def test_bwa_mapping():
        '''It test that the gmap doesn't map anything'''
        reference = join(TEST_DATA_DIR, 'blast/arabidopsis_genes')
        work_dir = NamedTemporaryDir()
        reference_fpath = join(work_dir.name, 'arabidopsis_genes')
        os.symlink(reference, reference_fpath)

        reads_fhand = NamedTemporaryFile(suffix='.sfastq')
        reads_fhand.write(SOLEXA)
        reads_fhand.flush()

        out_bam_fhand = NamedTemporaryFile()
        out_bam_fpath = out_bam_fhand.name
        out_bam_fhand.close()

        parameters = {'colorspace': False, 'reads_length':'short',
                      'threads':None, 'java_conf':None}
        map_reads_with_bwa(reference_fpath, reads_fhand.name, out_bam_fpath,
                           parameters)
        test_sam_fhand = NamedTemporaryFile(suffix='sam')
        bam2sam(out_bam_fpath, test_sam_fhand.name)
        result = open(test_sam_fhand.name).read()
        assert 'seq17' in result

        unmapped_fhand = StringIO.StringIO()
        parameters = {'colorspace': False, 'reads_length':'short',
                      'threads':None, 'java_conf':None,
                      'unmapped_fhand':unmapped_fhand}
        map_reads_with_bwa(reference_fpath, reads_fhand.name, out_bam_fpath,
                           parameters)
        assert 'seq17' in unmapped_fhand.getvalue()
        test_sam_fhand = NamedTemporaryFile(suffix='sam')
        bam2sam(out_bam_fpath, test_sam_fhand.name)
        result = open(test_sam_fhand.name).read()
        assert 'seq17' not in result