head 1.11; access; symbols pkgsrc-2023Q4:1.11.0.8 pkgsrc-2023Q4-base:1.11 pkgsrc-2023Q3:1.11.0.6 pkgsrc-2023Q3-base:1.11 pkgsrc-2023Q2:1.11.0.4 pkgsrc-2023Q2-base:1.11 pkgsrc-2023Q1:1.11.0.2 pkgsrc-2023Q1-base:1.11 pkgsrc-2022Q4:1.10.0.2 pkgsrc-2022Q4-base:1.10 pkgsrc-2022Q3:1.9.0.2 pkgsrc-2022Q3-base:1.9 pkgsrc-2022Q2:1.8.0.4 pkgsrc-2022Q2-base:1.8 pkgsrc-2022Q1:1.8.0.2 pkgsrc-2022Q1-base:1.8 pkgsrc-2021Q4:1.7.0.2 pkgsrc-2021Q4-base:1.7 pkgsrc-2021Q3:1.4.0.6 pkgsrc-2021Q3-base:1.4 pkgsrc-2021Q2:1.4.0.4 pkgsrc-2021Q2-base:1.4 pkgsrc-2021Q1:1.4.0.2 pkgsrc-2021Q1-base:1.4 pkgsrc-2020Q4:1.3.0.4 pkgsrc-2020Q4-base:1.3 pkgsrc-2020Q3:1.3.0.2 pkgsrc-2020Q3-base:1.3 pkgsrc-2020Q2:1.2.0.14 pkgsrc-2020Q2-base:1.2 pkgsrc-2020Q1:1.2.0.10 pkgsrc-2020Q1-base:1.2 pkgsrc-2019Q4:1.2.0.12 pkgsrc-2019Q4-base:1.2 pkgsrc-2019Q3:1.2.0.8 pkgsrc-2019Q3-base:1.2 pkgsrc-2019Q2:1.2.0.6 pkgsrc-2019Q2-base:1.2 pkgsrc-2019Q1:1.2.0.4 pkgsrc-2019Q1-base:1.2 pkgsrc-2018Q4:1.2.0.2 pkgsrc-2018Q4-base:1.2 pkgsrc-2018Q3:1.1.0.4 pkgsrc-2018Q3-base:1.1 pkgsrc-2018Q2:1.1.0.2 pkgsrc-2018Q2-base:1.1; locks; strict; comment @# @; 1.11 date 2023.02.25.13.50.38; author bacon; state Exp; branches; next 1.10; commitid aSK7KFXf3JGeAUeE; 1.10 date 2022.12.13.10.27.03; author adam; state Exp; branches; next 1.9; commitid CV8O1zaNSHQ7Qn5E; 1.9 date 2022.07.05.11.00.16; author adam; state Exp; branches; next 1.8; commitid RCR7pFtYhm7xcHKD; 1.8 date 2022.02.26.23.08.43; author bacon; state Exp; branches; next 1.7; commitid YxJUwP6Bau5XmbuD; 1.7 date 2021.12.17.15.01.27; author bacon; state Exp; branches; next 1.6; commitid 0Q2lguoOwZDOX0lD; 1.6 date 2021.10.26.10.03.40; author nia; state Exp; branches; next 1.5; commitid R64ULQLy8JYkZieD; 1.5 date 2021.10.07.13.19.40; author nia; state Exp; branches; next 1.4; commitid CQ422EVgQgYxGSbD; 1.4 date 2021.03.20.18.17.07; author bacon; state Exp; branches; next 1.3; commitid xHhEvARbUkdBL4MC; 1.3 date 2020.07.22.14.50.14; author bacon; state Exp; branches; next 1.2; commitid NAXI0k4BbuNRm5hC; 1.2 date 2018.11.06.10.24.14; author adam; state Exp; branches; next 1.1; commitid C9oASYM53yszYRYA; 1.1 date 2018.04.30.16.51.54; author bacon; state Exp; branches; next ; commitid 3VFXSN720JateuAA; desc @@ 1.11 log @biology/htslib: Update to 1.17 Numerous enhancements and fixes Changes: https://github.com/samtools/htslib/releases @ text @$NetBSD$ BLAKE2s (htslib-1.17.tar.bz2) = 01a90e639179c0f819a24f74cfe232963699c79b94c153e45f23a2bccac50373 SHA512 (htslib-1.17.tar.bz2) = 624ab449d57713dab2d34399926c065f8cff8a45e6fbe68e0bb518c601421f587b613caeb095f8639b1d67cdb4a65d658c85f942173bcaa48da026fe15def5d3 Size (htslib-1.17.tar.bz2) = 4619884 bytes @ 1.10 log @htslib: updated to 1.16 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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.9 2022/07/05 11:00:16 adam Exp $ d3 3 a5 3 BLAKE2s (htslib-1.16.tar.bz2) = 5a4620982ac745706107fd0646de630b2410d133b4966fffa304ef62bb345beb SHA512 (htslib-1.16.tar.bz2) = 9fa0b1f9bba50f889d4542825c9543fb3b34c13b4cc0e18940a66fafd130749574bfa2c2663d8b39f0b4ed2b298bf130367cda1b17b2929093d64b386730cbc5 Size (htslib-1.16.tar.bz2) = 4466776 bytes @ 1.9 log @htslib: updated to 1.15.1 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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.8 2022/02/26 23:08:43 bacon Exp $ d3 3 a5 3 BLAKE2s (htslib-1.15.1.tar.bz2) = 7d7498964c0bd934ba24450ebb86584f82606df788f3f126d76fd9e8fdd9d9b6 SHA512 (htslib-1.15.1.tar.bz2) = 69d0c7f3ac50a9b9c579e9b3479b6745fc30d0ac838ff14695cf4e3da593854350e345ed1f4a496931ef57395f3416da4316903488f3e641f1e00fec544f3620 Size (htslib-1.15.1.tar.bz2) = 4141140 bytes @ 1.8 log @biology/htslib: Update to 1.15 Several minor enhancements and bug fixes No API changes affecting existing packages Changes: https://github.com/samtools/htslib/tags @ text @d1 1 a1 1 $NetBSD$ d3 3 a5 3 BLAKE2s (htslib-1.15.tar.bz2) = 74f4c5e815b6276507762ca956232a44784bd6d085534c2853cbaf22a29127ce SHA512 (htslib-1.15.tar.bz2) = b87ce3eaa63a731d812953129f1c9aa857fe896ea9e924b7eb92173d8e624dd45e5582b3a97e7120ff7fe339e4d40148077424029626f50372b3f164093aa6cc Size (htslib-1.15.tar.bz2) = 4141168 bytes @ 1.7 log @biology/htslib: Update to 1.14 Numerous fixes and enhancements since 1.12 Changes: https://github.com/samtools/htslib/releases/tag/1.14 @ text @d3 3 a5 3 BLAKE2s (htslib-1.14.tar.bz2) = ef0d9f8c4e1dbf4102019cff4c715fb4033f66be0e9882c17c735ec356c6d392 SHA512 (htslib-1.14.tar.bz2) = 97893a067f368668a5e0b704ca6a6399458e30283f774b42dae752b5115b19eda9112a75ba3578109be587c345ef15b3a3fc8245191287f2cd4108ea8a8bec61 Size (htslib-1.14.tar.bz2) = 4136564 bytes @ 1.6 log @biology: Replace RMD160 checksums with BLAKE2s checksums All checksums have been double-checked against existing RMD160 and SHA512 hashes @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.5 2021/10/07 13:19:40 nia Exp $ d3 3 a5 3 BLAKE2s (htslib-1.12.tar.bz2) = 401ede511b47d29b4e3771f0fb32ef5b8265b38d10158d8c8fc645d3504c8fe8 SHA512 (htslib-1.12.tar.bz2) = a810c646561f5c8b3a19b73ac22ec5f25b04d4e88e1314988881a8120c54106591d1d65aa708bbe2608f0065ca8abe92bdd70ef59a0dd0cdf63ff45c10957092 Size (htslib-1.12.tar.bz2) = 4094458 bytes @ 1.5 log @biology: Remove SHA1 hashes for distfiles @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.4 2021/03/20 18:17:07 bacon Exp $ d3 1 a3 1 RMD160 (htslib-1.12.tar.bz2) = 3d93d91db8c382f42b8ad0843609cabd3b502b46 @ 1.4 log @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 @ text @d1 1 a1 1 $NetBSD$ a2 1 SHA1 (htslib-1.12.tar.bz2) = 8cab518f97bbdf43165320c3a4bdef1e9a42893a @ 1.3 log @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 @ text @d3 4 a6 7 SHA1 (htslib-1.10.2.tar.gz) = 0ac4b86e49556d7dcaa89d4cce2661c9ca706631 RMD160 (htslib-1.10.2.tar.gz) = 6d8b6a362297345420dc9acc544029276ce4b1b6 SHA512 (htslib-1.10.2.tar.gz) = 7a91c15ca1de35653d068dc57ae511ad791ae0bd8504867d4e60c46e813e58b441409541197cde3b2a37840e60331336aebc627ecbf5c64fca1af63dd05f8f9e Size (htslib-1.10.2.tar.gz) = 1452177 bytes SHA1 (patch-Makefile) = e13333dd97ecd6c6753d14c1b738d6e5934a2911 SHA1 (patch-cram_open__trace__file.c) = 49b47e13786317e652a8ec810cc91f10d21bb8ea SHA1 (patch-hfile__libcurl.c) = 2a143818f1099ef01c57a3c904060a76abb63f14 @ 1.2 log @htslib: updated to 1.9 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= 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. @ text @d1 1 a1 1 $NetBSD: distinfo,v 1.1 2018/04/30 16:51:54 bacon Exp $ d3 7 a9 4 SHA1 (htslib-1.9.tar.bz2) = 21be5187203df30637dda2e1133cae2e833ef050 RMD160 (htslib-1.9.tar.bz2) = 85d5211cc197931e73a0dc7ca0673426f2ff6d89 SHA512 (htslib-1.9.tar.bz2) = ddb0e2d970e4c2c27e203b064898f95cb7c187cd497c02fc7b4312dcea25669d0b6063d537687521e7a065f6daefa1ae897add2df4981037a187b499d08fdef7 Size (htslib-1.9.tar.bz2) = 1178859 bytes @ 1.1 log @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. @ text @d1 1 a1 1 $NetBSD$ d3 4 a6 4 SHA1 (htslib-1.8.tar.gz) = bc9dd2ca08de99b0b30bb7f5d64bfa0e8c3d35fd RMD160 (htslib-1.8.tar.gz) = 400ee0a4994c01e314394bd6a2dceedaa93ec7af SHA512 (htslib-1.8.tar.gz) = 888c815d5b202a624cfc99dfe4f795825defd4dcd2420153314096c8fe79532e0a21e0be6bd3b5a4f86dfa1e7c4524271b3f960ab871812abe5a1961d05d568c Size (htslib-1.8.tar.gz) = 1262465 bytes @