.. seq:module:: bio.bam

:seq:mod:`bio.bam`
------------------

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

.. seq:data:: BAM_FPAIRED



.. seq:data:: BAM_FPROPER_PAIR



.. seq:data:: BAM_FUNMAP



.. seq:data:: BAM_FMUNMAP



.. seq:data:: BAM_FREVERSE



.. seq:data:: BAM_FMREVERSE



.. seq:data:: BAM_FREAD1



.. seq:data:: BAM_FREAD2



.. seq:data:: BAM_FSECONDARY



.. seq:data:: BAM_FQCFAIL



.. seq:data:: BAM_FDUP



.. seq:data:: BAM_FSUPPLEMENTARY



.. seq:data:: AUX_TYPE_INT8



.. seq:data:: AUX_TYPE_UINT8



.. seq:data:: AUX_TYPE_INT16



.. seq:data:: AUX_TYPE_UINT16



.. seq:data:: AUX_TYPE_INT32



.. seq:data:: AUX_TYPE_UINT32



.. seq:data:: AUX_TYPE_FLOAT



.. seq:data:: AUX_TYPE_DOUBLE



.. seq:data:: AUX_TYPE_CHAR



.. seq:data:: AUX_TYPE_STRING



.. seq:data:: AUX_TYPE_ARRAY



.. seq:data:: AUX_TYPE_INT



.. seq:class:: SAMAux

   **Properties:**

      .. seq:attribute:: tag_type

            
                    String representing the type of this tag.
            
                      - "int": use ``i`` property for int value
                      - "float": use ``f`` property for float value
                      - "char": use ``A`` property for byte value
                      - "string": use ``Z`` property for string value
                      - "Array[int]": use ``B_len`` for array length and either ``B2i(index)`` to access elements
                      - "Array[float]": use ``B_len`` for array length and either ``B2f(index)`` to access elements
            


      .. seq:attribute:: i

            
                    Int value of this tag
            


      .. seq:attribute:: f

            
                    Float value of this tag
            


      .. seq:attribute:: A

            
                    Byte value of this tag
            


      .. seq:attribute:: Z

            
                    String value of this tag
            


      .. seq:attribute:: B_len

            
                    Array length of this tag
            


   **Magic methods:**

      .. seq:method:: __bool__()
         :noindex:

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

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

   **Methods:**

      .. seq:method:: B2i(idx : int)

            
                    `idx`th element of integer array comprising this tag
            


      .. seq:method:: B2f(idx : int)

            
                    `idx`th element of float array comprising this tag
            




.. seq:class:: SAMRecord

   **Properties:**

      .. seq:attribute:: name

            
                    Read name of this record
            


      .. seq:attribute:: query_name

            
                    Alias of `name`
            


      .. seq:attribute:: read

      .. seq:attribute:: seq

            
                    Record sequence
            


      .. seq:attribute:: qual

            
                    Record quality string
            


      .. seq:attribute:: cigar

            
                    Record `CIGAR`
            


      .. seq:attribute:: tid

            
                    Record contig ID
            


      .. seq:attribute:: flag

            
                    Record flag
            


      .. seq:attribute:: pos

            
                    Record position (0-based)
            


      .. seq:attribute:: locus

            
                    Record `Locus` consisting of `tid` and `pos`
            


      .. seq:attribute:: mate_tid

            
                    Contig ID in mate's record
            


      .. seq:attribute:: mate_pos

            
                    Position in mate's record (0-based)
            


      .. seq:attribute:: mate_locus

            
                    Record `Locus` of mate's record consisting of `mate_tid` and `mate_pos`
            


      .. seq:attribute:: mapq

            
                    Record's mapping quality
            


      .. seq:attribute:: insert_size

            
                    Record's insert size
            


      .. seq:attribute:: paired

            
                    Whether this record is paired
            


      .. seq:attribute:: proper_pair

            
                    Whether this record and its pair form a proper pair
            


      .. seq:attribute:: unmapped

            
                    Whether this record is unmapped
            


      .. seq:attribute:: mate_unmapped

            
                    Whether mate's record is unmapped
            


      .. seq:attribute:: reversed

            
                    Whether this record is reverse complemented on the reference
            


      .. seq:attribute:: mate_reversed

            
                    Whether this record's mate is reverse complemented on the reference
            


      .. seq:attribute:: read1

            
                    Whether this is the first read in the pair
            


      .. seq:attribute:: read2

            
                    Whether this is the second read in the pair
            


      .. seq:attribute:: secondary

            
                    Whether this is a seconday alignment
            


      .. seq:attribute:: qc_fail

            
                    Whether this record failed quality control checks
            


      .. seq:attribute:: duplicate

            
                    Whether this record is marked as a duplicate
            


      .. seq:attribute:: supplementary

            
                    Whether this record is supplementary
            


      .. seq:attribute:: endpos

            
                    The rightmost base position of an alignment on the reference genome
            


   **Magic methods:**

      .. seq:method:: __init__(htslib_record : _bam1_t)
         :noindex:

   **Methods:**

      .. seq:method:: aux(tag : str)

            
                    Returns the auxiliary tag with the specified key.
            




.. seq:class:: BAMReader

   **Magic methods:**

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

      .. seq:method:: __blocks__(size : int)
         :noindex:

      .. seq:method:: __seqs__()
         :noindex:

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

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

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

   **Methods:**

      .. seq:method:: seek(region : str)

      .. seq:method:: close()

      .. seq:method:: contigs()

      .. seq:method:: contig(rid : int)



.. seq:class:: SAMReader

   **Magic methods:**

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

      .. seq:method:: __seqs__()
         :noindex:

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

      .. seq:method:: __blocks__(size : int)
         :noindex:

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

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

   **Methods:**

      .. seq:method:: close()

      .. seq:method:: contigs()

      .. seq:method:: contig(rid : int)



.. seq:data:: CRAMReader



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



.. seq:function:: BAM(path : str, region : str = ".", copy : bool = True, num_threads : int = 0)



.. seq:function:: CRAM(path : str, region : str = ".", copy : bool = True, num_threads : int = 0)