Gert Hulselmans

In our case the different BAM files are mapped by different people (over the years). Would it be that hard to fix? Would a hasmap with chromosome name to tid...

> Notice that in the OP's case there are no `-r` options involved, so the BAM files are streamed sequentially and may not even be indexed. So now that there...

@colindaven We used the BAM files without problems for other parts of our analysis (as they only use one BAM file at the time and they can use the index...

I wrote some ugly code that rewrote the BAM header so the chromosome order was in the order I need and fixed all `tid` and `mtid` indexes so the match...

I ran it per chromosome and ran `bcftools concat` afterwards (but the first chromosomes are much bigger, so they take much more time than the latter ones). At the moment...

MPI parallel compression might not be needed. When using `zlib-ng` as zlib library, compression speed is 4 times faster: https://github.com/zlib-ng/zlib-ng/issues/908

This is probably technically more correct (no -wb) as this allows to still use additional options for subtractBed: ``` bash intersectBed -a allknownsnps.bed -b sample_snps.bed | subtractBed -a sample_snps.bed -b...

Is this supported now for BED input? It would be nice if a `sorted` option would allow it with BED file as input. ``` bedtools genomecov -sorted -bg -i test.sorted.bed...

@probonopd Adding this change is not enough. It seems that there are a lot of issues with files bigger than 2GiB: ``` $ ./zsync2 -v https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc8nr/region_based/hg19-regions-9species.all_regions.mc8nr.feather.zsync zsync2 version 2.0.0-alpha-1 (commit...

@probonopd I didn't know about that argument, but it doesn't work anyway as HPC clusters have glibc versions from a milion years ago: ``` ❯ ./zsync2-51-4e549b6-x86_64.AppImage --appimage-extract-and-run /tmp/appimage_extracted_81b6fb70f1742dd32187033f6bf21299/AppRun: /usr/lib64/libc.so.6: version...