:: bcf_str_missing



.. seq:function:: ptr_off[T](base : Ptr[byte], byte_offset : int)



.. seq:data:: char_pp



.. seq:data:: char_p



.. seq:function:: check_header_id(hdr : Ptr[_bcf_hdr_t], h1_type : i32, id : i32)



.. seq:function:: is_gt_fmt(hdr : Ptr[_bcf_hdr_t], fmt_id : i32)



.. seq:function:: bcf_float_is_missing(f : i32)



.. seq:function:: bcf_float_is_vector_end(f : i32)



.. seq:function:: bcf_gt_allele(val : int)



.. seq:class:: BCFHeaderMetaData

   **Properties:**

      .. seq:attribute:: type_code

   **Magic methods:**

      .. seq:method:: __new__(bcf_hdr : Ptr[_bcf_hdr_t], _type_code : int)
         :noindex:

      .. seq:method:: __len__()
         :noindex:

      .. seq:method:: __iter__()
         :noindex:



.. seq:class:: BCFHeaderContigs

   **Magic methods:**

      .. seq:method:: __new__(bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __iter__()
         :noindex:



.. seq:class:: BCFHeaderSamples

   **Magic methods:**

      .. seq:method:: __new__(bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

      .. seq:method:: __getitem__(index : int)
         :noindex:



.. seq:data:: METADATA_TYPES



.. seq:class:: BCFHeaderRecord

   **Properties:**

      .. seq:attribute:: hdr_type

      .. seq:attribute:: key

      .. seq:attribute:: value

      .. seq:attribute:: attrs

   **Magic methods:**

      .. seq:method:: __new__(bcf_hdr : Ptr[_bcf_hdr_t], bcf_hrec : Ptr[_bcf_hrec_t])
         :noindex:

      .. seq:method:: __getitem__(key : str)
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

   **Methods:**

      .. seq:method:: get(key : str)

      .. seq:method:: iterkeys()

      .. seq:method:: itervalues()

      .. seq:method:: iteritems()



.. seq:class:: BCFHeader

   **Properties:**

      .. seq:attribute:: info

      .. seq:attribute:: filters

      .. seq:attribute:: formats

      .. seq:attribute:: contigs

      .. seq:attribute:: samples

   **Magic methods:**

      .. seq:method:: __new__(bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __new__()
         :noindex:

      .. seq:method:: __iter__()
         :noindex:



.. seq:data:: VALUE_TYPES



.. seq:class:: BCFMetadata

   **Properties:**

      .. seq:attribute:: name

      .. seq:attribute:: bcf_type

      .. seq:attribute:: record

      .. seq:attribute:: description

   **Magic methods:**

      .. seq:method:: __new__(bcf_hdr : Ptr[_bcf_hdr_t], _type_code : int, _id : int)
         :noindex:



.. seq:class:: BCFAux

   **Properties:**

      .. seq:attribute:: val

      .. seq:attribute:: arr

      .. seq:attribute:: type_code

      .. seq:attribute:: is_array



.. seq:function:: bcf_get_value_count(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t], h1_type : i32, id : i32, sample : i32)



.. seq:function:: bcf_array_to_object(data : cobj, type_code : i32, n : i32, count : i64, scalar : i32)



.. seq:function:: bcf_info_get_value(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t], info : Ptr[_bcf_info_t])



.. seq:function:: try_unpack(bcf1 : Ptr[_bcf1_t], mode : i32)



.. seq:class:: VCFRecordInfo

   **Magic methods:**

      .. seq:method:: __new__(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

      .. seq:method:: __len__()
         :noindex:

   **Methods:**

      .. seq:method:: get_int(key : str)

      .. seq:method:: get_ints(key : str)

      .. seq:method:: get_float(key : str)

      .. seq:method:: get_floats(key : str)

      .. seq:method:: get_str(key : str)

      .. seq:method:: get_flag(key : str)



.. seq:class:: VCFRecordSample

   **Properties:**

      .. seq:attribute:: name

      .. seq:attribute:: alleles

   **Magic methods:**

      .. seq:method:: __new__(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t], index : int)
         :noindex:

      .. seq:method:: __str__()
         :noindex:



.. seq:class:: VCFRecordSamples

   **Magic methods:**

      .. seq:method:: __new__(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __len__()
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

      .. seq:method:: __getitem__(key : str)
         :noindex:



.. seq:class:: VCFRecordFormat

   **Magic methods:**

      .. seq:method:: __new__(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __len__()
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

      .. seq:method:: __getitem__(key : str)
         :noindex:



.. seq:class:: VCFRecordFilter

   **Magic methods:**

      .. seq:method:: __new__(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

      .. seq:method:: __getitem__(key : str)
         :noindex:

      .. seq:method:: __len__()
         :noindex:



.. seq:class:: VCFRecord

   **Properties:**

      .. seq:attribute:: info

      .. seq:attribute:: n_info

      .. seq:attribute:: chrom

      .. seq:attribute:: contig

      .. seq:attribute:: pos

      .. seq:attribute:: qual

      .. seq:attribute:: ref

      .. seq:attribute:: alts

      .. seq:attribute:: id

      .. seq:attribute:: rlen

   **Magic methods:**

      .. seq:method:: __new__(bcf1 : Ptr[_bcf1_t], bcf_hdr : Ptr[_bcf_hdr_t])
         :noindex:

      .. seq:method:: __str__()
         :noindex:



.. seq:class:: BCFReader

   **Properties:**

      .. seq:attribute:: _bcf_hdr

   **Magic methods:**

      .. seq:method:: __init__(path : str, unpack_all : bool, copy : bool, num_threads : int)
         :noindex:

      .. seq:method:: __iter__()
         :noindex:

      .. seq:method:: __enter__()
         :noindex:

      .. seq:method:: __exit__()
         :noindex:

   **Methods:**

      .. seq:method:: close()



.. seq:data:: VCFReader



.. seq:function:: BCF(path : str, unpack_all : bool = True, copy : bool = True, num_threads : int = 0)



.. seq:function:: VCF(path : str, unpack_all : bool = True, copy : bool = True, num_threads : int = 0)