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# Source code for samsifter.util.sam

    #!/usr/bin/env python3
    # -*- coding: utf-8 -*-
    """Reconstruction of reference sequences from CIGAR and MD tags in SAM files.

    Includes tests for various scenarios of clipping, insertion and deletion.

    .. moduleauthor:: Florian Aldehoff (f.aldehoff@student.uni-tuebingen.de)
    """

    import sys
    import re

    def decompress_cigar(cigar):
        """Decompress CIGAR string.

        Parameters
        ----------
        cigar : str
            full CIGAR string (numbers and letters)

        Returns
        -------
        cigar_ext : str
            decompressed CIGAR string (letters only)

        """
        cigar_ext = ""
        cigar_ops = re.findall('(\d+)(\D)', cigar)
        for (count, op) in cigar_ops:
            cigar_ext += op * int(count)
        return cigar_ext

    def decompress_md(md):
        """
        Decompress MD string.

        Parameters
        ----------
        md : str
          MD string from SAM file without MD:Z: prefix

        Returns
        -------
        md_ext : str
          extended MD string without MD:Z: prefix

        """
        md_ext = ""
        md_ops = re.findall('(\d*)(\D*)', md)
        for (match, mismatch) in md_ops:
            try:
                md_ext += '=' * int(match)
            except ValueError:
                # regex also catches empty string, can be safely ignored
                pass
            md_ext += mismatch.lstrip('^')
        return md_ext

    def reconstruct(read, cigar, md, verbose=False):
        """Reconstruct both the full and the aligned reference sequence.

        Uses imformation from CIGAR string and optional MD tag to reconstruct the
        reference sequence. The full reference sequence including indels, clips and
        skips and the aligned substring can be used for calculation of identity and
        post-mortem degradation.

        Note
        ----
        Padded references should work as well, but remain untested. Use at your own
        risk!

        Parameters
        ----------
        read : str
            Raw read sequence without gaps, can be clipped.
        cigar : str
            CIGAR string from SAM file
        md : str
            matching MD string from SAM file without MD:Z: prefix

        Returns
        -------
        ref_full : str
            full reference sequence including indels, clipped and skipped parts
        read_full : str
            full read sequence including indels, clipped and skipped parts
        ref_aln : str
            aligned part of reference sequence (can include gaps)
        read_aln : str
            aligned part of read sequence (clipped, can include gaps)
        """
        ref_full = ""
        read_full = ""
        ref_aln = ""
        read_aln = ""

        cigar_ext = decompress_cigar(cigar)
        md_ext = decompress_md(md)

        # reconstruct reference by CIGAR and MD
        read_idx = 0
        md_idx = 0
        for (idx, op) in enumerate(cigar_ext):
            if op in ('M', 'X'):          # alignment match|mismatch -> consult MD
                if md_ext[md_idx] == '=':
                    ref_full += read[read_idx]
                    ref_aln += read[read_idx]
                else:
                    ref_full += md_ext[md_idx]
                    ref_aln += md_ext[md_idx]
                read_full += read[read_idx]
                read_aln += read[read_idx]
                read_idx += 1
                md_idx += 1
            elif op == '=':                # certain match
                ref_full += read[read_idx]
                ref_aln += read[read_idx]
                read_full += read[read_idx]
                read_aln += read[read_idx]
                read_idx += 1
                md_idx += 1
            elif op == 'D':                # deletion from reference -> consult MD
                ref_full += md_ext[md_idx]
                ref_aln += md_ext[md_idx]
                read_full += '-'
                read_aln += '-'
                md_idx += 1
            elif op == 'I':                # insertion to reference
                ref_full += '-'
                ref_aln += '-'
                read_full += read[read_idx]
                read_aln += read[read_idx]
                read_idx += 1
            elif op == 'N':                # skipped region in reference (intron?)
                ref_full += 'X'
    #            ref_aln += 'N'
                read_full += '-'
    #            read_aln += 'N'
            elif op == 'H':                # hard clipping (5' or 3' only)
                ref_full += 'X'
    #            ref_aln += 'N'
                read_full += 'X'
    #            read_aln += 'N'
            elif op == 'S':                # soft clipping (5' or 3' only)
                ref_full += 'X'
    #            ref_aln += 'N'
                read_full += read[read_idx]
    #            read_aln += 'N'
                read_idx += 1
            elif op == 'P':                # ignore padding, aligning single reads
                pass
        return (ref_full, read_full, ref_aln, read_aln)

