Add region and buffer region

gwaspy/imputation/impute5_impute.py

@@ -32,6 +32,7 @@ def imputation(
  vcf: hb.ResourceGroup = None,
  reference_vcf: hb.ResourceGroup = None,
  region: str = None,
+ buffer_region: str = None,
  ncpu: int = 8,
  memory: str = 'highmem',
  storage: int = None,
@@ -60,6 +61,7 @@ def imputation(
  --m /root/gwaspy/resources/maps/b38/{chrom}.b38.gmap.gz \
  --g {vcf['vcf']} \
  --r {region} \
+ --buffer-region {buffer_region} \
  --out-gp-field \
  --o {j.imputed_chunk['chunk.bcf']} \
  --threads {ncpu}
@@ -142,17 +144,21 @@ def concatenate_imputed_chunks(
  f'https://raw.githubusercontent.com/odelaneau/shapeit5/main/resources/chunks/b38/4cM/chunks_chr{i}.txt',
  sep='\t', header=None,
  names=['index', 'chrom', 'irg', 'org', 'col5', 'col6', 'col7', 'col8'])
- imp_chunks_no_buffer = imputation_chunks['org'].tolist() # 4th column (with no buffer between chunks)
+ imputation_chunks = imputation_chunks[['irg', 'org']]
+ imp_chunks = list(imputation_chunks.itertuples(index=False, name=None))
+ # imp_chunks_no_buffer = imputation_chunks['org'].tolist() # 4th column (with no buffer between chunks)
 
  # Impute genotypes
  imputed_chunks = [
  imputation(
  b=batch,
  vcf=chrom_vcf,
  reference_vcf=ref_vcf,
+ region=imp_chunks[i][1],
+ buffer_region=imp_chunks[i][0],
  storage=round(vcf_size + ref_size + 5)
  ).imputed_chunk
- for i in range(len(imp_chunks_no_buffer))
+ for i in range(len(imp_chunks))
  ]
 
  # Concatenate imputed chunks