Add cpuid checks behind an HAVE_CPUID check.#116
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Fixes samtools#115. Testing compiler versions is tricky, especially given some vendors wrap up standard compilers as their own, but change version numbers (Apple, Intel) and compilers also often masquerade as another (eg setting GNUC). Instead we just check if it links. Note there's no guard around this here for x86-64, but that's done in the code itself. (In theory we may have cpuid on another architecture that we wish to use at some point.)
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Problems still to consider. How does this work from htslib, which although having this as a submodule doesn't run the configure script ind instead builds the source direct.
Htslib builds from source have htscodecs as a submodule, so both can update in sync. |
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I don't have an x86 machine handy to check on, but could this just be done with the built-in generic tests? e.g. |
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Good thought. Possibly. It'd need validating whether it also solves the problem on the Mac, but given it was a compiler warning about missing prototype as well as a link error it seems likely. I'll try it out. |
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So... pros and cons. The configure.ac is simpler: just 1 line as you suggest. However the code that uses it is now ugly, made more so by the 0/1 nature rather than defined/not-defined as used elsewhere in autoconf. Plus these will need to be added to the htslib Makefile too for when not using configure. Thoughts? |
Switch to use AC_CHECK_DECLS as suggested by jm18. It makes the C code a bit more complex, but is less code overall when we include the configure script.
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I added those changes as a separate commit anyway, so we can either squash them together which means we get the new mechanism, or drop that commit and keep my previous method. Both appear to work fine under linux. I'll validate MinGW |
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If you fill in the actions-if-found and/or actions-if-not-found arguments, you can have your own simpler choice of macros to be defined instead of getting the default actions. |
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I did initially try as you suggest, but the if-found action is called for each in turn, so it ends up as an OR instead of an AND operation which is what I need. You can do it with two queries, to create two simpler looking macros, which also means it can be turned into a if-defined query rather than "defined and !zero" check, but then you're just doubling up code somewhere else so it doesn't feel like a big win and is non-standard to boot. Anyway, given I cannot validate any of this as fixing the initial issue, I'll wait for feedback from @ryandesign. |
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I've tested this and can confirm that it fixes the build on MacOS X 10.7 (Lion) with a contemporary xcode, all running in a UTM virtual machine.
which I guess is all we can expect with the missing declarations. |
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What's the plan for htslib? We can put in a similar autoconf rule easily enough as it's minimal code to add. There's the Makefile though for when configure isn't used. If we do nothing it should continue to build, just defaulting without optimised implementations. I'm not sure I like that (but frankly I've never liked our ability to build without first running configure either as it's just a needless pitfall). Instead I would advise hard coding the macros to be "on", so the default non-configured is just to assume this stuff works. That's a reasonable assumption which should hold true everywhere given it still has an x86-64 CPU check anyway. |
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I expect htslib |
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My point was we don't need to have x86_64 checks in the Makefile as they're already in the source files. We can just define these to 1 on all platforms and it'll have no consequences elsewhere. We don't need extra fragile or complex code for platform detection when not using autoconf. |
gpertea
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Mar 17, 2025
Notice: this is the last SAMtools / HTSlib release where CRAM 3.0
will be the default CRAM version. From the next we will change to
CRAM 3.1 unless the version is explicitly specified, for example
using "samtools view -O cram,version=3.0".
Updates
-------
* Extend annot-tsv with several new command line options.
--delim permits use of other delimiters.
--headers for selection of other header formats.
--no-header-idx to suppress column index numbers in header.
Also removed -h as it is now short for --headers. Note --help
still works. (PR samtools#1779)
* Allow annot-tsv -a to rename annotations. (PR samtools#1709)
* Extend annot-tsv --overlap to be able to specify the overlap
fraction separately for source and target. (PR samtools#1811)
* Added new APIs to facilitate low-level CRAM container
manipulations, used by the new "samtools cat" region
filtering code. Functions are:
cram_container_get_coords()
cram_filter_container()
cram_index_extents()
cram_container_num2offset()
cram_container_offset2num()
cram_num_containers()
cram_num_containers_between()
Also improved cram_index_query() to cope with HTS_IDX_NOCOOR
regions. (PR samtools#1771)
* Bgzip now retains file modification and access times when
compressing and decompressing. (PR samtools#1727, fixes samtools#1718.
Requested by Gert Hulselmans.)
* Use FNV1a for string hashing in khash. The old algorithm was
particularly weak with base-64 style strings and lead to a large
number of collisions. (PR samtools#1806. Fixes samtools/samtools#2066,
reported by Hans-Joachim Ruscheweyh)
* Improve the speed of the nibble2base() function on Intel (PR samtools#1667,
PR samtools#1764, PR samtools#1786, PR samtools#1802, thanks to Ruben Vorderman) and ARM
(PR samtools#1795, thanks to John Marshall).
