pysam.bcftools.concat Ignores the -o Option

[shokrofont]

When using pysam.bcftools.concat to concatenate VCF files, the -o option (for specifying the output file) is ignored. Instead, the concatenated output is written to stdout. This behavior is unexpected and makes it difficult to directly specify an output file during concatenation.

import pysam
import pysam.bcftools
import os

def create_dummy_vcf(filename, chrom, pos, ref, alt):
    """Creates a dummy VCF file with minimal content."""
    header = (
        "##fileformat=VCFv4.2\n"
        f"##contig=<ID={chrom}>\n"  # Add contig definition
        "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"
    )
    content = f"{chrom}\t{pos}\t.\t{ref}\t{alt}\t.\tPASS\t.\n"
    
    with open(filename, "w") as vcf:
        vcf.write(header)
        vcf.write(content)

# Create two dummy VCF files
vcf1 = "dummy1.vcf"
vcf2 = "dummy2.vcf"
output_vcf = "concatenated.vcf"

create_dummy_vcf(vcf1, "chr1", 100, "A", "T")
create_dummy_vcf(vcf2, "chr1", 200, "G", "C")

# Attempt to concatenate using pysam.bcftools.concat
try:
    out = pysam.bcftools.concat( '-o', output_vcf, vcf1, vcf2, catch_stdout=True)    
    if os.path.exists(output_vcf):
        print(f"Output VCF successfully created: {output_vcf}")
    else:
        print(f"Output VCF not created as expected. Check stdout.")
        print(out)
except Exception as e:
    print(f"An error occurred: {e}")

# Clean up dummy files
os.remove(vcf1)
os.remove(vcf2)
if os.path.exists(output_vcf):
    os.remove(output_vcf)