Takeshi Gitano

Suggested branch changes in https://github.com/jamescasbon/PyVCF/tree/wip/82-add-call-data are not going to be included in the master branch and future releases?? Being able to add unexistent FORMAT fields is a quite interesting fact...

@dawe : You can check the open pull request in #136 . I'm currently dealing with most of the common vcf edit tasks (at least those affecting my daily work)...

Since I didn't get any feedback on the open pull request in https://github.com/jamescasbon/PyVCF/pull/136, I continued developing the add/edit functions on a separate and private repository, which is currently working. In...

Hi, @jamescasbon! I'd like to come back to this pull-request. Regarding your request on tests, I'm thinking of adding 2 vcf files from different sources (GATK and VarScan, with different...

Added test files (vct/test/gatk_sample.vcf, vcf/test/varscan_sample.vcf, also gzipped and tabix indexed). Created script for merging files (scripts/vcf_merge.py). Included example of merge command (scripts/merge_test.txt).

Sorry for having submitted all my changes & tests without a prior exhaustive revision. I'm checking all the points you listed in your last 2 comments, and will come back...

I think I'm ready with the changes for the moment. A brief list of the changes: - I've formatted the scripts and checked them with 'pep8 --max-line-length=100' - I've removed...

"Print" statements have been substituted to "sys.stderr.write" for compatibility with python 3

Since I haven't received any more feedback, I've decided to go through my pull request. I've made more consistent changes, regarding private methods being called from outside propietary classes and...

New changes included: - parser.py: Writer class: add_attr method created, for adding infos, formats, etc. - parser.py: Writer class: _init_ method: now this method does not write header until first...