Liguo Wang

I have the same problem (Python 3.8.3). The error message "ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()" means that...

This is fantastic. Wish I could help more, but I don't know Rust. Since you already implemented the bed-convert function, how it's speed compared to: 1) CrossMap 2) UCSC liftover...

This is fixed in v0.6.5 $ python3 ../../CrossMap-0.2.9.git/bin/CrossMap.py vcf v1.0_to_v1.1_rdna_merged.chain HG002_CHM13v1.0_CMRG_smallvar_v1.00_draft.vcf.gz chm13v2.0_maskedY.fa.gz out.vcf 2022-12-01 07:16:10 [INFO] Read the chain file "v1.0_to_v1.1_rdna_merged.chain" 2022-12-01 07:16:10 [INFO] Filter out variants [reference_allele == alternative_allele]...

please try: `pip3 install git+https://github.com/liguowang/cpgtools.git`

I just updated the PyPI package. Maybe you could also try: `pip install cpgtools`

We used our internally developed code to do the "union". As an alternative, you could select the longest transcript from each gene.

Thanks, Thomas. What is the appropriate place to put the `src/__init__.py`?

Don't understand what you meant, but I do realize there is an issue here. The "noCompAllele" option cannot deal with variants that have **multiple alternative alleles**.

Looks like you cannot use cpgtools for DNA methylation data generated from Pacbio. If my understanding is correct, Pacbio methylation data is mostly binary calls (methylated for unmethylated). Don't know...

Hi Solivehong Genotypes in the "ALT" field can only be IUPAC characters plus dot (.), dash (-) and star (*). please double-check. Liguo