* bgzf_getline() will now warn if it encounters UTF-16 data. (PR
samtools#1487, thanks to John Marshall)
* Speed up bgzf_read(). While this does not reduce CPU
significantly, it does increase the maximum parallelism
available permitting 10-15% faster decoding. (PR samtools#1772, PR
samtools#1800, Issue samtools#1798)
* Speed up faidx by use of better isgraph methods (PR samtools#1797) and
whole-line reading (PR samtools#1799, thanks to John Marshall).
* Speed up kputll() function, speeding up BAM -> SAM conversion by
about 5% and also samtools depth. (PR samtools#1805)
* Added more example code, covering fasta/fastq indexing, tabix
indexing and use of the thread pool. (PR samtools#1666)
Build Changes
-------------
* Code warning fixes for pedantic compilers (PR samtools#1777) and avoid some
undefined behaviour (PR samtools#1810, PR samtools#1816, PR samtools#1828).
* Windows based CI has been migrated from AppVeyor to GitHub Actions.
(PR samtools#1796, PR samtools#1803, PR samtools#1808)
* Miscellaneous minor build infrastructure and code fixes. (PR samtools#1807,
PR samtools#1829, both thanks to John Marshall)
* Updated htscodecs submodule to version 1.6.1 (PR samtools#1828)
* Fixed an awk script in the Makefile that only worked with gawk. (PR
samtools#1831)
Bug fixes
---------
* Fix small OSS-Fuzz reported issues with CRAM encoding and long
CIGARS and/or illegal positions. (PR samtools#1775, PR samtools#1801, PR samtools#1817)
* Fix issues with on-the-fly indexing of VCF/BCF (bcftools
--write-index) when not using multiple threads. (PR samtools#1837.
Fixes samtools/bcftools#2267, reported by Giulio Genovese)
* Stricter limits on POS / MPOS / TLEN in sam_parse1(). This fixes a
signed overflow reported by OSS-Fuzz and should help prevent other
as-yet undetected bugs. (PR samtools#1812)
* Check that the underlying file open worked for preload: URLs.
Fixes a NULL pointer dereference reported by OSS-Fuzz. (PR samtools#1821)
* Fix an infinite loop in hts_itr_query() when given extremely large
positions which cause integer overflow. Also adds hts_bin_maxpos()
and hts_idx_maxpos() functions. (PR samtools#1774, thanks to John Marshall
and reported by Jesus Alberto Munoz Mesa)
* Fix an out of bounds read in hts_itr_multi_next() when switching
chromosomes. This bug is present in releases 1.11 to 1.20. (PR
samtools#1788. Fixes samtools/samtools#2063, reported by acorvelo)
* Work around parsing problems with colons in CHROM names. Fixes
samtools/bcftools#2139. (PR samtools#1781, John Marshall / James Bonfield)
* Correct the CPU detection for Mac OS X 10.7. cpuid is used by
htscodecs (see samtools/htscodecs#116), and the corresponding
changes in htslib are PR samtools#1785. Reported by Ryan Carsten Schmidt.
* Make BAM zero-length intervals work the same as CRAM; permitted
and returning overlapping records. (PR samtools#1787. Fixes
samtools/samtools#2060, reported by acorvelo)
* Replace assert() with abort() in BCF synced reader. This is not an
ideal solution, but it gives consistent behaviour when compiling
with or without NDEBUG. (PR samtools#1791, thanks to Martin Pollard)
* Fixed failure to change the write block size on compressed SAM or
VCF files due to an internal type confusion. (PR samtools#1826)
* Fixed an out-of-bounds read in cram_codec_iter_next() (PR samtools#1832)
diekhans
added a commit
to diekhans/htslib
that referenced
this pull request
May 27, 2025
htslib release 1.21:
The primary user-visible changes in this release are updates to
the annot-tsv tool and some speed improvements. Full details of
other changes and bugs fixed are below.
Notice: this is the last SAMtools / HTSlib release where CRAM 3.0
will be the default CRAM version. From the next we will change to
CRAM 3.1 unless the version is explicitly specified, for example
using "samtools view -O cram,version=3.0".
Updates
-------
* Extend annot-tsv with several new command line options.
--delim permits use of other delimiters.
--headers for selection of other header formats.
--no-header-idx to suppress column index numbers in header.
Also removed -h as it is now short for --headers. Note --help
still works. (PR samtools#1779)
* Allow annot-tsv -a to rename annotations. (PR samtools#1709)
* Extend annot-tsv --overlap to be able to specify the overlap
fraction separately for source and target. (PR samtools#1811)
* Added new APIs to facilitate low-level CRAM container
manipulations, used by the new "samtools cat" region
filtering code. Functions are:
cram_container_get_coords()
cram_filter_container()
cram_index_extents()
cram_container_num2offset()
cram_container_offset2num()
cram_num_containers()
cram_num_containers_between()
Also improved cram_index_query() to cope with HTS_IDX_NOCOOR
regions. (PR samtools#1771)
* Bgzip now retains file modification and access times when
compressing and decompressing. (PR samtools#1727, fixes samtools#1718.
