refactor chrom.sizes locales, add default genomemodel func

bedboss/refgenome_validator/chrom_sizes/ucsc_hg19.chrom.sizes

@@ -90,4 +90,4 @@ chrUn_gl000231	27386
 chrUn_gl000229	19913
 chrM	16571
 chrUn_gl000226	15008
-chr18_gl000207_random	4262
+chr18_gl000207_random	4262

bedboss/refgenome_validator/chrom_sizes/ucsc_mm10.chrom.sizes

@@ -0,0 +1,66 @@
+chr1	195471971
+chr2	182113224
+chrX	171031299
+chr3	160039680
+chr4	156508116
+chr5	151834684
+chr6	149736546
+chr7	145441459
+chr10	130694993
+chr8	129401213
+chr14	124902244
+chr9	124595110
+chr11	122082543
+chr13	120421639
+chr12	120129022
+chr15	104043685
+chr16	98207768
+chr17	94987271
+chrY	91744698
+chr18	90702639
+chr19	61431566
+chr5_JH584299_random	953012
+chrX_GL456233_random	336933
+chrY_JH584301_random	259875
+chr1_GL456211_random	241735
+chr4_GL456350_random	227966
+chr4_JH584293_random	207968
+chr1_GL456221_random	206961
+chr5_JH584297_random	205776
+chr5_JH584296_random	199368
+chr5_GL456354_random	195993
+chr4_JH584294_random	191905
+chr5_JH584298_random	184189
+chrY_JH584300_random	182347
+chr7_GL456219_random	175968
+chr1_GL456210_random	169725
+chrY_JH584303_random	158099
+chrY_JH584302_random	155838
+chr1_GL456212_random	153618
+chrUn_JH584304	114452
+chrUn_GL456379	72385
+chr4_GL456216_random	66673
+chrUn_GL456393	55711
+chrUn_GL456366	47073
+chrUn_GL456367	42057
+chrUn_GL456239	40056
+chr1_GL456213_random	39340
+chrUn_GL456383	38659
+chrUn_GL456385	35240
+chrUn_GL456360	31704
+chrUn_GL456378	31602
+chrUn_GL456389	28772
+chrUn_GL456372	28664
+chrUn_GL456370	26764
+chrUn_GL456381	25871
+chrUn_GL456387	24685
+chrUn_GL456390	24668
+chrUn_GL456394	24323
+chrUn_GL456392	23629
+chrUn_GL456382	23158
+chrUn_GL456359	22974
+chrUn_GL456396	21240
+chrUn_GL456368	20208
+chrM	16299
+chr4_JH584292_random	14945
+chr4_JH584295_random	1976

bedboss/refgenome_validator/chrom_sizes/ucsc_mm39.chrom.sizes

@@ -0,0 +1,61 @@
+chr1	195154279
+chr2	181755017
+chrX	169476592
+chr3	159745316
+chr4	156860686
+chr5	151758149
+chr6	149588044
+chr7	144995196
+chr10	130530862
+chr8	130127694
+chr14	125139656
+chr9	124359700
+chr11	121973369
+chr13	120883175
+chr12	120092757
+chr15	104073951
+chr16	98008968
+chr17	95294699
+chrY	91455967
+chr18	90720763
+chr19	61420004
+chr5_JH584299v1_random	953012
+chrX_GL456233v2_random	559103
+chrY_JH584301v1_random	259875
+chr1_GL456211v1_random	241735
+chr1_GL456221v1_random	206961
+chr5_JH584297v1_random	205776
+chr5_JH584296v1_random	199368
+chr5_GL456354v1_random	195993
+chr5_JH584298v1_random	184189
+chrY_JH584300v1_random	182347
+chr7_GL456219v1_random	175968
+chr1_GL456210v1_random	169725
+chrY_JH584303v1_random	158099
+chrY_JH584302v1_random	155838
+chr1_GL456212v1_random	153618
+chrUn_JH584304v1	114452
+chrUn_GL456379v1	72385
+chrUn_GL456366v1	47073
+chrUn_GL456367v1	42057
+chr1_GL456239v1_random	40056
+chrUn_GL456383v1	38659
+chrUn_GL456385v1	35240
+chrUn_GL456360v1	31704
+chrUn_GL456378v1	31602
+chrUn_MU069435v1	31129
+chrUn_GL456389v1	28772
+chrUn_GL456372v1	28664
+chrUn_GL456370v1	26764
+chrUn_GL456381v1	25871
+chrUn_GL456387v1	24685
+chrUn_GL456390v1	24668
+chrUn_GL456394v1	24323
+chrUn_GL456392v1	23629
+chrUn_GL456382v1	23158
+chrUn_GL456359v1	22974
+chrUn_GL456396v1	21240
+chrUn_GL456368v1	20208
+chrM	16299
+chr1_MU069434v1_random	8412
+chr4_JH584295v1_random	1976

bedboss/refgenome_validator/refgenomevalidator.py

@@ -22,7 +22,9 @@ class RefValidator:
     """
 
     def __init__(
-        self, genome_models: List[GenomeModel], igd_path: Optional[str] = None
+        self,
+        genome_models: Optional[List[GenomeModel]] = None,
+        igd_path: Optional[str] = None,
     ):
         """
         Initialization method
@@ -31,6 +33,8 @@ def __init__(
         :param str igd_path: path to a local IGD file containing ALL excluded ranges intervals for IGD overlap assessment, if not provided these metrics are not computed.
 
         """
+        if not genome_models:
+            genome_models = self.build_default_models()
 
         if isinstance(genome_models, str):
             genome_models = list(genome_models)
@@ -381,6 +385,32 @@ def process_igd_stats(self, igd_stats: dict):
         """
         pass
 
+    def build_default_models(self):
+        """
+        Builds a default list of GenomeModels from the chrom.sizes folder.
+        Uses file names as genome alias.
+
+        return list[GenomeModel]
+        """
+
+        chrm_sizes_directory = os.path.join(
+            os.path.curdir, os.path.abspath("./chrom_sizes")
+        )
+        all_genome_models = []
+        for root, dirs, files in os.walk(chrm_sizes_directory):
+            for file in files:
+                if file.endswith(".sizes"):
+                    # print(os.path.join(root, file))
+                    # Get file name
+                    name = os.path.basename(file)
+
+                    curr_genome_model = GenomeModel(
+                        genome_alias=name, chrom_sizes_file=file
+                    )
+                    all_genome_models.append(curr_genome_model)
+
+        return all_genome_models
+
 
 # ----------------------------
 # Helper Functions