    """
    tests for reference reconstruction method
    """

    def test_deletion_snp_no_delim(verbose=False):
        """Tests reconstruction despite missing 0 delimiter after deletion in MD.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
        cigar = "37M4D8M"
        md = "G36^CCTTTC6"
        """
        CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA    AAAAAAAA    read
        |||||||||||||||||||||||||||||||||||||----||||||||    extended CIGAR
        G||||||||||||||||||||||||||||||||||||CCTTTC||||||    extended MD
        GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA    full reference
        CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA    full read
        GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA    aligned reference
        CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA    aligned read
        """
        ref_full = "GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA"
        read_full = "CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA"
        ref_aln = "GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA"
        read_aln = "CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\tSNP after deletion without 0 delimiter"
              % (rec_ref_full == ref_full
                 and rec_read_full == read_full
                 and rec_ref_aln == ref_aln
                 and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln and
                rec_read_aln == read_aln)

    def test_deletion_snp_0_delim(verbose=False):
        """Tests reference reconstruction with 0 delimiter after deletion in MD.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
        cigar = "37M4D8M"
        md = "G36^CCTT0TC6"
        """
        CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA    AAAAAAAA    read
        |||||||||||||||||||||||||||||||||||||----||||||||    extended CIGAR
        G||||||||||||||||||||||||||||||||||||CCTTTC||||||    extended MD
        GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA    full reference
        CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA    full read
        GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA    aligned reference
        CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA    aligned read
        """
        ref_full  = "GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA"
        read_full = "CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA"
        ref_aln   = "GTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTTCAAAAAA"
        read_aln  = "CTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA----AAAAAAAA"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\tSNP after deletion with 0 delimiter"
              % (rec_ref_full == ref_full
                 and rec_read_full == read_full
                 and rec_ref_aln == ref_aln
                 and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln
                and rec_read_aln == read_aln)

    def test_insertion(verbose=False):
        """Tests reference reconstruction with insertion to reference.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "GCCTTCCGCGTCGGCGAGGACGGCCCCACCCACCAGCCCAT"
        cigar = "1M1I39M"
        md = "2A2G2C31"
        """
        GCCTTCCGCGTCGGCGAGGACGGCCCCACCCACCAGCCCAT    read (41bp)
        MIMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM    extended CIGAR (41bp)
        = =A==G==C===============================    extended MD (40bp) ! shift by del
        G-CATCGGCCTCGGCGAGGACGGCCCCACCCACCAGCCCAT    full reference
        GCCTTCCGCGTCGGCGAGGACGGCCCCACCCACCAGCCCAT    full read
        G-CATCGGCCTCGGCGAGGACGGCCCCACCCACCAGCCCAT    aligned reference
        GCCTTCCGCGTCGGCGAGGACGGCCCCACCCACCAGCCCAT    aligned read
        """
        ref_full  = "G-CATCGGCCTCGGCGAGGACGGCCCCACCCACCAGCCCAT"
        read_full = "GCCTTCCGCGTCGGCGAGGACGGCCCCACCCACCAGCCCAT"
        ref_aln   = "G-CATCGGCCTCGGCGAGGACGGCCCCACCCACCAGCCCAT"
        read_aln  = "GCCTTCCGCGTCGGCGAGGACGGCCCCACCCACCAGCCCAT"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\tinsertion into reference" % (rec_ref_full == ref_full
                                                and rec_read_full == read_full
                                                and rec_ref_aln == ref_aln
                                                and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln
                and rec_read_aln == read_aln)

    def test_skipped_intron(verbose=False):
        """Tests reference reconstruction with skipped intron.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "GTGTAACCCTCAGAATA"
        cigar = "9M32N8M"
        md = "17"
        """
        GTGTAACCC                                TCAGAATA    read (17bp)
        MMMMMMMMMNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNMMMMMMMM    extended CIGAR (49bp)
        =========                                ========    extended MD (17bp)
        GTGTAACCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCAGAATA    full reference
        GTGTAACCC--------------------------------TCAGAATA    full read
        GTGTAACCC                                TCAGAATA    aligned reference
        GTGTAACCC                                TCAGAATA    aligned read
        """
        ref_full  = "GTGTAACCCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTCAGAATA"
        read_full = "GTGTAACCC--------------------------------TCAGAATA"
        ref_aln   = "GTGTAACCCTCAGAATA"
        read_aln  = "GTGTAACCCTCAGAATA"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\tskipped intron" % (rec_ref_full == ref_full
                                      and rec_read_full == read_full
                                      and rec_ref_aln == ref_aln
                                      and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln
                and rec_read_aln == read_aln)

    def test_hard_clipping_front(verbose=False):
        """Tests reference reconstruction with hard clipped 5' read.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA"
        cigar = "23H37M"
        md = "36G"
        """
                               ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA    read (37bp)
        HHHHHHHHHHHHHHHHHHHHHHHMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM    extended CIGAR (50bp)
                               ====================================G    extended MD (37bp)
        NNNNNNNNNNNNNNNNNNNNNNNATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG    full reference
        NNNNNNNNNNNNNNNNNNNNNNNATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA    full read
                               ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG    aligned reference
                               ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA    aligned read
        """
        ref_full  = "XXXXXXXXXXXXXXXXXXXXXXXATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG"
        read_full = "XXXXXXXXXXXXXXXXXXXXXXXATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA"
        ref_aln   = "ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG"
        read_aln  = "ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\t5' hard clipping" % (rec_ref_full == ref_full
                                        and rec_read_full == read_full
                                        and rec_ref_aln == ref_aln
                                        and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln
                and rec_read_aln == read_aln)

