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CVS log for pkgsrc/biology/htslib/Makefile

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Revision 1.30 / (download) - annotate - [select for diffs], Wed Dec 28 15:27:16 2022 UTC (5 weeks ago) by bacon
Branch: MAIN
Changes since 1.29: +2 -2 lines
Diff to previous 1.29 (colored)

Change MAINTAINER= to OWNER= on mission-critical packages

Revision 1.29 / (download) - annotate - [select for diffs], Tue Dec 13 10:27:03 2022 UTC (7 weeks, 2 days ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2022Q4-base, pkgsrc-2022Q4
Changes since 1.28: +8 -10 lines
Diff to previous 1.28 (colored)

htslib: updated to 1.16


Make hfile_s3 refresh AWS credentials on expiry in order to make HTSlib work better with AWS IAM credentials, which have a limited lifespan.

Allow BAM headers between 2GB and 4GB in size once more. This is not permitted in the BAM specification but was allowed in an earlier version of HTSlib. There is now a warning at 2GB and a hard failure at 4GB.

Improve error message when failing to load an index.

Permit MM (base modification) tags containing . and ? suffixes. These define implicit vs explicit coordinates. See the SAM tags specification for details.

Warn if spaces instead of tabs are detected in a VCF file to prevent confusion.

Add an sclen filter expression keyword. This is the length of a soft-clip, both left and right end. It may be combined with qlen (qlen-sclen) to obtain the number of bases in the query sequence that have been aligned to the genome ie it provides a way to compare local-alignment vs global-alignment length.

Improve error messages for CRAM reference mismatches. If the user specifies the wrong reference, the CRAM slice header MD5sum checks fail. We now report the SQ line M5 string too so it is possible to validate against the whole chr in the ref.fa file. The error message has also been improved to report the reference name instead of #num. Finally, we now hint at the likely cause, which counters the misleading samtools supplied error of "truncated or corrupt" file.

Expose more of the CRAM API and add new functionality to extract the reference from a CRAM file.

Improvements to the implementation of embedded references in CRAM where no external reference is specified.

The CRAM writer now allows alignment records with RG:Z: aux tags that don't have a corresponding @RG ID in the file header. Previously these tags would have been silently dropped. HTSlib will complain whenever it has to add one though, as such tags do not conform to recommended practice for the SAM, BAM and CRAM formats.

Set tab delimiter in man page for tabix GFF3 sort.

When using libdeflate, the 1...9 scale of BGZF compression levels is now remapped to the 1...12 range used by libdeflate instead of being passed directly. In particular, HTSlib levels 8 and 9 now map to libdeflate levels 10 and 12, so it is possible to select the highest (but slowest) compression offered by libdeflate.

The VCF variant API has been extended so that it can return separate flags for INS and DEL variants as well as the existing INDEL one. These flags have not been added to the old bcf_get_variant_types() interface as it could break existing users. To access them, it is necessary to use new functions bcf_has_variant_type() and bcf_has_variant_types().

The missing, but trivial, le_to_u8() function has been added to hts_endian.

bcf_format_gt() now works properly on big-endian platforms.

Revision 1.28 / (download) - annotate - [select for diffs], Wed Oct 26 10:31:14 2022 UTC (3 months, 1 week ago) by wiz
Branch: MAIN
Changes since 1.27: +2 -1 lines
Diff to previous 1.27 (colored)

*: bump PKGREVISION for libunistring shlib major bump

Revision 1.27 / (download) - annotate - [select for diffs], Tue Jul 5 11:00:16 2022 UTC (6 months, 4 weeks ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2022Q3-base, pkgsrc-2022Q3
Changes since 1.26: +3 -4 lines
Diff to previous 1.26 (colored)

htslib: updated to 1.15.1


Security fix: Fixed broken error reporting in the sam_cap_mapq() function, due to a missing hts_log() parameter. Prior to this fix it was possible to abuse the log message format string by passing a specially crafted alignment record to this function.

