Pull in latest htscodecs and improve portability #1628
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- Speed up fqz_qual_stats function - Speed up fqcomp encoding through memory prefetching - Optimise fqzcomp decoder - Remove prefetching from c_simple_mode.h - Autoconf improvements - Updates for 1.5.0 release - Only use the ARM NEON 32-way unrolled rANS on AArch64. - Add include of config.h to test programs. - Add FreeBSD to the CI tests - On AMD, don't always use AVX512 in preference to AVX2. - Add a -b option to change block size for rans4x16 test.
This caused problems on freebsd, and is no longer needed now the test sources include config.h
HTSlib uses POSIX and XSI functions, so to be strictly conforming POSIX says it should define _XOPEN_SOURCE before any standard headers are included. Some system headers may use this to enable or disable declarations for these functions. Define it unconditionally in configure, unless it has already been set by the user via CPPFLAGS etc. This mirrors what happens if you build HTSlib by typing "make" without running configure first. As it is now set by default, other locations where _XOPEN_SOURCE may be altered are removed. Co-authored-by: Rob Davies <rmd+git@sanger.ac.uk>
To stop check_spaces.pl from tripping up on it.
Some of them were using it already, and it's slightly more portable on platforms (mainly BSDs) that don't put perl in /usr/bin/. Happily most of them do put env in the same place these days...
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Pulls in the latest version of htscodecs, including a change to add
#include "config.h"to the htscodecs test sources, allowing a hack (which didn't work on FreeBSD) that set_POSIX_C_SOURCEwhen building them to be removed.configureis also changed so that it adds#define _XOPEN_SOURCE 600by default toconfig.hinstead of relying on thePTHREAD_MUTEX_RECURSIVEtest to do it, which allows that test and various other places that set_XOPEN_SOURCEto be removed. I've set the author of the commit that does this to @jmarshall as it's mostly his work - hopefully that's OK.The other commits fix some minor annoyances when running
make maintainer-checkon a repository whereconfigurehas been run; and makes all the perl scripts use#!/usr/bin/env perl(some already did) so that they work on platforms like FreeBSD which put perl in/usr/local/bin.Fixes #1606
Closes #1608