Noteworthy changes in release 1.17 (21st February 2023) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * A new API for iterating through a BAM record's aux field. (PR#1354, addresses #1319. Thanks to John Marshall) * Text mode for bgzip. Allows bgzip to compress lines of text with block breaks at newlines. (PR#1493, thanks to Mike Lin for the initial version PR#1369) * Make tabix support CSI indices with large positions. Unlike SAM and VCF files, BED files do not set a maximum reference length which hindered CSI support. This change sets an arbitrary large size of 100G to enable it to work. (PR#1506) * Add a fai_line_length function. Exposes the internal line-wrap length. (PR#1516) * Check for invalid barcode tags in fastq output. (PR#1518, fixes samtools#1728. Reported by Poshi) * Warn if reference found in a CRAM file is not contained in the specified reference file. (PR#1517 and PR#1521, adds diagnostics for #1515. Reported by Wei WeiDeng) * Add a faidx_seq_len64 function that can return sequence lengths longer than INT_MAX. At the same time limit faidx_seq_len to INT_MAX output. Also add a fai_adjust_region to ensure given ranges do not go beyond the end of the requested sequence. (PR#1519) * Add a bcf_strerror function to give text descriptions of BCF errors. (PR#1510) * Add CRAM SQ/M5 header checking when specifying a fasta file. This is to prevent creating a CRAM that cannot be decoded again. (PR#1522. In response to samtools#1748 though not a direct fix) * Improve support for very long input lines (> 2Gbyte). This is mostly useful for tabix which does not do much interpretation of its input. (PR#1542, a partial fix for #1539) * Speed up load_ref_portion. This function has been sped up by about 7x, which speeds up low-depth CRAM decoding by about 10%. (PR#1551) * Expand CRAM API to cope with new samtools cram_size command. (PR#1546) * Merges neighbouring I and D ops into one op within pileup. This means 4M1D1D1D3M is reported as 4M3D3M. Fixing this in sam.c means not only is samtools mpileup now looking better, but any tool using the mpileup API will be getting consistent results. (PR#1552, fixes the last remaining part of samtools#139) * Update the API documentation for bgzf_mt as it refered to a previous iteration. (PR#1556, fixes #1553. Reported by Raghavendra Padmanabhan) Build changes ------------- * Use POSIX grep in testing as egrep and fgrep are considered obsolete. (PR#1509, thanks to David Seifert) * Switch to building libdefalte with cmake for Cirris CI. (PR#1511) * Ensure strings in config_vars.h are escaped correctly. (PR#1530, fixes #1527. Reported by Lucas Czech) * Easier modification of shared library permissions during install. (PR#1532, fixes #1525. Reported by StephDC) * Fix build on ancient compilers. Added -std=gnu90 to build tests so older C compilers will still be happy. (PR#1524, fixes #1523. Reported by Martin Jakt) * Switch MacOS CI tests to an ARM-based image. (PR#1536) * Cut down the number of embed_ref=2 tests that get run. (PR#1537) * Add symbol versions to libhts.so. This is to aid package developers. (PR#1560 addresses #1505, thanks to John Marshall. Reported by Stefan Bruens) * htscodecs now updated to v1.4.0. (PR#1563) * Cleaned up misleading system error reports in test_bgzf. (PR#1565) Bug fixes --------- * VCF. Fix n-squared complexity in sample line with many adjacent tabs [fuzz]. (PR#1503) * Improved bcftools detection and reporting of bgzf decode errors. (PR#1504, thanks to Lilian Janin. PR#1529 thanks to Bergur Ragnarsson, fixes #1528. PR#1554) * Prevent crash when the only FASTA entry has no sequence [fuzz]. (PR#1507) * Fixed typo in sam.h documentation. (PR#1512, thanks to kojix2) * Fix buffer read-overrun in bam_plp_insertion_mod. (PR#1520) * Fix hash keys being left behind by bcf_hdr_remove. (PR#1535, fixes #1533. Reported by Giulio Genovese in #842) * Make bcf_hdr_idinfo_exists more robust by checking id value exists. (PR#1544, fixes #1538. Reported by Giulio Genovese) * CRAM improvements. Fixed crash with multi-threaded CRAM. Fixed a bug in the codec parameter learning for CRAM 3.1 name tokeniser. Fixed Cram compression container substitution matrix generation, (PR#1558, PR#1559 and PR#1562) Noteworthy changes in release 1.16 (18th August 2022) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Make hfile_s3 refresh AWS credentials on expiry in order to make HTSlib work better with AWS IAM credentials, which have a limited lifespan. (PR#1462 and PR#1474, addresses #344) * 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. (PR#1421, fixes #1420 and samtools#1613. Reported by John Marshall and