add support for unmmapped bams (#98)

* add support for unmmapped bams

* fix _validate_bam_file for ubam

* Add tests to make sure proper calls made with unmapped option

---------

Co-authored-by: Yash Patel <yashpatel@mednet.ucla.edu>

CHANGELOG.md

@@ -10,7 +10,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ## [Unreleased]
 ### Added
 - Add validation flowchart
-
+- Add support for unmapped BAM
 ---
 
 ## [5.0.0] - 2024-02-16
@@ -72,7 +72,7 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 
 ### Fixed
 
-### Removed 
+### Removed
 - Remove deprecated parameter options from README
 - Remove inaccessible design doc link from README
 - Remove directory checking

pipeval/validate/__main__.py

@@ -16,7 +16,7 @@ def positive_integer(arg):
 
 def add_subparser_validate(subparsers:argparse._SubParsersAction):
     """ Parse arguments """
-    parser = subparsers.add_parser(
+    parser:argparse.ArgumentParser = subparsers.add_parser(
         name = 'validate',
         help = 'Validate one or more file(s)',
         description = 'Validate one or more file(s)',
@@ -26,6 +26,8 @@ def add_subparser_validate(subparsers:argparse._SubParsersAction):
     parser.add_argument('path', help='One or more paths of files to validate', type=str, nargs='+')
     parser.add_argument('-r', '--cram-reference', default=None, \
         help='Path to reference file for CRAM')
+    parser.add_argument('-u', '--unmapped-bam', action='store_true',
+        help='Input is unmmapped BAM.')
     parser.add_argument('-p', '--processes', type=positive_integer, default=1, \
         help='Number of processes to run in parallel when validating multiple files')
     parser.add_argument('-t', '--test-integrity', action='store_true', \

pipeval/validate/validate.py

@@ -47,6 +47,7 @@ def _validate_file(
         `args` must contain the following:
         `path` is a required argument with a value of list of files
         `cram_reference` is a required argument with either a string value or None
+        `unmapped_bam` is a required argument of boolean variable
     '''
     _path_exists(path)
 

pipeval/validate/validate_types.py

@@ -3,5 +3,5 @@
 
 ValidateArgs = namedtuple(
     'args',
-    'path, cram_reference, processes, test_integrity'
+    'path, cram_reference, unmapped_bam, processes, test_integrity'
 )

pipeval/validate/validators/bam.py

@@ -6,14 +6,22 @@
 
 from pipeval.validate.validate_types import ValidateArgs
 
-def _validate_bam_file(path:Path):
+def _validate_bam_file(path:Path, unmapped_bam:bool):
     '''Validates bam file'''
+    args = [str(path)]
+    if unmapped_bam:
+        args.append('-u')
     try:
-        pysam.quickcheck(str(path))
+        pysam.quickcheck(*args)
     except pysam.SamtoolsError as err:
         raise ValueError("samtools bam check failed. " + str(err)) from err
 
-    bam_head: pysam.IteratorRowHead = pysam.AlignmentFile(str(path)).head(1)
+    kwargs = {
+        'filename': str(path)
+    }
+    if unmapped_bam:
+        kwargs['check_sq'] = False
+    bam_head: pysam.IteratorRowHead = pysam.AlignmentFile(**kwargs).head(1)
     if next(bam_head, None) is None:
         raise ValueError("pysam bam check failed. No reads in " + str(path))
 
@@ -35,5 +43,5 @@ def _check_bam(path:Path, args:Union[ValidateArgs,Dict[str, Union[str,list]]]):
     `args` must contains the following:
         `cram_reference` is a required key with either a string value or None
     '''
-    _validate_bam_file(path)
+    _validate_bam_file(path, args.unmapped_bam)
     _check_bam_index(path)

test/unit/test_validate.py

@@ -2,7 +2,7 @@
 # pylint: disable=C0114
 from pathlib import Path
 from argparse import Namespace, ArgumentTypeError
-from unittest.mock import Mock, mock_open
+from unittest.mock import Mock, mock_open, MagicMock
 import warnings
 import zlib
 import gzip
@@ -110,7 +110,13 @@ def test__path_exists__errors_for_non_existing_path(mock_path):
 @mock.patch('pipeval.validate.files.Path', autospec=True)
 def test__check_compressed__raises_warning_for_uncompressed_path(mock_path, mock_magic):
     mock_magic.return_value = 'text/plain'
-    test_args = ValidateArgs(path=[], cram_reference=None, processes=1, test_integrity=False)
+    test_args = ValidateArgs(
+        path=[],
+        cram_reference=None,
+        unmapped_bam=False,
+        processes=1,
+        test_integrity=False
+    )
 
