(issue #881) Fix add_meta function in libcbcf.pyx, so meta-information lines in he…

[lltw]

…ader added with this function have double-quoting rules in accordance to rules specified in VCF4.2 and VCF4.3 specifications

[AndreasHeger]

Thanks!

[kishwarshafin]

Hello,

Not sure what happened here, with this code:

sq_id = sq
 n = self.fasta_handler.get_chromosome_sequence_length(sq)
items = [('ID', sq_id), 
         ('length', ln)]
header.add_meta(key='contig', items=items)

I keep getting:

Traceback (most recent call last):
  File "/home/kishwar/Kishwar/software/pepper/venv/bin/pepper_snp", line 11, in <module>
    load_entry_point('pepper-polish==0.0.6', 'console_scripts', 'pepper_snp')()
  File "/home/kishwar/Kishwar/software/pepper/venv/lib/python3.6/site-packages/pepper_polish-0.0.6-py3.6-linux-x86_64.egg/pepper_snp/pepper_snp.py", line 428, in main
    FLAGS.probability_threshold)
  File "/home/kishwar/Kishwar/software/pepper/venv/lib/python3.6/site-packages/pepper_polish-0.0.6-py3.6-linux-x86_64.egg/pepper_snp/modules/python/FindSNPCandidates.py", line 59, in find_candidates
    vcf_file.write_vcf_records(contig, all_candidates, reference_dict, positions)
  File "/home/kishwar/Kishwar/software/pepper/venv/lib/python3.6/site-packages/pepper_polish-0.0.6-py3.6-linux-x86_64.egg/pepper_snp/modules/python/VcfWriter.py", line 89, in write_vcf_records
    filter='PASS', alleles=alleles, GT=gt, GQ=60)
  File "pysam/libcbcf.pyx", line 4398, in pysam.libcbcf.VariantFile.new_record
  File "pysam/libcbcf.pyx", line 2074, in pysam.libcbcf.VariantHeader.new_record
  File "pysam/libcbcf.pyx", line 3061, in pysam.libcbcf.VariantRecord.contig.__set__
ValueError: Invalid chromosome/contig

However, works fine on 0.15.2