R C Mueller) * Improve error message when failing to load an index. (PR#1468, example of the problem samtools#1637) * Permit MM (base modification) tags containing "." and "?" suffixes. These define implicit vs explicit coordinates. See the SAM tags specification for details. (PR#1423 and PR#1426, fixes #1418. PR#1469, fixes #1466. Reported by cjw85) * Warn if spaces instead of tabs are detected in a VCF file to prevent confusion. (PR#1328, fixes bcftools#1575. Reported by ketkijoshi278) * 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. (PR#1441 and PR/samtools#1661, fixes #1436. Requested by Chang Y) * 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. (PR#1427, fixes samtools#1640. Reported by Jian-Guo Zhou) * Expose more of the CRAM API and add new functionality to extract the reference from a CRAM file. (PR#1429 and PR#1442) * Improvements to the implementation of embedded references in CRAM where no external reference is specified. (PR#1449, addresses some of the issues in #1445) * 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. (PR#1480, fixes #1479. Reported by Alex Leonard) * Set tab delimiter in man page for tabix GFF3 sort. (PR#1457. Thanks to Colin Diesh) * 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. (PR#1488, fixes #1477. Reported by Gert Hulselmans) * 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(). (PR#1467) * The missing, but trivial, `le_to_u8()` function has been added to hts_endian. (PR#1494, Thanks to John Marshall) * bcf_format_gt() now works properly on big-endian platforms. (PR#1495, Thanks to John Marshall) Build changes ------------- These are compiler, configuration and makefile based changes. * Update htscodecs to version 1.3.0 for new SIMD code + various fixes. Updates the htscodecs submodule and adds changes necessary to make HTSlib build the new SIMD codec implementations. (PR#1438, PR#1489, PR#1500) * Fix clang builds under mingw. Under mingw, clang requires dllexport to be applied to both function declarations and function definitions. (PR#1435, PR#1497, PR#1498 fixes #1433. Reported by teepean) * Fix curl type warning with gcc 12.1 on Windows. (PR#1443) * Detect ARM Neon support and only build appropriate SIMD object files. (PR#1451, fixes #1450. Thanks to John Marshall) * `make print-config` now reports extra CFLAGS that are needed to build the SIMD parts of htscodecs. These may be of use to third-party build systems that don't use HTSlib's or htscodecs' build infrastructure. (PR#1485. Thanks to John Marshall) * Fixed some Makefile dependency issues for the "check"/"test" targets and plugins. In particular, "make check" will now build the "all" target, if not done already, before running the tests. (PR#1496) Bug fixes --------- * Fix bug when reading position -1 in BCF (0 in VCF), which is used to indicate telomeric regions. The BCF reader was incorrectly assuming the value stored in the file was unsigned, so a VCF->BCF->VCF round-trip would change it from 0 to 4294967296. (PR#1476, fixes #1475 and bcftools#1753. Reported by Rodrigo Martin) * Various bugs and quirks have been fixed in the filter expression engine, mostly related to the handling of absent tags, and the is_true flag. Note that as a result of these fixes, some filter expressions may give different results: - Fixed and-expressions including aux tag values which could give an invalid true result depending on the order of terms. - The expression `![NM]` is now true if only `NM` does not exist. In earlier versions it would also report true for tags like `NM:i:0` which exist but have a value of zero. - The expression `[X1] != 0` is now false when `X1` does not exist. Earlier versions would return true for this comparison when the tag was missing. - NULL values due to missing tags now propagate through string, bitwise and mathematical operations. Logical operations always treat them as false. (PR#1463, fixes samtools#1670. Reported by Gert Hulselmans; PR#1478, fixes samtools#1677. Reported by johnsonzcode) * Fix buffer overrun in bam_plp_insertion_mod. Memory now grows to the proper size needed for base modification data. (PR#1430, fixes samtools#1652. Reported by hd2326) * Remove limit of returned size from fai_retrieve(). (PR#1446, fixes samtools#1660. Reported by Shane McCarthy) * Cap hts_getline() return value at INT_MAX. Prevents hts_getline() from returning a negative number (a fail) for very long string length values. (PR#1448. Thanks to John Marshall) * Fix breakend detection and test bcf_set_variant_type(). (PR#1456, fixes #1455. Thanks to Martin Pollard) * Prevent arrays of BCF_BT_NULL values found in BCF files from