     with pytest.warns(UserWarning):
         _check_compressed(mock_path, test_args)
@@ -132,7 +138,13 @@ def test__check_compressed__passes_compression_check(
     compression_mime):
     mock_magic.return_value = compression_mime
     mock_integrity.return_value = None
-    test_args = ValidateArgs(path=[], cram_reference=None, processes=1, test_integrity=False)
+    test_args = ValidateArgs(
+        path=[],
+        cram_reference=None,
+        unmapped_bam=False,
+        processes=1,
+        test_integrity=False
+    )
 
     with warnings.catch_warnings():
         warnings.filterwarnings("error")
@@ -147,14 +159,46 @@ def test__validate_bam_file__empty_bam_file(mock_pysam):
     test_path = Path('empty/valid/bam')
 
     with pytest.raises(ValueError):
-        _validate_bam_file(test_path)
+        _validate_bam_file(test_path, unmapped_bam=False)
+
+@mock.patch('pipeval.validate.validators.bam.pysam')
+def test__validate_bam_file__quickcheck_called_with_unmapped(mock_pysam):
+    mock_alignment_file = Mock()
+    mock_alignment_file.head.return_value = iter(['read1'])
+    mock_quickcheck = Mock()
+
+    mock_pysam.quickcheck = mock_quickcheck
+    mock_pysam.AlignmentFile.return_value = mock_alignment_file
+
+    test_path = 'empty/valid/bam'
+    test_unmapped_option = '-u'
+
+    _validate_bam_file(test_path, unmapped_bam=True)
+    mock_quickcheck.assert_called_with(test_path, test_unmapped_option)
+
+@mock.patch('pipeval.validate.validators.bam.pysam')
+def test__validate_bam_file__alignmentfile_called_with_unmapped(mock_pysam):
+    mock_alignment_file = MagicMock()
+    mock_alignment_file.__iter__.return_value = ['read1']
+    mock_quickcheck = Mock()
+
+    mock_pysam.quickcheck = mock_quickcheck
+    mock_pysam.AlignmentFile = mock_alignment_file
+
+    test_path = 'empty/valid/bam'
+    test_unmapped_option = False
+
+    _validate_bam_file(test_path, unmapped_bam=True)
+    mock_alignment_file.assert_called_with(
+        **{'filename': test_path, 'check_sq': test_unmapped_option}
+    )
 
 @mock.patch('pipeval.validate.validators.bam.Path', autospec=True)
 def test__validate_bam_file__quickcheck_fails(mock_path):
     mock_path.exists.return_value = False
 
     with pytest.raises(ValueError):
-        _validate_bam_file(mock_path)
+        _validate_bam_file(mock_path, unmapped_bam=False)
 
 @mock.patch('pipeval.validate.validators.bam.pysam', autospec=True)
 def test__check_bam_index__no_index_file_error(mock_pysam):
@@ -247,7 +291,13 @@ def test__validate_vcf_file__passes_vcf_validation(mock_call):
     _validate_vcf_file('some/file')
 
 def test__run_validate__passes_validation_no_files():
-    test_args = ValidateArgs(path=[], cram_reference=None, processes=1, test_integrity=False)
+    test_args = ValidateArgs(
+        path=[],
+        cram_reference=None,
+        unmapped_bam=False,
+        processes=1,
+        test_integrity=False
+    )
     run_validate(test_args)
 
 @pytest.mark.parametrize(
@@ -273,6 +323,7 @@ def test___validation_worker__fails_with_failing_checks(
     test_args = ValidateArgs(
         path=[test_path],
         cram_reference=None,
+        unmapped_bam=False,
         processes=1,
         test_integrity=False)
     mock_path_resolve.return_value = test_path
@@ -292,6 +343,7 @@ def test__run_validate__passes_on_all_valid_files(
     test_args = ValidateArgs(
         path=[test_path],
         cram_reference=None,
+        unmapped_bam=False,
         processes=1,
         test_integrity=False)
 
@@ -309,6 +361,7 @@ def test__run_validate__fails_with_failing_file(
     test_args = ValidateArgs(
         path=[test_path],
         cram_reference=None,
+        unmapped_bam=False,
         processes=1,
         test_integrity=False)
     expected_code = 1
@@ -352,6 +405,7 @@ def test__validate_file__checks_compression(
     test_args = ValidateArgs(
         path=[],
         cram_reference=None,
+        unmapped_bam=False,
         processes=1,
         test_integrity=False)
 
@@ -369,6 +423,7 @@ def test__run_validate__fails_on_unresolvable_symlink(mock_path_resolve):
     test_args = ValidateArgs(
         path=[test_path],
         cram_reference=None,
+        unmapped_bam=False,
         processes=1,
         test_integrity=False)
 
@@ -394,6 +449,7 @@ def test___validation_worker__passes_proper_validation(
     test_args = ValidateArgs(
         path=[test_path],
         cram_reference=None,
+        unmapped_bam=False,
         processes=1,
         test_integrity=False)