Work Item 2: Refactor from PyVCF to PyVCF3

[crashfrog]

PyVCF is end-of-life and doesn't support Python 3; PyVCF3 is a fork that supports Python 3. Figure out why these tests don't pass:

======================================================================
ERROR: test_1_filter_regions (test.test_cfsan_snp_pipeline.SnpPipelineLambdaVirusTest)
Run filter_regions and verify var.flt_preserved.vcf and var.flt_removed.vcf contains expected contents for each sample.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 150, in setUp
    self.compare_file('metrics.tsv')
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 81, in compare_file
    match = filecmp.cmp(correct_result_file, result_file, shallow=False)
  File "/home/chet/.pyenv/versions/3.10.4/lib/python3.10/filecmp.py", line 54, in cmp
    s2 = _sig(os.stat(f2))
FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpksh0rotb/testLambdaVirus/metrics.tsv'

======================================================================
ERROR: test_2_merge_sites (test.test_cfsan_snp_pipeline.SnpPipelineLambdaVirusTest)
Run merge_sites and verify snplist.txt contains expected contents.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 171, in test_2_merge_sites
    self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'snplist.txt')
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 96, in run_function_test
    funct(args)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/cfsan_snp_pipeline.py", line 585, in run_command_from_args
    args.func(args)  # this executes the function previously associated with the subparser with set_defaults
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/merge_sites.py", line 83, in merge_sites
    utils.global_error("Error: all %d VCF files were missing or empty." % bad_file_count)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/utils.py", line 572, in global_error
    sys.exit(100)
SystemExit: 100

======================================================================
ERROR: test_3_call_consensus (test.test_cfsan_snp_pipeline.SnpPipelineLambdaVirusTest)
Run call_consensus and verify consensus.fasta and consensus.vcf contain expected contents for each sample.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 189, in test_3_call_consensus
    self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, os.path.join(dir, 'consensus.fasta'))
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 96, in run_function_test
    funct(args)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/cfsan_snp_pipeline.py", line 585, in run_command_from_args
    args.func(args)  # this executes the function previously associated with the subparser with set_defaults
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/call_consensus.py", line 109, in call_consensus
    utils.global_error("Error: cannot call consensus without the snplist file.")
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/utils.py", line 572, in global_error
    sys.exit(100)
SystemExit: 100

======================================================================
ERROR: test_4_create_snp_matrix (test.test_cfsan_snp_pipeline.SnpPipelineLambdaVirusTest)
Run snp_matrix and verify snpma.fasta contains expected contents.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 199, in test_4_create_snp_matrix
    self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'snpma.fasta')
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 96, in run_function_test
    funct(args)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/cfsan_snp_pipeline.py", line 585, in run_command_from_args
    args.func(args)  # this executes the function previously associated with the subparser with set_defaults
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/snp_matrix.py", line 97, in create_snp_matrix
    utils.global_error("Error: all %d consensus fasta files were missing or empty." % bad_file_count)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/utils.py", line 572, in global_error
    sys.exit(100)
SystemExit: 100

======================================================================
ERROR: test_5_create_snp_reference_seq (test.test_cfsan_snp_pipeline.SnpPipelineLambdaVirusTest)
Run create_snp_reference_seq and verify referenceSNP.fasta contains expected contents.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 208, in test_5_create_snp_reference_seq
    self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'referenceSNP.fasta')
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 96, in run_function_test
    funct(args)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/cfsan_snp_pipeline.py", line 585, in run_command_from_args
    args.func(args)  # this executes the function previously associated with the subparser with set_defaults
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/snp_reference.py", line 64, in create_snp_reference_seq
    utils.global_error("Error: cannot create the snp reference sequence without the snplist file.")
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/utils.py", line 572, in global_error
    sys.exit(100)
SystemExit: 100

======================================================================
ERROR: test_6_calculate_snp_distances (test.test_cfsan_snp_pipeline.SnpPipelineLambdaVirusTest)
Run calculate_snp_distances and verify snp_distance_pairwise.tsv contains expected contents.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 216, in test_6_calculate_snp_distances
    self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'snp_distance_pairwise.tsv')
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 96, in run_function_test
    funct(args)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/cfsan_snp_pipeline.py", line 585, in run_command_from_args
    args.func(args)  # this executes the function previously associated with the subparser with set_defaults
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/distance.py", line 61, in calculate_snp_distances
    utils.global_error("Error: cannot calculate sequence distances without the snp matrix file.")
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/utils.py", line 572, in global_error
    sys.exit(100)
SystemExit: 100

======================================================================
ERROR: test_7_calculate_snp_distances (test.test_cfsan_snp_pipeline.SnpPipelineLambdaVirusTest)
Run calculate_snp_distances and verify snp_distance_matrix.tsv contains expected contents.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 224, in test_7_calculate_snp_distances
    self.run_function_test(cfsan_snp_pipeline.run_command_from_args, args, 'snp_distance_matrix.tsv')
  File "/mnt/c/Users/crash/Documents/snp-pipeline/test/test_cfsan_snp_pipeline.py", line 96, in run_function_test
    funct(args)
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/cfsan_snp_pipeline.py", line 585, in run_command_from_args
    args.func(args)  # this executes the function previously associated with the subparser with set_defaults
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/distance.py", line 61, in calculate_snp_distances
    utils.global_error("Error: cannot calculate sequence distances without the snp matrix file.")
  File "/mnt/c/Users/crash/Documents/snp-pipeline/snppipeline/utils.py", line 572, in global_error
    sys.exit(100)
SystemExit: 100

----------------------------------------------------------------------
Ran 31 tests in 20.040s

FAILED (errors=7)
Test failed: <unittest.runner.TextTestResult run=31 errors=7 failures=0>
error: Test failed: <unittest.runner.TextTestResult run=31 errors=7 failures=0>