Vasimuddin Md comments

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                                            Vasimuddin Md

Add magic number to new indexes that have same name

We will make sure that we have different names for different kinds of indices.

Feature request: Limit memory usage during index step.

@rhpvorderman @WANGchuang715 we are looking into this, hopefully, we will have a solution soon.

Feature request: Limit memory usage during index step.

You used an older release. Please try with the latest release v2.1 and check. The index size is reduced in the latest release. We are looking into reducing the memory...

run error with CLWB instructions

The binary required clwb instruction it seems. Could you compile it from source and check.

Difference between bwa 0.7.17 and bwa-mem2 2.1: Asterisk instead of read sequence

Please provide the following details: Which ref. genome you used? Command lines used for both bwa-mem and bwa-mem2 Which mode was run: sse/avx/avx512? the stderr logs prints this info Will...

Difference between bwa 0.7.17 and bwa-mem2 2.1: Asterisk instead of read sequence

Thanks. For a quick check: could you try with same number of threads for bwa-mem and bwa-mem2 runs? Right now it is 125 for bwa-mem and 25 for bwa-mem2.

Difference between bwa 0.7.17 and bwa-mem2 2.1: Asterisk instead of read sequence

Ok cool. Will look into this and get back.

Standard error of bwa-mem2 output contained non-ASCII

Is bwa-mem2 version 2.1 working/printing correctly in the current setting?

Standard error of bwa-mem2 output contained non-ASCII

Could be a system issue, not sure. You can try running on some other system and check, or share the inputs and I can check on my end. Is your...

Standard error of bwa-mem2 output contained non-ASCII

you can check the output correctness by comparing it with the original bwa-mem run output on the same data. Highly unlikely that the log mess would lead to incorrect/corruption in...