jamescasbon/PyVCF — pull request #55 by cmclean (2012-06-25 20:52:02+00:00)
Title: Modifications to have Writer output match Reader input

The following are small changes to make vcf Writer output more consistent with common VCF input files.

Modify Writer to output FILTER field properly:
* Writes as ";"-delimited string rather than the Python list representation
* Writes non-existent or "PASS" filters as "PASS" rather than "."

Modify Writer to output INFO field properly:
* Writes Flag outputs just as present, not using the X=Y format
* E.g. the DB flag to indicate presence in dbSNP will be written as "DB", rather than as "DB=True"

Modify Writer to allow different line terminator to be used:
* Default remains "\r\n" for backward compatibility