fixref supports standard fasta ref by pysam

hxj5 / xcltk

Toolkit for XClone preprocessing to detect CNVs from scRNA-seq data

Apache License 2.0

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Closed huangyh09 closed 3 years ago

huangyh09 commented 3 years ago

Hi Xianjie,

I added pysam to fetch the ref allele from the standard fasta, which might make the interface simpler. The codes could be further optimised though.

Also, I noticed that it still has bug in supporting compressed output file in vcf.gz, while uncompressed format is fine.

Yuanhua