    def test_hard_clipping_end(verbose=False):
        """Tests reference reconstruction with hard clipped 3' read.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
        cigar = "44M6H"
        md = "44"
        """
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA        read (44bp)
        MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMHHHHHH  extended CIGAR (50bp)
        ============================================        extended MD (44bp)
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANNNNNN  full reference
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANNNNNN  full read
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA        aligned reference
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA        aligned read
        """
        ref_full  = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAXXXXXX"
        read_full = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAXXXXXX"
        ref_aln   = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
        read_aln  = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\t3' hard clipping" % (rec_ref_full == ref_full
                                        and rec_read_full == read_full
                                        and rec_ref_aln == ref_aln
                                        and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln
                and rec_read_aln == read_aln)

    def test_soft_clipping_front(verbose=False):
        """Tests reference reconstruction with soft clipped 5' read.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "GGGGGGGGGGGGGGGGGGGGGGGATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA"
        cigar = "23S37M"
        md = "36G"
        """
        GGGGGGGGGGGGGGGGGGGGGGGATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA    read (50bp)
        SSSSSSSSSSSSSSSSSSSSSSSMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM    extended CIGAR (50bp)
                               ====================================G    extended MD (37bp)
        NNNNNNNNNNNNNNNNNNNNNNNATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG    full reference
        NNNNNNNNNNNNNNNNNNNNNNNATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA    full read
                               ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG    aligned reference
                               ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA    aligned read
        """
        ref_full  = "XXXXXXXXXXXXXXXXXXXXXXXATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG"
        read_full = "GGGGGGGGGGGGGGGGGGGGGGGATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA"
        ref_aln   = "ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCG"
        read_aln  = "ATGAGAGTTTGATCCTGGCTCAGGACGAACGCTGGCA"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\t5' soft clipping" % (rec_ref_full == ref_full
                                        and rec_read_full == read_full
                                        and rec_ref_aln == ref_aln
                                        and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln
                and rec_read_aln == read_aln)

    def test_soft_clipping_end(verbose=False):
        """Tests reference reconstruction with soft clipped 3' read.

        Parameters
        ----------
        verbose : bool
            Print additional output to STDOUT, defaults to False.

        Returns
        -------
        bool
            True if test was successful, otherwise False.
        """
        read = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGG"
        cigar = "44M6S"
        md = "44"
        """
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGG    read (44bp)
        MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMSSSSSS    extended CIGAR (50bp)
        ============================================          extended MD (44bp)
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANNNNNN    full reference
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAANNNNNN    full read
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA          aligned reference
        GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA          aligned read
        """
        ref_full  = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAXXXXXX"
        read_full = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGGGG"
        ref_aln   = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"
        read_aln  = "GTTTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"

        (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(read, cigar, md, verbose)
        if verbose:
            print(rec_ref_full + "\treconstructed reference")
            print(ref_full + "\tactual reference")
            print(rec_read_full + "\treconstructed read")
            print(read_full + "\tactual read")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(ref_aln + "\tactual aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")
            print(read_aln + "\tactual aligned read")
        print("%s\t3' soft clipping" % (rec_ref_full == ref_full
                                        and rec_read_full == read_full
                                        and rec_ref_aln == ref_aln
                                        and rec_read_aln == read_aln,))
        return (rec_ref_full == ref_full
                and rec_read_full == read_full
                and rec_ref_aln == ref_aln
                and rec_read_aln == read_aln)

    def main(argv):
        """Runs simple tests of the reference reconstruction method."""
        tests = [test_deletion_snp_no_delim(verbose=False),
                 test_deletion_snp_0_delim(verbose=False),
                 test_insertion(verbose=False),
                 test_skipped_intron(verbose=False),
                 test_hard_clipping_front(verbose=False),
                 test_hard_clipping_end(verbose=False),
                 test_soft_clipping_front(verbose=False),
                 test_soft_clipping_end(verbose=False)]
        print("passed %i out of %i tests"
              % (tests.count(True), len(tests)))

        # process command line arguments
        if len(argv) == 4:
            print()
            (rec_ref_full, rec_read_full, rec_ref_aln, rec_read_aln) = reconstruct(argv[1], argv[2], argv[3], verbose=True)
            print(rec_ref_full + "\treconstructed reference")
            print(rec_ref_aln + "\treconstructed aligned reference")
            print(rec_read_aln + "\treconstructed aligned read")

        exit()

    if __name__ == "__main__":
        main(sys.argv)

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