HTSlib now uses libhtscodecs release 1.2.2. This fixes a number of bugs where invalid compressed data could trigger usage of uninitialised values.

Fixed excessive memory used by multi-threaded SAM output on long reads.

Fixed a bug where tabix would misinterpret region specifiers starting at position 0. It will also now warn if the file being indexed is supposed to be 1-based but has positions less than or equal to 0.

The VCF header parser will now issue a warning if it finds an INFO header with Type=Flag but Number not equal to 0. It will also ignore the incorrect Number so the flag can be used.

Revision 1.26 / (download) - annotate - [select for diffs], Tue Jun 28 11:31:00 2022 UTC (7 months ago) by wiz
Branch: MAIN
Changes since 1.25: +2 -1 lines
Diff to previous 1.25 (colored)

*: recursive bump for perl 5.36

Revision 1.25 / (download) - annotate - [select for diffs], Sat Feb 26 23:08:43 2022 UTC (11 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2022Q2-base, pkgsrc-2022Q2, pkgsrc-2022Q1-base, pkgsrc-2022Q1
Changes since 1.24: +1 -1 lines
Diff to previous 1.24 (colored)

biology/htslib: Update to 1.15

Several minor enhancements and bug fixes
No API changes affecting existing packages

Revision 1.24 / (download) - annotate - [select for diffs], Fri Dec 17 15:01:27 2021 UTC (13 months, 2 weeks ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2021Q4-base, pkgsrc-2021Q4
Changes since 1.23: +2 -3 lines
Diff to previous 1.23 (colored)

biology/htslib: Update to 1.14

Numerous fixes and enhancements since 1.12


Revision 1.23 / (download) - annotate - [select for diffs], Wed Dec 8 16:03:23 2021 UTC (13 months, 3 weeks ago) by adam
Branch: MAIN
Changes since 1.22: +2 -2 lines
Diff to previous 1.22 (colored)

revbump for icu and libffi

Revision 1.22 / (download) - annotate - [select for diffs], Wed Sep 29 19:00:20 2021 UTC (16 months ago) by adam
Branch: MAIN
Changes since 1.21: +2 -2 lines
Diff to previous 1.21 (colored)

revbump for boost-libs

Revision 1.21 / (download) - annotate - [select for diffs], Mon May 24 19:49:11 2021 UTC (20 months, 1 week ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2021Q3-base, pkgsrc-2021Q3, pkgsrc-2021Q2-base, pkgsrc-2021Q2
Changes since 1.20: +2 -2 lines
Diff to previous 1.20 (colored)

*: recursive bump for perl 5.34

Revision 1.20 / (download) - annotate - [select for diffs], Wed Apr 21 13:24:24 2021 UTC (21 months, 1 week ago) by adam
Branch: MAIN
Changes since 1.19: +2 -1 lines
Diff to previous 1.19 (colored)

revbump for boost-libs

Revision 1.19 / (download) - annotate - [select for diffs], Sat Mar 20 18:17:07 2021 UTC (22 months, 2 weeks ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2021Q1-base, pkgsrc-2021Q1
Changes since 1.18: +6 -4 lines
Diff to previous 1.18 (colored)

biology/htslib: Update to 1.12
biology/bcftools: Update to 1.12
biology/samtools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.10
Minimized pkgsrc patches in all three packages
Moved htslib to custom tarball since Github-generated distfiles are incomplete

Revision 1.18 / (download) - annotate - [select for diffs], Mon Aug 31 18:06:39 2020 UTC (2 years, 5 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2020Q4-base, pkgsrc-2020Q4, pkgsrc-2020Q3-base, pkgsrc-2020Q3
Changes since 1.17: +2 -2 lines
Diff to previous 1.17 (colored)

*: bump PKGREVISION for perl-5.32.

