James Bonfield

If we or someone else is to do the leg work for this, we need to know what problem we're actually trying to solve. Specifically: > Currently, the SOVERSION is...

I'm sorry, but why is GSL "doing it wrong too"? Your own output shows it has 0 removed and 0 changed functions, only added ones. Maybe I'm just being thick,...

> Then when a user has htslib-1.12 and samtools-1.12 installed, and types `rpm -Uvh samtools-1.16.….rpm`, the samtools update can fail with “your installed htslib package does not provide `libhts.so.3(HTSLIB_1.14)`” or...

> Manually adding `Requires: libhts3 >= 1.13` solves this problem on e.g. openSUSE, because only libhts3==1.13 satisfies both the manual and automatic dependencies (libhts3==1.16 also does, libhts4=* does not). Doing...

Thank you. I understand this now. So it's simply an issue that the X package has incomplete dependencies as it hasn't correctly specified the minimum version of htslib it needs....

Many thanks for this John. It's a great start to backfill the historical data. We'll look at automation to keep it up to date via nm/awk hackery or similar. (And...

You can try ```strace -f -tT samtools view ...``` to show the time taken for each system call. That may help to show where any delays are happening. I'm not...

I just did this myself and see ~2sec in select timeouts. ``` $ strace -o tr -ftT samtools view -H "https://s3-us-west-1.amazonaws.com/ilmn.htslib-test/test.bam" > /dev/null $ fgrep 'select(4, [3]' tr 29431 15:21:48...

Good spot on that typo. The realloc issue sadly turns up in a lot of places. Eg a grep of realloc in htslib/cram/\*.c I see 39 reallocs of which only...

I'm curious what the data looks like, having no experience at all with bedgraph. Is it purely a rname, pos, depth table, or does it have various layers at different...