causing bcf_fmt_array() to call exit() as the type is unsupported. These are now tested for and caught by bcf_record_check(), which returns an error code instead. (PR#1486) * Improved detection of fasta and fastq files that have very long comments following identifiers. (PR#1491, thanks to John Marshall. Fixes samtools/samtools#1689, reported by cjw85) * Fixed a SEGV triggered by giving a SAM file to `samtools import`. (PR#1492) Noteworthy changes in release 1.15.1 (7th April 2022) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Security fix: Fixed broken error reporting in the sam_prob_realn() function, due to a missing hts_log() parameter. Prior to this fix (i.e., in HTSlib versions 1.8 to 1.15) it was possible to abuse the log message format string by passing a specially crafted alignment record to this function. (PR#1406) * HTSlib now uses libhtscodecs release 1.2.2. This fixes a number of bugs where invalid compressed data could trigger usage of uninitialised values. (PR#1416) * Fixed excessive memory used by multi-threaded SAM output on long reads. (Part of PR#1384) * 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. (PR#1411) * 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. (PR#1415) Noteworthy changes in release 1.15 (21st February 2022) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Features and Updates -------------------- * Bgzip now has a --keep option to not remove the input file after compressing. (PR#1331) * Improved file format detection so some BED files are no longer detected as FASTQ or FASTA. (PR#1350, thanks to John Marshall) * Added xz (lzma), zstd and D4 formats to the file type detection functions. We don't actively support reading these data types, but function calls and htsfile can detect them. (PR#1340, thanks to John Marshall) * CRAM now also uses libdeflate for read-names if the libdeflate version is new enough (1.9 onwards). Previously we used zlib for this due to poor performance of libdeflate. This gives a slight speed up and reduction in file size. (PR#1383) * The VCF and BCF readers will now issue a warning if contig, INFO or FORMAT IDs do not match the formats described in the VCFv4.3 specification. Note that while the invalid names will mostly still be accepted, future updates will convert the warnings to errors causing files including invalid names to be rejected. (PR#1389) Build changes ------------- These are compiler, configuration and makefile based changes. * HTSlib now uses libhtscodecs release 1.2.1. * Improved support for compiling and linking against HTSlib with Microsoft Visual Studio. (PR#1380, #1377, #1375. Thanks to Aidan Bickford and John Marshall) * Various internal CI improvements. Bug fixes --------- * Fixed CRAM index queries for HTSJDK output (PR#1388, reported by Chris Norman). Note this also fixes writing CRAM writing, to match the specification (and HTSJDK), from version 3.1 onwards. * Fixed CRAM index queries when required-fields settings are selected to ignore CIGARs (PR#1372, reported by Giulio Genovese). * Unmapped but placed (having chr/pos) are now included in the BAM indices. (PR#1352, thanks to John Marshall) * CRAM now honours the filename##idx##index nomenclature for specifying non-standard index locations. (PR#1360, reported by Michael Cariaso) * Minor CRAM v1.0 read-group fix (PR#1349, thanks to John Marshall) * Permit .fa and .fq file type detection as synonyms for FASTA and FASTQ. (PR#1386). * Empty VCF format fields are now output ":.:" as instead of "::". (PR#1370) * Repeated bcf_sr_seek calls now work. (PR#1363, reported by Giulio Genovese) * Bcf_remove_allele_set now works on unpacked BCF records. (PR#1358, reported by Brent Pedersen). * The hts_parse_decimal() function used to read numbers in region lists is now better at rejecting non-numeric values. In particular it now rejects a lone 'G' instead of interpreting it as '0G', i.e. zero. (PR#1396, PR#1400, reported by SSSimon Yang; thanks to John Marshall). * Improve support for GPU issues listed by -Wdouble-promotion. (PR#1365, reported by David Seisert) * Fix example code in header file documentation. (PR#1381, Thanks to Aidan Bickford) Noteworthy changes in release 1.14 (22nd October 2021) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Features and Updates -------------------- * Added a keep option to bgzip to leave the original file untouched. This brings bgzip into line with gzip. (PR #1331, thanks to Alex Petty) * "endpos" has been added to the filter language, giving the position of the rightmost mapped base as measured by the CIGAR string. For unmapped reads it is the same as "pos". (PR #1307, thanks to John Marshall) * Interfaces have been added to interpret the new base modification tags added to the SAMtags document in samtools/hts-specs#418. (PR #1132) * New API functions hts_flush()/sam_flush()/bcf_flush() for flushing output htsFile/samFile/vcfFile streams. (PR #1326, thanks to John Marshall) * The synced_bcf_reader now sorts lines with symbolic alleles by END tag as well as POS. (PR #1321) * Added synced_bcf_reader options BCF_SR_REGIONS_OVERLAP and BCF_SR_TARGETS_OVERLAP for better control of records that start outside the desired region but overlap it are handled. Fixes samtools/bcftools#1420 and samtools/bcftools#1421 raised by John Marshall. (PR #1327) * HTSlib will now accept long-cigar CG:B: tags made by htsjdk which don't quite follow the specification properly (using signed values instead of unsigned). Thanks to Colin Diesh for reporting an example file. (PR #1317) * The warning printed when the BGZF reader finds a file with no EOF block has been changed to be less alarming. Unfortunately some third-party BGZF encoders don't write EOF blocks at the end of files. Thanks to Keiran Raine for reporting an example file. (PR #1323) * The FASTA and FASTQ readers get an option to skip over the first item on the header line, and use the second as the read name. It allows the original name to be restored on some of the fastq files served from the European Nucleotide Archive (ENA). (PR #1325) * HTSlib is now more strict when parsing the VCF samples line (beginning #CHROM). It will only accept tabs between the mandatory field names and sample names must be separated with tabs. (PR #1328) * HTSlib will now warn if it looks like the header has been corrupted by diagnostic messages from the program that made it. This can happen when using `nohup`, which by default mixes stdout and stderr into the same stream. (PR#1339, thanks to John Marshall) * File format detection will now recognise signatures for XZ, Zstd and D4 files (note that HTSlib will not read them yet). (PR #1340, thanks to John Marshall) Build changes ------------- These are compiler, configuration and makefile based changes. * Some redundant tests have been removed from the test harness, speeding it up. (PR #1308) * The version.sh script now works better on shallow checkouts. (PR #1324) * A check-untracked Makefile target has been added to catch untracked files (mostly) left by the test harness. (PR #1324) Bug fixes --------- * Fixed a case where flushing the thread pool could very occasionally cause a deadlock. (PR #1309) * Fixed a bug where some CRAM files could fail to decode if the required_fields option was in use. Thanks to Matt Sexton for reporting the issue. (PR #1314, fixes samtools/samtools#1475) * Fixed a regression where the S3 plugin could not read public files unless you supplied some Amazon credentials. Thanks to Chris Saunders for reporting. (PR #1332, fixes samtools/samtools#1491) * Fixed a possible CRAM thread deadlock discovered by @ryancaicse. (PR #1330, fixes #1329) * Some set-but-unused variables have been removed. (PR #1334) * Fixed a bug which prevented "flag.read2" from working in the filter language unless it was at the end of the expression. Thanks to Vamsi Kodali for reporting the issue. (PR #1342) * Fixed a memory leak that could happen if CRAM fails to inflate a LZMA block. (PR #1340, thanks to John Marshall) Noteworthy changes in release 1.13 (7th July 2021) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Features and Updates -------------------- * In case a PG header line has multiple ID tags supplied by other applications, the header API now selects the first one encountered as the identifying tag and issues a warning when detecting subsequent ID tags. (#1256; fixed samtools/samtools#1393) * VCF header reading function (vcf_hdr_read) no longer tries to download a remote index file by default. (#1266; fixes #380) * Support reading and writing FASTQ format in the same way as SAM, BAM or CRAM. Records read from a FASTQ file will be treated as unmapped data. (#1156) * Added GCP requester pays bucket access. Thanks to @indraniel. (#1255) * Made mpileup's overlap removal choose which copy to remove at random instead of always removing the second one. This avoids strand bias in experiments where the +ve and -ve strand reads always appear in the same order. (#1273; fixes samtools/bcftools#1459) * It is now possible to use platform specific BAQ parameters. This also selects long-read parameters for read lengths bigger than 1kb, which helps bcftools mpileup call SNPs on PacBio CCS reads. (#1275) * Improved bcf_remove_allele_set. This fixes a bug that