Revision 1.17 / (download) - annotate - [select for diffs], Wed Jul 22 15:36:55 2020 UTC (2 years, 6 months ago) by bacon
Branch: MAIN
Changes since 1.16: +3 -2 lines
Diff to previous 1.16 (colored)

bioloty/htslib: Correct bl2 (ABI bump, not API)

Also add -if to autoreconf

Revision 1.16 / (download) - annotate - [select for diffs], Wed Jul 22 14:50:14 2020 UTC (2 years, 6 months ago) by bacon
Branch: MAIN
Changes since 1.15: +13 -8 lines
Diff to previous 1.15 (colored)

biology/htslib: Upgrade to 1.10.2

Numerous enhancements and bug fixes since 1.9, including:

Elimited refernce file size limits
SAM header API
On-the-fly indexing
Improved Amazon S3 interface

This package contains a patch for recent libcurl not in the upstream release

Revision 1.15 / (download) - annotate - [select for diffs], Fri May 22 10:55:57 2020 UTC (2 years, 8 months ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2020Q2-base, pkgsrc-2020Q2
Changes since 1.14: +2 -2 lines
Diff to previous 1.14 (colored)

revbump after updating security/nettle

Revision 1.14 / (download) - annotate - [select for diffs], Wed May 6 14:04:19 2020 UTC (2 years, 8 months ago) by adam
Branch: MAIN
Changes since 1.13: +2 -2 lines
Diff to previous 1.13 (colored)

revbump after boost update

Revision 1.13 / (download) - annotate - [select for diffs], Sun Mar 8 16:48:52 2020 UTC (2 years, 10 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2020Q1-base, pkgsrc-2020Q1
Changes since 1.12: +2 -2 lines
Diff to previous 1.12 (colored)

*: recursive bump for libffi

Revision 1.12 / (download) - annotate - [select for diffs], Sun Jan 26 17:30:46 2020 UTC (3 years ago) by rillig
Branch: MAIN
Changes since 1.11: +2 -2 lines
Diff to previous 1.11 (colored)

all: migrate homepages from http to https

pkglint -r --network --only "migrate"

As a side-effect of migrating the homepages, pkglint also fixed a few
indentations in unrelated lines. These and the new homepages have been
checked manually.

Revision 1.11 / (download) - annotate - [select for diffs], Sat Jan 18 21:48:47 2020 UTC (3 years ago) by jperkin
Branch: MAIN
Changes since 1.10: +2 -2 lines
Diff to previous 1.10 (colored)

*: Recursive revision bump for openssl 1.1.1.

Revision 1.10 / (download) - annotate - [select for diffs], Sun Jan 12 20:20:04 2020 UTC (3 years ago) by ryoon
Branch: MAIN
Changes since 1.9: +2 -2 lines
Diff to previous 1.9 (colored)

*: Recursive revbump from devel/boost-libs

Revision 1.9 / (download) - annotate - [select for diffs], Thu Aug 22 12:22:51 2019 UTC (3 years, 5 months ago) by ryoon
Branch: MAIN
CVS Tags: pkgsrc-2019Q4-base, pkgsrc-2019Q4, pkgsrc-2019Q3-base, pkgsrc-2019Q3
Changes since 1.8: +2 -2 lines
Diff to previous 1.8 (colored)

Recursive revbump from boost-1.71.0

Revision 1.8 / (download) - annotate - [select for diffs], Sun Aug 11 13:18:00 2019 UTC (3 years, 5 months ago) by wiz
Branch: MAIN
Changes since 1.7: +2 -2 lines
Diff to previous 1.7 (colored)

Bump PKGREVISIONs for perl 5.30.0

Revision 1.7 / (download) - annotate - [select for diffs], Sat Jul 20 22:46:10 2019 UTC (3 years, 6 months ago) by wiz
Branch: MAIN
Changes since 1.6: +2 -2 lines
Diff to previous 1.6 (colored)

*: recursive bump for nettle 3.5.1

Revision 1.6 / (download) - annotate - [select for diffs], Mon Jul 1 04:07:57 2019 UTC (3 years, 7 months ago) by ryoon
Branch: MAIN
Changes since 1.5: +2 -2 lines
Diff to previous 1.5 (colored)

