Martin Pollard

Another way you can check for undefined behaviour is to compile with `-fsanitize=address`. This is a bit faster but may catch if the issue is caused by a bad memory...

Looks good to me, if we get any complaints we could consider uplifting functions on request to htslib.

Hi, Got a few questions and comments: 1. What does -t do that -cp doesn't? 2. Could you fix up the indentation? It will make reviewing the patch easier. 3....

The reason we don't generate an identical BAM file to samtools 0.1.19 is that this version of samtools can generate an invalid BAM file. Specifically because this version ignores the...

Technically shouldn't it be the symbolic allele , the dot allele being missing data?

The issue is not with file sizes greater than 2 gigabytes, it is if the SAM is mapped to a reference contains chromosomes/scaffolds/contigs that are larger than 2 gigabases (which...

You have me curious now. I assume you’re running samtools 1.9? Also what mapper did you use and which reference? Try this to stream it rather than standard fopen: cat...

According to that grep your header has 65 million lines in it. That’s what is breaking the format. I would suggest you check to see whether you have mostly @RG...

BAM uses a signed 32 bit integer to hold position data. Thus about 2 billion is the largest chromosome size it can represent. BAI has similar issues. We recommend you...

Because it is not correct to assume /tmp, for example on my Mac (and every Mac) TMPDIR is defined to something other than /tmp. `declare -x TMPDIR="/var/folders/03/3h2pdngd2k3d9_h3cb_mv554000dhq/T/"` See also POSIX:...