No option to flush VariantFile.write() (or at least undocumented)

[blex-max]

Output is not written until the program completes. Is this something that could be added? Many thanks for your work.

[jmarshall]

Much as with ordinary Python I/O streams, you should call myvariantfile.close() when you have finished writing to it to ensure the output is flushed and the file closed in a timely fashion.

Alternatively VariantFile, AlignmentFile, etc can be used as context managers, so that the following would ensure the file is closed at the end of the with statement:

with pysam.VariantFile('foo.vcf', 'w') as f:
    f.write(record)
    …etc…

Pysam could do more for flushing these files while writing them: there is an underlying HTSlib hts_flush() function that VariantFile, AlignmentFile, etc could expose as a flush() method. However I suspect most code would not really benefit from being able to do this.

[blex-max]

In my case I'd like to be able to watch 'tail filename' output as it is produced, I find it useful for debugging