Requested by Gert Hulselmans.)
* Use FNV1a for string hashing in khash. The old algorithm was
particularly weak with base-64 style strings and lead to a large
number of collisions. (PR samtools#1806. Fixes samtools/samtools#2066,
reported by Hans-Joachim Ruscheweyh)
* Improve the speed of the nibble2base() function on Intel (PR samtools#1667,
PR samtools#1764, PR samtools#1786, PR samtools#1802, thanks to Ruben Vorderman) and ARM
(PR samtools#1795, thanks to John Marshall).
* bgzf_getline() will now warn if it encounters UTF-16 data. (PR
samtools#1487, thanks to John Marshall)
* Speed up bgzf_read(). While this does not reduce CPU
significantly, it does increase the maximum parallelism
available permitting 10-15% faster decoding. (PR samtools#1772, PR
samtools#1800, Issue samtools#1798)
* Speed up faidx by use of better isgraph methods (PR samtools#1797) and
whole-line reading (PR samtools#1799, thanks to John Marshall).
* Speed up kputll() function, speeding up BAM -> SAM conversion by
about 5% and also samtools depth. (PR samtools#1805)
* Added more example code, covering fasta/fastq indexing, tabix
indexing and use of the thread pool. (PR samtools#1666)
Build Changes
-------------
* Code warning fixes for pedantic compilers (PR samtools#1777) and avoid some
undefined behaviour (PR samtools#1810, PR samtools#1816, PR samtools#1828).
* Windows based CI has been migrated from AppVeyor to GitHub Actions.
(PR samtools#1796, PR samtools#1803, PR samtools#1808)
* Miscellaneous minor build infrastructure and code fixes. (PR samtools#1807,
PR samtools#1829, both thanks to John Marshall)
* Updated htscodecs submodule to version 1.6.1 (PR samtools#1828)
* Fixed an awk script in the Makefile that only worked with gawk. (PR
samtools#1831)
Bug fixes
---------
* Fix small OSS-Fuzz reported issues with CRAM encoding and long
CIGARS and/or illegal positions. (PR samtools#1775, PR samtools#1801, PR samtools#1817)
* Fix issues with on-the-fly indexing of VCF/BCF (bcftools
--write-index) when not using multiple threads. (PR samtools#1837.
Fixes samtools/bcftools#2267, reported by Giulio Genovese)
* Stricter limits on POS / MPOS / TLEN in sam_parse1(). This fixes a
signed overflow reported by OSS-Fuzz and should help prevent other
as-yet undetected bugs. (PR samtools#1812)
* Check that the underlying file open worked for preload: URLs.
Fixes a NULL pointer dereference reported by OSS-Fuzz. (PR samtools#1821)
* Fix an infinite loop in hts_itr_query() when given extremely large
positions which cause integer overflow. Also adds hts_bin_maxpos()
and hts_idx_maxpos() functions. (PR samtools#1774, thanks to John Marshall
and reported by Jesus Alberto Munoz Mesa)
* Fix an out of bounds read in hts_itr_multi_next() when switching
chromosomes. This bug is present in releases 1.11 to 1.20. (PR
samtools#1788. Fixes samtools/samtools#2063, reported by acorvelo)
* Work around parsing problems with colons in CHROM names. Fixes
samtools/bcftools#2139. (PR samtools#1781, John Marshall / James Bonfield)
* Correct the CPU detection for Mac OS X 10.7. cpuid is used by
htscodecs (see samtools/htscodecs#116), and the corresponding
changes in htslib are PR samtools#1785. Reported by Ryan Carsten Schmidt.
* Make BAM zero-length intervals work the same as CRAM; permitted
and returning overlapping records. (PR samtools#1787. Fixes
samtools/samtools#2060, reported by acorvelo)
* Replace assert() with abort() in BCF synced reader. This is not an
ideal solution, but it gives consistent behaviour when compiling
with or without NDEBUG. (PR samtools#1791, thanks to Martin Pollard)
* Fixed failure to change the write block size on compressed SAM or
VCF files due to an internal type confusion. (PR samtools#1826)
* Fixed an out-of-bounds read in cram_codec_iter_next() (PR samtools#1832)
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Fixes #115.
Testing compiler versions is tricky, especially given some vendors wrap up standard compilers as their own, but change version numbers (Apple, Intel) and compilers also often masquerade as another (eg setting GNUC).
Instead we just check if it links. Note there's no guard around this here for x86-64, but that's done in the code itself. (In theory we may have cpuid on another architecture that we wish to use at some point.)