Grammatikati Konstantin

Repo needs maintainer not only because of cooperation, but because of several breaking changes: - https://github.com/Illumina/ExpansionHunter/issues/160 - https://github.com/Illumina/ExpansionHunter/issues/168 - https://github.com/Illumina/ExpansionHunter/issues/165 @egor-dolzhenko Do you still maintain this repo?

As we can see in [code](https://github.com/humanlongevity/HLA/blob/master/bin/typer.sh#L50-L52): ```sh if [ "$FULL" = true ]; then $BIN/full.r $OUT/${ID}.tsv.dna $OUT/${ID}.hla $OUT/${ID}.hla.full fi ``` running with `--full` only run one extra script `full.r` and...

Same problem here, Oracle Linux 9

Looks like here is the first reason: https://github.com/Illumina/ExpansionHunter/issues/160 And this is the second reason: https://github.com/Illumina/ExpansionHunter/issues/168 Upgrading `googletest` to `1.11.0` and adding `#include ` to [GraphCoordinates.cpp](https://github.com/Illumina/ExpansionHunter/blob/master/ehunter/thirdparty/graph-tools-master-0cd9399/src/graphcore/GraphCoordinates.cpp) helps. ```sh sed -i '/GIT_TAG/s/release-1.10.0/release-1.11.0/'...

Hello, I've experienced issues whose origin are from these changes (I think) - that's why I'm posing here (issue should be reopened maybe?): I've checked [VCF spec](https://samtools.github.io/hts-specs/VCFv4.2.pdf) and found what...

According to spec - second one is correct because only it has correct ALT in POS. And how can you differentiate which one G is deleted in nature? Aren't they...

@liguowang Hello, do we have fix for this issue?

I've installed `b0` version: ``` #11 [ 7/10] RUN cd "/soft" && wget -q .../distr/CrossMap-0.6.5b0.tar.gz -O "/soft/CrossMap-0.6.5b0.tar.gz" && tar -xzf "/soft/CrossMap-0.6.5b0.tar.gz" && cd "/soft/CrossMap-0.6.5b0" && pip3 install --no-cache-dir . #11...

@liguowang Issue is not fixed - do you have any other ides how to fix it?

@liguowang If you need help with fix or feedback - we can try, but we don't know where to look at now.