Recursive revbump from boost-1.70.0

Revision 1.5 / (download) - annotate - [select for diffs], Thu Dec 13 19:51:42 2018 UTC (4 years, 1 month ago) by adam
Branch: MAIN
CVS Tags: pkgsrc-2019Q2-base, pkgsrc-2019Q2, pkgsrc-2019Q1-base, pkgsrc-2019Q1, pkgsrc-2018Q4-base, pkgsrc-2018Q4
Changes since 1.4: +2 -1 lines
Diff to previous 1.4 (colored)

revbump for boost 1.69.0

Revision 1.4 / (download) - annotate - [select for diffs], Tue Nov 6 10:24:14 2018 UTC (4 years, 2 months ago) by adam
Branch: MAIN
Changes since 1.3: +12 -17 lines
Diff to previous 1.3 (colored)

htslib: updated to 1.9

If ./configure fails, make will stop working until either configure is re-run successfully, or make distclean is used. This makes configuration failures more obvious.

The default SAM version has been changed to 1.6. This is in line with the latest version specification and indicates that HTSlib supports the CG tag used to store long CIGAR data in BAM format.

bgzip integrity check option '--test'

Faidx can now index fastq files as well as fasta. The fastq index adds an extra column to the .fai index which gives the offset to the quality values. New interfaces have been added to htslib/faidx.h to read the fastq index and retrieve the quality values. It is possible to open a fastq index as if fasta (only sequences will be returned), but not the other way round.

New API interfaces to add or update integer, float and array aux tags.

Add level=<number> option to hts_set_opt() to allow the compression level to be set. Setting level=0 enables uncompressed output.

Improved bgzip error reporting.

Better error reporting when CRAM reference files can't be opened.

Fixes to make tests work properly on Windows/MinGW - mainly to handle line ending differences.

Efficiency improvements:

Small speed-up for CRAM indexing.

Reduce the number of unnecessary wake-ups in the thread pool.

Avoid some memory copies when writing data, notably for uncompressed BGZF output.

Bug fixes:

Fix multi-region iterator bugs on CRAM files.

Fixed multi-region iterator bug that caused some reads to be skipped incorrectly when reading BAM files.

Fixed synced_bcf_reader() bug when reading contigs multiple times.

Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when removing samples.

Fixed bug where the VCF record ref length was calculated incorrectly if an INFO END tag was present. (71b00a)

Fixed warnings found when compiling with gcc 8.1.0.

sam_hdr_read() and sam_hdr_write() will now return an error code if passed a NULL file pointer, instead of crashing.

Fixed possible negative array look-up in sam_parse1() that somehow escaped previous fuzz testing.

Fixed bug where cram range queries could incorrectly report an error when using multiple threads.

Fixed very rare rANS normalisation bug that could cause an assertion failure when writing CRAM files.

Revision 1.3 / (download) - annotate - [select for diffs], Wed Aug 22 09:42:59 2018 UTC (4 years, 5 months ago) by wiz
Branch: MAIN
CVS Tags: pkgsrc-2018Q3-base, pkgsrc-2018Q3
Changes since 1.2: +2 -1 lines
Diff to previous 1.2 (colored)

Recursive bump for perl5-5.28.0

Revision 1.2 / (download) - annotate - [select for diffs], Wed Jul 4 13:40:09 2018 UTC (4 years, 7 months ago) by jperkin
Branch: MAIN
Changes since 1.1: +2 -2 lines
Diff to previous 1.1 (colored)

*: Move SUBST_STAGE from post-patch to pre-configure

Performing substitutions during post-patch breaks tools such as mkpatches,
making it very difficult to regenerate correct patches after making changes,
and often leading to substituted string replacements being committed.

Revision 1.1 / (download) - annotate - [select for diffs], Mon Apr 30 16:51:54 2018 UTC (4 years, 9 months ago) by bacon
Branch: MAIN
CVS Tags: pkgsrc-2018Q2-base, pkgsrc-2018Q2

biology/htslib: import htslib-1.8

HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.

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