ragtag_utilities/ContigAlignment.py
def _get_primary_alignment(self):
        """
        Get the offset corresponding to the 'primary' (longest) alignment.
        Only consider alignments to the 'best' reference sequence.
        """
        max_index = -1
        max_len = -1
        for i in self._get_best_ref_alns():
            this_len = self._ref_aln_lens[i]
            if this_len > max_len:
                max_len = this_len
                max_index = i
        self.primary_alignment = max_index

        Get the offset corresponding to the 'primary' (longest) alignment.
        Only consider alignments to the 'best' reference sequence.
        
Get the offset corresponding to the 'primary' (longest) alignment.
Only consider alignments to the 'best' reference sequence.
Get the offset corresponding to the ' primary ' ( longest ) alignment . Only consider alignments to the ' best ' reference sequence .
def _get_primary_alignment(self):
        max_index = -1
        max_len = -1
        for i in self._get_best_ref_alns():
            this_len = self._ref_aln_lens[i]
            if this_len > max_len:
                max_len = this_len
                max_index = i
        self.primary_alignment = max_index
def _get_primary_alignment ( self ) : max_index = - 1 max_len = - 1 for i in self . _get_best_ref_alns ( ) : this_len = self . _ref_aln_lens [ i ] if this_len > max_len : max_len = this_len max_index = i self . primary_alignment = max_index
Get the offset corresponding to the 'primary' (longest) alignment.
Get the offset corresponding to the ' primary ' ( longest ) alignment .
"""
        Get the offset corresponding to the 'primary' (longest) alignment.
        Only consider alignments to the 'best' reference sequence.
        """
self