ragtag_utilities/ContigAlignment.py
def has_internal_ref_cuttings(self, max_term_dist):
        """
        This is when a reference sequence is well contained within a query sequence, yet there are parts of the
        reference sequence that don't align. Should be used after filtering an merging.
        :return:
        """
        self.sort_by_query()
        for i in range(self.num_alns):

            # For each reference/query alignment terminus, determine if it is close to the sequence terminus
            ref_left_end, ref_right_end = self.ref_start_end(i, max_term_dist)
            query_left_end, query_right_end = self.query_start_end(i, max_term_dist)

            if not query_left_end and not query_right_end:
                if not ref_left_end or not ref_right_end:
                    return True

        return False

        This is when a reference sequence is well contained within a query sequence, yet there are parts of the
        reference sequence that don't align. Should be used after filtering an merging.
        :return:
        
This is when a reference sequence is well contained within a query sequence, yet there are parts of the
reference sequence that don't align. Should be used after filtering an merging.
This is when a reference sequence is well contained within a query sequence yet there are parts of the reference sequence that don ' t align . Should be used after filtering an merging .
def has_internal_ref_cuttings(self, max_term_dist):
        self.sort_by_query()
        for i in range(self.num_alns):
            ref_left_end, ref_right_end = self.ref_start_end(i, max_term_dist)
            query_left_end, query_right_end = self.query_start_end(i, max_term_dist)
            if not query_left_end and not query_right_end:
                if not ref_left_end or not ref_right_end:
                    return True
        return False
def has_internal_ref_cuttings ( self , max_term_dist ) : self . sort_by_query ( ) for i in range ( self . num_alns ) : ref_left_end , ref_right_end = self . ref_start_end ( i , max_term_dist ) query_left_end , query_right_end = self . query_start_end ( i , max_term_dist ) if not query_left_end and not query_right_end : if not ref_left_end or not ref_right_end : return True return False
This is when a reference sequence is well contained within a query sequence, yet there are parts of the
reference sequence that don't align.
This is when a reference sequence is well contained within a query sequence yet there are parts of the reference sequence that don ' t align .
"""
        This is when a reference sequence is well contained within a query sequence, yet there are parts of the
        reference sequence that don't align. Should be used after filtering an merging.
        :return:
        """ # For each reference/query alignment terminus, determine if it is close to the sequence terminus
None
self
max_term_dist