marekkokot

Thanks for pointing this. I configured my environment to use .clang-format file and reformated my changes. If something is wrong let me know.

Hi, hmm this is surprising. Could you please upload the smallest possible example input file causing this behavior and the full command line you have used? I thought I fixed...

Hi, I cannot see the attachments. I created the input myself, like this: ``` @alph-63_S41_R1_001:2/1 cD:i:1 cE:f:0.000000 cM:i:0 GACTACTACATCTATGCTATCATCTGATGCTGAGCTGATGCATGTCATGCTA + IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII ``` but it seems to give ok results: ```...

This bug is a little nasty because it is a consequence of some assumptions we made developing the first versions of KMC, i.e., that reads are short. Later, we added...

For future me: it seems there is a buffer overflow in `skipSingleBGZFBlock`.

This is a little more complex. KMC reads input files twice. The first time, only a very small portion of it for adjustments for better balancing. After this file is...

Hi, Stage one is also multithreaded. The best thread usage is when there are many gzipped input files. If sf, sp, sr are all used KMC will read these parameters,...

Oh, I see. BAM files are handled a little differently, but it should not matter here. KMC may, in fact, read from a couple of files at the same time,...

Try to add `-ci1` to your command. `-f` is probably unnecessary. `-cx` causes removing all k-mers with counters below x (`No. of k-mers below min. threshold : 5403715`), the default...

Hello! Thank you very much for reporting this. There were indeed performance-related issue in the code. It was caused because of some characteristics of this particular dataset. I think I...