test v0.1.3

fix bugs related to boolean values for CLI

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "vstolib"
-version = "0.1.2"
+version = "0.1.3"
 edition = "2021"
 
 [package.metadata.maturin]

examples/outputs/hg002_sniffles2_overlap.tsv

@@ -1,3 +1,3 @@
 variant_id	variant_call_id	sample_id	chromosome_1	position_1	chromosome_2	position_2	variant_type	reference_allele	alternate_allele	source_id	phase_block_id	clone_id	nucleic_acid	variant_calling_method	sequencing_platform	filter	quality_score	precise	variant_subtype	variant_size	reference_allele_read_count	alternate_allele_read_count	total_read_count	alternate_allele_fraction	alternate_allele_read_ids	variant_sequences	tags	attributes	position_1_annotation_annotator	position_1_annotation_annotator_version	position_1_annotation_gene_id	position_1_annotation_gene_id_stable	position_1_annotation_gene_name	position_1_annotation_gene_strand	position_1_annotation_gene_type	position_1_annotation_gene_version	position_1_annotation_region	position_1_annotation_species	position_2_annotation_annotator	position_2_annotation_annotator_version	position_2_annotation_gene_id	position_2_annotation_gene_id_stable	position_2_annotation_gene_name	position_2_annotation_gene_strand	position_2_annotation_gene_type	position_2_annotation_gene_version	position_2_annotation_region	position_2_annotation_species
-1	HG002_dna_sniffles2_INS_1_chr1:10863_chr1:10863	HG002	chr1	10863	chr1	10863	INS	N	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA	hg002			dna	sniffles2	PACBIO	PASS	45.0	True		48	5	8	13	0.615	m64011_190901_095311/23725469/ccs;m64011_190830_220126/131269927/ccs;m64012_190921_234837/125634487/ccs;m64012_190921_234837/58460920/ccs;m64011_190901_095311/150538373/ccs;m64011_190830_220126/102304431/ccs;m64011_190901_095311/166070209/ccs;m64011_190830_220126/70254798/ccs	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA		ID=Sniffles2.INS.5S0;PRECISE=True;SVTYPE=INS;SVLEN=48;END=10863;SUPPORT=8;RNAMES=m64011_190901_095311/166070209/ccs,m64012_190921_234837/125634487/ccs,m64011_190830_220126/70254798/ccs,m64011_190901_095311/150538373/ccs,m64011_190830_220126/102304431/ccs,m64012_190921_234837/58460920/ccs,m64011_190830_220126/131269927/ccs,m64011_190901_095311/23725469/ccs;COVERAGE=11,12,13,13,13;STRAND=-;AF=0.615;STDEV_LEN=14.341;STDEV_POS=0.0;SUPPORT_LONG=0;GT=0/1;GQ=27;DR=5;DV=8																				
+1	HG002_dna_sniffles2_INS_1_chr1:10863_chr1:10863	HG002	chr1	10863	chr1	10863	INS	N	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA	hg002			dna	sniffles2	PACBIO	PASS	45.0	True		48	5	8	13	0.615	m64012_190921_234837/58460920/ccs;m64011_190830_220126/131269927/ccs;m64012_190921_234837/125634487/ccs;m64011_190830_220126/102304431/ccs;m64011_190901_095311/166070209/ccs;m64011_190830_220126/70254798/ccs;m64011_190901_095311/23725469/ccs;m64011_190901_095311/150538373/ccs	CAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA		ID=Sniffles2.INS.5S0;PRECISE=True;SVTYPE=INS;SVLEN=48;END=10863;SUPPORT=8;RNAMES=m64011_190901_095311/166070209/ccs,m64012_190921_234837/125634487/ccs,m64011_190830_220126/70254798/ccs,m64011_190901_095311/150538373/ccs,m64011_190830_220126/102304431/ccs,m64012_190921_234837/58460920/ccs,m64011_190830_220126/131269927/ccs,m64011_190901_095311/23725469/ccs;COVERAGE=11,12,13,13,13;STRAND=-;AF=0.615;STDEV_LEN=14.341;STDEV_POS=0.0;SUPPORT_LONG=0;GT=0/1;GQ=27;DR=5;DV=8																				
 2	HG002_dna_sniffles2_INS_2_chr1:10863_chr1:10863	HG002	chr1	10863	chr1	10863	INS	N	CAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA	hg002			dna	sniffles2	PACBIO	PASS	51.0	True		134	8	5	13	0.385	m64011_190901_095311/14353347/ccs;m64011_190901_095311/142478143/ccs;m64011_190830_220126/95815702/ccs;m64011_190901_095311/177932654/ccs;m64011_190901_095311/101253601/ccs	CAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGGGCCGGCGCAGGCGCAGAGACACATGCTAGCGCGTCCAGGGGAGGAGGCGTGGCA		ID=Sniffles2.INS.6S0;PRECISE=True;SVTYPE=INS;SVLEN=134;END=10863;SUPPORT=5;RNAMES=m64011_190901_095311/177932654/ccs,m64011_190901_095311/101253601/ccs,m64011_190901_095311/14353347/ccs,m64011_190901_095311/142478143/ccs,m64011_190830_220126/95815702/ccs;COVERAGE=11,12,13,13,13;STRAND=+-;AF=0.385;STDEV_LEN=0.0;STDEV_POS=0.0;SUPPORT_LONG=0;GT=0/1;GQ=27;DR=8;DV=5																				

