pysam pysam/libcbcf.pyx error when opening vcf.format file

[minjaf]

Hi! When running cue, I am getting an error:

[E::bcf_hdr_parse_sample_line] Could not parse the "#CHROM.." line, either FORMAT is missing or spaces are present instead of tab
s:                                                                                                                               
        #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT                                                   
                                                                                                                                 
Traceback (most recent call last):                                                                                               
  File "pysam/libcbcf.pyx", line 4355, in pysam.libcbcf.VariantFile.open                                                         
  File "pysam/libcbcf.pyx", line 2210, in pysam.libcbcf.makeVariantHeader                                                        
ValueError: cannot create VariantHeader                                                                                          
                                                                                                                                 
During handling of the above exception, another exception occurred:                                                              
                                                                                                                                 
Traceback (most recent call last):                                                                                               
  File "/home/vsfishman/soft/cue/engine/call.py", line 183, in <module>                                                          
    min_score=data_config.min_qual_score, min_len=data_config.min_sv_len)                                                        
  File "/home/vsfishman/soft/cue/seq/io.py", line 360, in bed2vcf                                                                
    vcf_format_file = get_vcf_format_variant_file(vcf_fname + ".format", chr_index.contigs())                                    
  File "/home/vsfishman/soft/cue/seq/io.py", line 327, in get_vcf_format_variant_file                                            
    vcf_file = VariantFile(vcf_fname)                                                                                            
  File "pysam/libcbcf.pyx", line 4117, in pysam.libcbcf.VariantFile.__init__
  File "pysam/libcbcf.pyx", line 4357, in pysam.libcbcf.VariantFile.open
ValueError: file `b'/mnt/10tb/home/vsfishman/genomes/process/1000206901/reports//svs.vcf.format'` does not have valid header (mod
e=`b'r'`) - is it VCF/BCF format?

I believe this is because when pysam is installed with new htclib (>=1.14), which does not accept empty vcf with format field:
samtools/htslib#1328 (comment)

I suggest replacing the line 326 of io.py
vcf.write("#%s\n" % "\t".join(["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO", "FORMAT"]))
with:
vcf.write("#%s\n" % "\t".join(["CHROM", "POS", "ID", "REF", "ALT", "QUAL", "FILTER", "INFO"]))

in this case, FORMAT will be added later on when actually writing records to the vcf file.

[jkalleberg]

@minjaf Thank you for this! I also encountered this error with the tutorial, but your fix seems to work for me.

[prmunn]

Thanks @minjaf - your fix worked for me too!