German Tischler

I have changed the program so it uses filenames of an input and an output file instead of stdin and stdout. As for the valdiating method: I think another step...

It is not something I have seen. Would it be possible to get line numbers in the trace? ________________________________________ Von: James Bonfield ***@***.***> Gesendet: Donnerstag, 6. Mai 2021 17:00 An:...

Try using bamcat instead. This will not open all input files at the same time. If you want the output to be sorted then use ``` bamcat level=0 in1.bam in2.bam...

You can try whether a multiple stage merge is faster, i.e. use bammerge to merge subsets, then merge the pre merged files. bammerge currently has no support for doing multiple...

Hello Brad, so far I have no idea where the memory could be going. Would it be possible to run the debug version ( binaries at https://github.com/gt1/biobambam2/releases/download/2.0.57-release-20160918185932/biobambam2-2.0.57-release-20160918185932-x86_64-etch-linux-gnu-debug.tar.gz ) using commandline...

Hi, I cannot access the file, but I would assume the rest of the alignments for the read in question are marked as secondary or supplementary. bamcollate2 filters these out...

bamcollate2 currently does not handle cases well with secondary alignments. I would suggest you try the latest bamsort with sort order queryname_HI for this. This should collate alignment pairs including...

Hi, I am happy to look into it, but the problem is that you are asking for a BAM index (BAI/CSI) on an output file which is sorted in query...

What would make you think writing to stdout will buffer in case of a full filesystem? Anyway, consider a call like ``` strace -f bash -c "src/bammerge in.bam >out.bam" ```...

Hi, could you retry with the latest version?