stopped iteration over alleles prematurely, marks removed alleles as 'missing' and does automatic lazy unpacking. (#1288; fixes #1259) * Improved compression metrics for unsorted CRAM files. This improves the choice of codecs when handling unsorted data. (#1291) * Linear index entries for empty intervals are now initialised with the file offset in the next non-empty interval instead of the previous one. This may reduce the amount of data iterators have to discard before reaching the desired region, when the starting location is in a sequence gap. Thanks to @carsonh for reporting the issue. (#1286; fixes #486) * A new hts_bin_level API function has been added, to compute the level of a given bin in the binning index. (#1286) * Related to the above, a new API method, hts_idx_nseq, now returns the total number of contigs from an index. (#1295 and #1299) * Added bracket handling to bcf_hdr_parse_line, for use with ##META lines. Thanks to Alberto Casas Ortiz. (#1240) Build changes ------------- These are compiler, configuration and makefile based changes. * HTSlib now uses libhtscodecs release 1.1.1. * Added a curl/curl.h check to configure and improved INSTALL documentation on build options. Thanks to Melanie Kirsche and John Marshall. (#1265; fixes #1261) * Some fixes to address GCC 11.1 warnings. (#1280, #1284, #1285; fixes #1283) * Supports building HTSlib in a separate directory. Thanks to John Marshall. (#1277; fixes #231) * Supports building HTSlib on MinGW 32-bit environments. Thanks to John Marshall. (#1301) Bug fixes --------- * Fixed hts_itr_query() et al region queries: fixed bug introduced in HTSlib 1.12, which led to iterators producing very few reads for some queries (especially for larger target regions) when unmapped reads were present. HTSlib 1.11 had a related problem in which iterators would omit a few unmapped reads that should have been produced; cf #1142. Thanks to Daniel Cooke for reporting the issue. (#1281; fixes #1279) * Removed compressBound assertions on opening bgzf files. Thanks to Gurt Hulselmans for reporting the issue. (#1258; fixed #1257) * Duplicate sample name error message for a VCF file now only displays the duplicated name rather the entire same name list. (#1262; fixes samtools/bcftools#1451) * Fix to make samtools cat work on CRAMs again. (#1276; fixes samtools/samtools#1420) * Fix for a double memory free in SAM header creation. Thanks to @ihsineme. (#1274) * Prevent assert in bcf_sr_set_regions. Thanks to Dr K D Murray. (#1270) * Fixed crash in knet_open() etc stubs. Thanks to John Marshall. (#1289) * Fixed filter expression "cigar" on unmapped reads. Stop treating an empty CIGAR string as an error. Thanks to Chang Y for reporting the issue. (#1298, fixes samtools/samtools#1445) * Bug fixes in the bundled copy of htscodecs: - Fixed an uninitialized access in the name tokeniser decoder. (samtools/htscodecs#23) - Fixed a bug with name tokeniser and variable number of names per slice, causing it to incorrectly report an error on certain valid inputs. (samtools/htscodecs#24) Noteworthy changes in release 1.12 (17th March 2021) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Features and Updates -------------------- * Added experimental CRAM 3.1 and 4.0 support. (#929) These should not be used for long term data storage as the specification still needs to be ratified by GA4GH and may be subject to changes in format. (This is highly likely for 4.0). However it may be tested using: test/test_view -t ref.fa -C -o version=3.1 in.bam -p out31.cram For smaller but slower files, try varying the compression profile with an additional "-o small". Profile choices are fast, normal, small and archive, and can be applied to all CRAM versions. * Added a general filtering syntax for alignment records in SAM/BAM/CRAM readers. (#1181, #1203) An example to find chromosome spanning read-pairs with high mapping quality: 'mqual >= 30 && mrname != rname' To find significant sized deletions: 'cigar =~ "[0-9]{2}D"' or 'rlen - qlen > 10'. To report duplicates that aren't part of a "proper pair": 'flag.dup && !flag.proper_pair' More details are in the samtools.1 man page under "FILTER EXPRESSIONS". * The knet networking code has been removed. It only supported the http and ftp protocols, and a better and safer alternative using libcurl has been available since release 1.3. If you need access to ftp:// and http:// URLs, HTSlib should be built with libcurl support. (#1200) * The old htslib/knetfile.h interfaces have been marked as deprecated. Any code still using them should be updated to use hFILE instead. (#1200) * Added an introspection API