Grammatikati Konstantin

Thanks for your data, we've tested on BWA 0.7.18 and latest (master) bwa-mem2 - we cannot test at 0.7.17 and 2.2.1 due to compilation errors on Ubuntu 22.04 https://github.com/lh3/bwa/issues/387 https://github.com/bwa-mem2/bwa-mem2/issues/207....

@lh3 We've tested on the same references both times, differences between results of tests are based on reference, but described bug is on the same reference, and we cannot reproduce...

@lh3 You are talking about screenshot from @Miciac in first post? It is only screenshot in issue. According to provided commands - reference should be same, but coverage is different,...

Does this check actually checks base image? Documentation doesn't have any info about it. Is there any way to ignore only current case of this check (not all check entirely)?...

Thanks for fast answer, maybe there are any workarounds - like `PATH1=${PATH1:-}:/new-path1` or `PYTHONPATH="$SOFT/Stranger-${STRANGER_VERSION}/local/lib/python3.10/dist-packages:${PYTHONPATH:-''}"`? To ensure that user is aware about empty variable?

@tonistiigi This variable is not always unset - it depends from base image and there are no universal syntax for both declared and undeclared state (like `PATH1=${PATH1:-}:/new-path1`) - so we...

We've found reason for empty result - we used `/ref/human_g1k_v37.list` from `v1.2.0` `scan` command for `v1.2.2` (we don't know that they will change after update). ``` ==> human_g1k_v37.list_v1.2.0 (71504K size)...

We'll test v1.3.0 today, when we test it we got error about same genome for `scan` and `msi` commands and decided to downgrade to 1.2.2 first. We completely forgot about...

Can you help me with new naming? Before we have `"${outputPrefix}_somatic"` and `"${outputPrefix}_germline"` - now we have `"${outputPrefix}_unstable"` and `"${outputPrefix}_all"`. Is this correct match? According to https://github.com/xjtu-omics/msisensor-pro/blob/35c39bb122e579c8fe97d405990a3d126030b850/cpp/sample.cpp#L40 - looks like...

Here is a comparison (`v1.3.0` - left, `v1.2.2` - right):  ``` Total loading windows: 5812 Total loading homopolymer and microsatellites: 2678803 *** Summary information *** Number of total sites:...