examples/run_vstol_diff.sh

@@ -5,6 +5,8 @@ vstol diff \
   --query-tsv-file ../test/data/hg002_cutesv.tsv \
   --num-threads 1 \
   --max-neighbor-distance 10 \
+  --match-all-breakpoints no \
+  --match-variant-types no \
   --output-tsv-file outputs/hg002_sniffles2_private.tsv
 
 vstol diff \
@@ -14,4 +16,6 @@ vstol diff \
   --query-tsv-file ../test/data/hg002_cutesv.tsv \
   --num-threads 1 \
   --max-neighbor-distance 10 \
+  --match-all-breakpoints no \
+  --match-variant-types no \
   --output-tsv-file outputs/hg002_merged_variants_private.tsv

examples/run_vstol_intersect.sh

@@ -5,5 +5,7 @@ vstol intersect \
   --tsv-file ../test/data/hg002_svim.tsv \
   --num-threads 4 \
   --max-neighbor-distance 10 \
+  --match-all-breakpoints yes \
+  --match-variant-types yes \
   --output-tsv-file outputs/hg002_intersecting_variants.tsv
 

examples/run_vstol_merge.sh

@@ -6,5 +6,7 @@ vstol merge \
   --tsv-file ../test/data/hg002_svim.tsv \
   --num-threads 4 \
   --max-neighbor-distance 10 \
+  --match-all-breakpoints yes \
+  --match-variant-types yes \
   --output-tsv-file outputs/hg002_merged_variants.tsv
 

pyproject.toml

@@ -21,7 +21,7 @@ build-backend = "maturin"
 
 [project]
 name = "vstol"
-version = "0.1.2"
+version = "0.1.3"
 requires-python = ">=3.10"
 keywords = [
     "somatic variants",

python/vstolib/cli/cli_diff.py

@@ -26,6 +26,7 @@
 from ..default import *
 from ..logging import get_logger
 from ..main import diff
+from ..utilities import str2bool
 from ..variants_list import VariantsList
 
 
@@ -99,23 +100,25 @@ def add_cli_diff_arg_parser(
     parser_optional.add_argument(
         "--match-all-breakpoints", '-b',
         dest="match_all_breakpoints",
-        type=bool,
+        type=str2bool,
         required=False,
         default=DIFF_MATCH_ALL_BREAKPOINTS,
-        help="If true, two VariantCall objects are considered an intersect "
+        help="If 'yes', two VariantCall objects are considered an intersect "
              "if both pairs of breakpoints match (start1==start2 AND end1==end2). "
-             "If false, two VariantCall objects are considered an intersect "
-             "if one of the breakpoint pairs matches (start1==start2 OR end1==end2). Default: %r."
+             "If 'no', two VariantCall objects are considered an intersect "
+             "if one of the breakpoint pairs matches (start1==start2 OR end1==end2). Default: %s"
              % DIFF_MATCH_ALL_BREAKPOINTS
     )
     parser_optional.add_argument(
         "--match-variant-types", '-m',
         dest="match_variant_types",
-        type=bool,
+        type=str2bool,
         required=False,
         default=DIFF_MATCH_VARIANT_TYPES,
-        help="If true, two VariantCall objects are considered an intersect "
-             "if the (super) variant types are the same (default: %r)."
+        help="If 'yes', two VariantCall objects are considered an intersect "
+             "if the (super) variant types are the same. "
+             "If 'no', two VariantCall objects are considered an intersect "
+             "even if the (super) variant types are different (default: %s)."
              % DIFF_MATCH_VARIANT_TYPES
     )
     parser.set_defaults(which='diff')

