#===========================================================================
#
#                           PUBLIC DOMAIN NOTICE
#              National Center for Biotechnology Information
#
# This software/database is a "United States Government Work" under the
# terms of the United States Copyright Act.  It was written as part of
# the author's official duties as a United States Government employee and
# thus cannot be copyrighted.  This software/database is freely available
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#
# Although all reasonable efforts have been taken to ensure the accuracy
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# Government disclaim all warranties, express or implied, including
# warranties of performance, merchantability or fitness for any particular
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#===========================================================================
#
import sys
import traceback

from ngs import NGS
from ngs.ErrorMsg import ErrorMsg
from ngs.ReadCollection import ReadCollection
from ngs.Alignment import Alignment
from ngs.AlignmentIterator import AlignmentIterator
from ngs.Reference import Reference

def run(acc, refName, start, stop):
    # open requested accession using SRA implementation of the API
    with NGS.openReadCollection(acc) as run:
        run_name = run.getName()
    
        # get requested reference
        with run.getReference(refName) as ref:
            # start iterator on requested range
            with ref.getAlignmentSlice(start, stop-start+1, Alignment.primaryAlignment) as it:
                i = 0
                while it.nextAlignment():
                    print ("{}\t{}\t{}\t{}\t{}".format(
                        it.getReadId(),
                        it.getReferenceSpec(),
                        it.getAlignmentPosition(),
                        it.getLongCigar(False),
                        it.getAlignedFragmentBases(),
                        ))
                    i += 1
                print ("Read {} alignments for {}".format(i, run_name))


if len(sys.argv) != 5:
    print ("Usage: AlignSliceTest accession reference start stop\n")
    exit(1)
else:
    try:
        run(sys.argv[1], sys.argv[2], int(sys.argv[3]), int(sys.argv[4]))
    except ErrorMsg as x:
        print (x)
        traceback.print_exc()
        # x.printStackTrace - not implemented
        exit(1)
    except BaseException as x:
        traceback.print_exc()
        exit(1)