.. seq:module:: bio.bwa

:seq:mod:`bio.bwa`
------------------

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

.. seq:data:: BWA_LIB



.. seq:class:: bntann1_t



.. seq:class:: bntamb1_t



.. seq:class:: bntseq_t



.. seq:class:: mem_alnreg_t

   **Properties:**

      .. seq:attribute:: rb

      .. seq:attribute:: re

      .. seq:attribute:: qb

      .. seq:attribute:: qe

      .. seq:attribute:: rid

      .. seq:attribute:: score

      .. seq:attribute:: true_score

      .. seq:attribute:: sub

      .. seq:attribute:: alt_score

      .. seq:attribute:: csub

      .. seq:attribute:: sub_n

      .. seq:attribute:: w

      .. seq:attribute:: seedcov

      .. seq:attribute:: secondary

      .. seq:attribute:: secondary_all



.. seq:class:: mem_aln_t

   **Properties:**

      .. seq:attribute:: pos

      .. seq:attribute:: rid

      .. seq:attribute:: rev

      .. seq:attribute:: alt

      .. seq:attribute:: mapq

      .. seq:attribute:: NM

      .. seq:attribute:: cigar

      .. seq:attribute:: score

      .. seq:attribute:: sub

      .. seq:attribute:: alt_score



.. seq:class:: mem_alnreg_v

   **Magic methods:**

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

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

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

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



.. seq:class:: bwaidx_t

   **Methods:**

      .. seq:method:: name(aln : mem_aln_t)



.. seq:function:: mem_opt_init()



.. seq:function:: bwa_fill_scmat( : i32,  : i32,  : Ptr[i8])



.. seq:function:: bwa_idx_load( : cobj,  : i32)



.. seq:function:: mem_align1( : Ptr[mem_alnreg_v],  : cobj,  : cobj,  : Ptr[bntseq_t],  : cobj,  : i32,  : Ptr[byte])



.. seq:function:: mem_reg2aln( : Ptr[mem_aln_t],  : cobj,  : Ptr[bntseq_t],  : cobj,  : i32,  : Ptr[byte],  : Ptr[mem_alnreg_t])



.. seq:function:: options(match_score : int = 1, mismatch_score : int = 4, open_del : int = 6, open_ins : int = 6, extend_del : int = 1, extend_ins : int = 1, bandwidth : int = 100, zdrop : int = 100, clip_penalty : Tuple[int, int] = (5, 5), unpaired_penalty : int = 17)



.. seq:class:: BWA

   **Magic methods:**

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

      .. seq:method:: __new__(opt : cobj, hint : str)
         :noindex:

   **Methods:**

      .. seq:method:: name(aln : mem_aln_t)

      .. seq:method:: reg2aln(s : seq, reg : mem_alnreg_t)

      .. seq:method:: align(s : seq)