Martin Pollard

Avoid failing to recognise failed filesystem reads and bail rather than processing uninitialised data.

Platform: Ubuntu 22.04 LTS Compiler: gcc (Ubuntu 11.2.0-19ubuntu1) 11.2.0 gcc 11 now defines __rdtsc which results in a compile error. ``` src/utils.h:60:34: error: ‘long long unsigned int __rdtsc()’ redeclared inline...

GCC 11 now defines __rdtsc so make definition test conditional on GCC version

2

As far as I can tell GCC 11 (used in Ubuntu Jammy and later) now defines __rdtsc in it's intrinsics. Therefore util.h definition of this should be conditional on gcc...

Add magic number to new indexes that have same name

5

Would it be possible to add some kind of magic number to the indices which you increment if you make a breaking change please? Either that or always use a...

Feature request - Shared memory for reference between processes

2

BWA MEM has a shared memory feature that allowed copies of the reference database to be shared between two or more processes. This was little used because the reference had...

Fix how stats handles Supp reads on alternate haplotypes

3

Fix how stats handles Supp reads on alternate haplotypes by treating them similar to reads flagged secondary. Fix typo in getopt_long case statement where it's case 1 rather than case...

samtools collate should respect TMPDIR in generate_prefix()

11

#### Are you using the latest version of [samtools] samtools 1.10 #### Please describe your environment. linux #### Please specify the steps taken to generate the issue, the command you...

Ensure compiling on aarch64 is seamless by default by autodetecting aarch64 using POSIX standard `uname -m`

Fixes #199

On ARM chips such as AWS's Graviton the information given in the raw model and vendor name is rather generic and thus meaningless. However if we and thus lscpu has...