Fix on-the-fly indexing of VCF w.r.t virtual offsets.#1837
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When using bcftools view --write-index -o out.vcf.gz the virtual file offsets can differ depending on whether we do a bgzf_tell before or after a flush. Specifically it could point to the last byte in the current BGZF block or the first byte in the next BGZF block. Ultimately both of these resolve to the same physical location, but in some situations the former may mean attempting to read zero bytes (the remainder of the bgzf block). This has been known in the past to be misinterpreted as an EOF. (See samtools/samtools#1861) It also means the contents of the index produced by --write-index and a separate bcftools index command can yield different results, albeit both representing the same data. The fix for the samtools / bcftools issue above (samtools#1672) when multi-threading inadvertently recreated the bug when not multi-threading. Fixes samtools/bcftools#2267
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gpertea
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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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When using bcftools view --write-index -o out.vcf.gz the virtual file offsets can differ depending on whether we do a bgzf_tell before or after a flush. Specifically it could point to the last byte in the current BGZF block or the first byte in the next BGZF block. Ultimately both of these resolve to the same physical location, but in some situations the former may mean attempting to read zero bytes (the remainder of the bgzf block). This has been known in the past to be misinterpreted as an EOF. (See samtools/samtools#1861)
It also means the contents of the index produced by --write-index and a separate bcftools index command can yield different results, albeit both representing the same data.
The fix for the samtools / bcftools issue above (#1672) when multi-threading inadvertently recreated the bug when not multi-threading.
Fixes samtools/bcftools#2267