malonge

#!/usr/bin/env python
import argparse


def delta2paf():
    """
    Essentially a translation of paftools.js delta2paf

    https://github.com/lh3/minimap2/tree/master/misc
    """

malonge

import re
import gzip
import argparse


def main():
    message = """
    Summarize the rate of edits (insertion, deletion, mismatch) from minimap2 alignments of a query to a target.
    For each alignment, the rate is defined as the number of edits divided by the alignment length 
    with respect to the query. 

malonge

#!/usr/bin/python3
import argparse
from collections import defaultdict

"""
This utility converts a SAM file to a nucmer delta file.

SAM files must contain an NM tag, which is default in minimap2 alignments.  
"""

malonge

#!/usr/bin/env python

import re
import gzip
import argparse
from collections import defaultdict


class Alignment:
    def __init__(self, in_r_start, in_r_end, in_q_start, in_q_end, in_cigar, in_strand, in_num_matches, in_aln_len, in_num_mismatches):