Dave Lawrence

@hyanwong FYI you can get them out via: ``` import cyvcf2 c2_reader = cyvcf2.Reader("./my_vcf.vcf") for k in ['fileformat', 'fileDate', 'source', 'reference']: try: print("%s = %s" % (k, c2_reader.get_header_type(k)[k])) except: pass...

On the topic of missing values for FORMAT fields: ```gt_alt_depths``` returns -1 for missing values while ```format()``` - returns -2147483648, which is -(2^31) or all bits set signed int32 -...

Hi, as an example here's the script to download and generate RefSeq for 37: https://github.com/SACGF/cdot/blob/main/generate_transcript_data/refseq_transcripts_grch37.sh There's scripts for 38 and Ensembl in the same directory. Will join up on slack...

Yes - exactly as Reece said - HGVS requires a way to get sequences (SeqRepo) and transcripts (UTA/cdot) You can install them all locally, for SeqRepo copy/paste the 3 command...

Hi, I've added the issues to the cdot repo (linked above) please add any further info if you need. I hope to be able to find time within a few...

Hi @roysomak4 - I've released a new version of cdot (0.2.8) that handles protein identifiers (so c_to_p works) and also all of the possible transcripts for a given position (this...

Hi, this was due to an off by 1 error (I assumed var_g.posedit.pos.start.base would be 1 past the end) I've fixed it and upgraded cdot, the data files haven't changed...

Hi, yeah it takes a while to builds the interval tree, but it only does so lazily when you need it. If you don't use that functionality it should be...

The Python spec for contextmanger says: https://docs.python.org/2/library/contextlib.html > The function being decorated must return a generator-iterator when called. This iterator must yield exactly one value So you're not allowed to...

>> Please try exactly as below (i.e., removing the UTA connect string) The issue only occurs with a local UTA w/Postgres url. It works fine for me when I don't...