[I/O] VCFReader crashes when reading from regions that are empty

[edawson]

When reading a VCF and parsing a specific region, the reader can crash if that region contains no variants. This can happen if the region is truly empty or if the tabix index is invalid.

The solution is probably to place a guard around the call to concat to check if any of the VCF dataframes are not empty:

if any([not df.empty for df in df_list]):
  concat(df_list)

and return an empty dataframe if no concat-able datframes exist.

I've placed a stacktrace here, but it's from a VCF with an invalid tabix index, so it's maybe not the best example.

/home/eric/vcfs/LP6005441-DNA_B01.annotated.nh.vcf.gz
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
 in 
     10 
     11 sgdp_pon = pon.PanelOfNormals()
---> 12 sgdp_pon.from_vcf_list(sgdp_list, merge_columns=["chrom", "start_pos", "end_pos", "ref", "alt"], info_keys=["AC"], regions=["22"], usePandas=False)

~/sandbox/somatic-vc/somaticdf/pon.py in from_vcf_list(self, vcf_list, merge_columns, regions, info_keys, tags, count_variable, usePandas)
    109         for i in range(0, len(vcf_list)):
    110             print(vcf_list[i])
--> 111             d = read_func(vcf_list[i], regions, tags=tags, info_keys=info_keys)
    112 
    113             if not d.empty:

~/sandbox/somatic-vc/somaticdf/utils.py in read_vcf_to_df(vcf_file, regions, num_threads, tags, info_keys, filter_keys, format_keys, chunk_size)
    130     Read a VCF file into a cuDF Variant DataFrame.
    131     """
--> 132     ret = cudf.DataFrame(read_vcf_to_pandas(vcf_file, regions=regions, num_threads=num_threads, tags=tags, info_keys=info_keys, filter_keys=filter_keys, format_keys=format_keys, chunk_size=chunk_size))
    133     return ret
    134 

~/sandbox/somatic-vc/somaticdf/utils.py in read_vcf_to_pandas(vcf_file, regions, num_threads, tags, info_keys, filter_keys, format_keys, chunk_size)
    137     Read a VCF file into a PANDAS Variant DataFrame.
    138     """
--> 139     v = VCFReader(vcf_file, regions=regions, num_threads=num_threads, tags=tags, require_genotype=False, info_keys=info_keys, format_keys=format_keys, filter_keys=filter_keys, chunksize=chunk_size)
    140     df = v.dataframe
    141     df = set_default_types(df)

~/sandbox/somatic-vc/VariantWorks/variantworks/io/vcfio.py in __init__(self, vcf, bams, is_fp, require_genotype, tags, info_keys, filter_keys, format_keys, regions, num_threads, chunksize, sort, unbounded_val_max_cols)
    172 
    173         # Parse the VCF
--> 174         self._parallel_parse_vcf()
    175 
    176     @property

~/sandbox/somatic-vc/VariantWorks/variantworks/io/vcfio.py in _parallel_parse_vcf(self)
    646         # Generate final DataFrame from intermediate DataFrames computed by
    647         # individual threads.
--> 648         self._dataframe = pd.concat(df_list, ignore_index=True)
    649 
    650         # Manually set strict data types of specific fields

~/anaconda3/envs/ashg/lib/python3.7/site-packages/pandas/core/reshape/concat.py in concat(objs, axis, join, ignore_index, keys, levels, names, verify_integrity, sort, copy)
    279         verify_integrity=verify_integrity,
    280         copy=copy,
--> 281         sort=sort,
    282     )
    283 

~/anaconda3/envs/ashg/lib/python3.7/site-packages/pandas/core/reshape/concat.py in __init__(self, objs, axis, join, keys, levels, names, ignore_index, verify_integrity, copy, sort)
    327 
    328         if len(objs) == 0:
--> 329             raise ValueError("No objects to concatenate")
    330 
    331         if keys is None:

ValueError: No objects to concatenate