Metadata modification and others minor updates #30
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While writing VCF metadata with the Writer class, ordering could put the vcf file format metadata after others metadata, causing warnings while dealing with VCF and breaking analises with the last BCF tools
e to explain why this merge is necessary,
bunop
changed the title
The Writer class make use of csv.writer which by default uses the windows encoding line terminator while writing files. Forced to use the standard '\n' newline
I'm trying to fix tests and resolve bugs when comparing records
Checking record equality (only by positions on chromosome). Only
a test fails:
Traceback (most recent call last):
File "/home/paolo/Projects/cyvcf/test/test_vcf.py", line 767, in testApplyMultipleFilters
assert s == 0
AssertionError
This seems a problem inside pyvcf library, used only for tests
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Dear Aaron,
here some minor fixes to your library:
self.metadata,self.infos,self.filters,self.formatsinReaderclass from dictionaries tocollections.OrderedDict: By usingWriterclass, those records will be placed in random order to output file. The VCF file format records (eg.##fileformat=VCFv4.1) must be the first record in a VCF file, or other VCF processing softwares will fail (bcftools) or raise warningscfriedlinein your pull request #29install_requires = ["cython"],in setup.py in order to check and installcythonwhile installing cyvcfWritermethod force thecsv.writerto use the standard linux line terminator\n, not the default windows\r\nRegards,
Paolo