python/vstolib/cli/cli_intersect.py

@@ -26,6 +26,7 @@
 from ..default import *
 from ..logging import get_logger
 from ..main import intersect
+from ..utilities import str2bool
 from ..variants_list import VariantsList
 
 
@@ -91,23 +92,25 @@ def add_cli_intersect_arg_parser(
     parser_optional.add_argument(
         "--match-all-breakpoints", '-b',
         dest="match_all_breakpoints",
-        type=bool,
+        type=str2bool,
         required=False,
         default=INTERSECT_MATCH_ALL_BREAKPOINTS,
-        help="If true, two VariantCall objects are considered an intersect "
+        help="If 'yes', two VariantCall objects are considered an intersect "
              "if both pairs of breakpoints match (start1==start2 AND end1==end2). "
-             "If false, two VariantCall objects are considered an intersect "
-             "if one of the breakpoint pairs matches (start1==start2 OR end1==end2). Default: %r."
+             "If 'no', two VariantCall objects are considered an intersect "
+             "if one of the breakpoint pairs matches (start1==start2 OR end1==end2). Default: %s"
              % INTERSECT_MATCH_ALL_BREAKPOINTS
     )
     parser_optional.add_argument(
         "--match-variant-types", '-m',
         dest="match_variant_types",
-        type=bool,
+        type=str2bool,
         required=False,
         default=INTERSECT_MATCH_VARIANT_TYPES,
-        help="If true, two VariantCall objects are considered an intersect "
-             "if the (super) variant types are the same (default: %r)."
+        help="If 'yes', two VariantCall objects are considered an intersect "
+             "if the (super) variant types are the same. "
+             "If 'no', two VariantCall objects are considered an intersect "
+             "even if the (super) variant types are different (default: %s)."
              % INTERSECT_MATCH_VARIANT_TYPES
     )
     parser.set_defaults(which='intersect')

python/vstolib/cli/cli_merge.py

@@ -26,6 +26,7 @@
 from ..default import *
 from ..logging import get_logger
 from ..main import merge
+from ..utilities import str2bool
 from ..variants_list import VariantsList
 
 
@@ -88,23 +89,27 @@ def add_cli_merge_arg_parser(
              % MERGE_MAX_NEIGHBOR_DISTANCE
     )
     parser_optional.add_argument(
-        "--match-all-breakpoints", '-m',
+        "--match-all-breakpoints", '-b',
         dest="match_all_breakpoints",
-        type=bool,
+        type=str2bool,
         required=False,
         default=MERGE_MATCH_ALL_BREAKPOINTS,
-        help="If true, for two VariantCall objects to be considered "
-             "intersecting, all breakpoints must match or be near each other (default: %r)."
+        help="If 'yes', two VariantCall objects are considered an intersect "
+             "if both pairs of breakpoints match (start1==start2 AND end1==end2). "
+             "If 'no', two VariantCall objects are considered an intersect "
+             "if one of the breakpoint pairs matches (start1==start2 OR end1==end2). Default: %s"
              % MERGE_MATCH_ALL_BREAKPOINTS
     )
     parser_optional.add_argument(
-        "--match-variant-types", '-a',
+        "--match-variant-types", '-m',
         dest="match_variant_types",
-        type=bool,
+        type=str2bool,
         required=False,
         default=MERGE_MATCH_VARIANT_TYPES,
-        help="If true, for two VariantCall objects to be considered "
-             "intersecting, the variant types must be the same (default: %r)."
+        help="If 'yes', two VariantCall objects are considered an intersect "
+             "if the (super) variant types are the same. "
+             "If 'no', two VariantCall objects are considered an intersect "
+             "even if the (super) variant types are different (default: %s)."
              % MERGE_MATCH_VARIANT_TYPES
     )
     parser.set_defaults(which='merge')

python/vstolib/default.py

@@ -37,8 +37,8 @@
 
 """diff"""
 DIFF_MAX_NEIGHBOR_DISTANCE = 1000
-DIFF_MATCH_ALL_BREAKPOINTS = False
-DIFF_MATCH_VARIANT_TYPES = False
+DIFF_MATCH_ALL_BREAKPOINTS = 'no'
+DIFF_MATCH_VARIANT_TYPES = 'no'
 
 
 """filter"""
@@ -53,16 +53,16 @@
 """intersect"""
 # Maximum neighbor distance (bases).
 INTERSECT_MAX_NEIGHBOR_DISTANCE = 10
-INTERSECT_MATCH_ALL_BREAKPOINTS = True
-INTERSECT_MATCH_VARIANT_TYPES = True
+INTERSECT_MATCH_ALL_BREAKPOINTS = 'yes'
+INTERSECT_MATCH_VARIANT_TYPES = 'yes'
 
 
 
 """merge"""
 # Maximum neighbor distance (bases).
 MERGE_MAX_NEIGHBOR_DISTANCE = 10
-MERGE_MATCH_ALL_BREAKPOINTS = True
-MERGE_MATCH_VARIANT_TYPES = True
+MERGE_MATCH_ALL_BREAKPOINTS = 'yes'
+MERGE_MATCH_VARIANT_TYPES = 'yes'
 
 
 """overlap"""

python/vstolib/utilities.py

@@ -139,6 +139,7 @@ def retrieve_from_dict(
                            default_value=default_value,
                            type=type)
 
+
 def retrieve_from_list(
         lst: list,
         index: int,
@@ -164,3 +165,13 @@ def retrieve_from_list(
     return get_typed_value(value=value,
                            default_value=default_value,
                            type=type)
+
+
+def str2bool(v):
+    if v.lower() in ('yes', 'true', 't', 'y', '1'):
+        return True
+    elif v.lower() in ('no', 'false', 'f', 'n', '0'):
+        return False
+    else:
+        raise Exception('Boolean value expected.')
+

test/test_diff.py

@@ -5,7 +5,7 @@
 from vstolib.constants import VariantTypes
 
 
-def test_diff_sniffles2_variants_list(
+def test_diff_1(
         sniffles2_variants_list,
         cutesv_variants_list,
         pbsv_variants_list,
@@ -24,7 +24,7 @@ def test_diff_sniffles2_variants_list(
     )
 
 
-def test_diff_bnd():
+def test_diff_2():
     variant_call_11 = VariantCall(
         id='variant_call_11',
         sample_id='sample1',
@@ -128,3 +128,51 @@ def test_diff_bnd():
     assert 'variant_call_12' in variants_list.variant_call_ids
     assert 'variant_call_13' in variants_list.variant_call_ids
     assert 'variant_call_14' not in variants_list.variant_call_ids
+
+
+def test_diff_3():
+    variant_call_11 = VariantCall(
+        id='variant_call_11',
+        sample_id='sample1',
+        chromosome_1='chr1',
+        position_1=100,
+        chromosome_2='chr5',
+        position_2=500,
+        variant_type=VariantTypes.TRANSLOCATION,
+        reference_allele='T',
+        alternate_allele=''
+    )
+
+    variant_call_21 = VariantCall(
+        id='variant_call_21',
+        sample_id='sample2',
+        chromosome_1='chr1',
+        position_1=101,
+        chromosome_2='chr1',
+        position_2=101,
+        variant_type=VariantTypes.INSERTION,
+        reference_allele='C',
+        alternate_allele='CTACTACTGGT'
+    )
+
+    variant_11 = Variant(id='variant_11')
+    variant_21 = Variant(id='variant_21')
+    variant_11.add_variant_call(variant_call=variant_call_11)
+    variant_21.add_variant_call(variant_call=variant_call_21)
+
+    variants_list_1 = VariantsList()
+    variants_list_2 = VariantsList()
+    variants_list_1.add_variant(variant=variant_11)
+    variants_list_2.add_variant(variant=variant_21)
+
+    variants_list = diff(
+        target_variants_list=variants_list_1,
+        query_variants_lists=[variants_list_2],
+        max_neighbor_distance=1000,
+        num_threads=1,
+        match_all_breakpoints=False,
+        match_variant_types=False
+    )
+
+    assert 'variant_call_11' not in variants_list.variant_call_ids
+