for checking some of the capabilities provided by HTSlib. (#1170) Thanks also to John Marshall for contributions. (#1222) - `hfile_list_schemes`: returns the number of schemes found - `hfile_list_plugins`: returns the number of plugins found - `hfile_has_plugin`: checks if a specific plugin is available - `hts_features`: returns a bit mask with all available features - `hts_test_feature`: test if a feature is available - `hts_feature_string`: return a string summary of enabled features * Made performance improvements to `probaln_glocal` method, which speeds up mpileup BAQ calculations. (#1188) - Caching of reused loop variables and removal of loop invariants - Code reordering to remove instruction latency. - Other refactoring and tidyups. * Added a public method for constructing a BAM record from the component pieces. Thanks to Anders Kaplan. (#1159, #1164) * Added two public methods, `sam_parse_cigar` and `bam_parse_cigar`, as part of a small CIGAR API (#1169, #1182). Thanks to Daniel Cameron for input. (#1147) * HTSlib, and the included htsfile program, will now recognise the old RAZF compressed file format. Note that while the format is detected, HTSlib is unable to read it. It is recommended that RAZF files are uncompressed with `gunzip` before using them with HTSlib. Thanks to John Marshall (#1244); and Matthew J. Oldach who reported problems with uncompressing some RAZF files (samtools/samtools#1387). * The S3 plugin now has options to force the address style. It will recognise the addressing_style and host_bucket entries in the respective aws .credentials and s3cmd .s3cfg files. There is also a new HTS_S3_ADDRESS_STYLE environment variable. Details are in the htslib-s3-plugin.7 man file (#1249). Build changes ------------- These are compiler, configuration and makefile based changes. * Added new Makefile targets for the applications that embed HTSlib and want to run its test suite or clean its generated artefacts. (#1230, #1238) * The CRAM codecs are now obtained via the htscodecs submodule, hence when cloning it is now best to use "git clone --recursive". In an existing clone, you may use "git submodule update --init" to obtain the htscodecs submodule checkout. * Updated CI test configuration to recurse HTSlib submodules. (#1359) * Added Cirrus-CI integration as a replacement for Travis, which was phased out. (#1175; #1212) * Updated the Windows image used by Appveyor to 'Visual Studio 2019'. (#1172; fixed #1166) * Fixed a buglet in configure.ac, exposed by the release 2.70 of autoconf. Thanks to John Marshall. (#1198) * Fixed plugin linking on macOS, to prevent symbol conflict when linking with a static HTSlib. Thanks to John Marshall. (#1184) * Fixed a clang++9 error in `cram_io.h`. Thanks to Pjotr Prins. (#1190) * Introduced $(ALL_CPPFLAGS) to allow for more flexibility in setting the compiler flags. Thanks to John Marshall. (#1187) * Added 'fall through' comments to prevent warnings issued by Clang on intentional fall through case statements, when building with `-Wextra flag`. Thanks to John Marshall. (#1163) * Non-configure builds now define _XOPEN_SOURCE=600 to allow them to work when the `gcc -std=c99` option is used. Thanks to John Marshall. (#1246) Bug fixes --------- * Fixed VCF `#CHROM` header parsing to only separate columns at tab characters. Thanks to Sam Morris for reporting the issue. (#1237; fixed samtools/bcftools#1408) * Fixed a crash reported in `bcf_sr_sort_set`, which expects REF to be present. (#1204; fixed samtools/bcftools#1361) * Fixed a bcf synced reader bug when filtering with a region list, and the first record for a chromosome had the same position as the last record for the previous chromosome. (#1254; fixed samtools/bcftools#1441) * Fixed a bug in the overlapping logic of mpileup, dealing with iterating over CIGAR segments. Thanks to `@wulj2` for the analysis. (#1202; fixed #1196) * Fixed a tabix bug that prevented setting the correct number of lines to be skipped in a region file. Thanks to Jim Robinson for reporting it. (#1189; fixed #1186) * Made `bam_itr_next` an alias for `sam_itr_next`, to prevent it from crashing when working with htsFile pointers. Thanks to Torbjörn Klatt for reporting it. (#1180; fixed #1179) * Fixed once per outgoing multi-threaded block `bgzf_idx_flush` assertion, to accommodate situations when a single record could span multiple blocks. Thanks to `@lacek`. (#1168; fixed samtools/samtools#1328) * Fixed assumption of pthread_t being a non-structure, as permitted by POSIX. Thanks also to John Marshall and Anders Kaplan. (#1167, #1153, #1153) * Fixed the minimum offset of a BAI index bin, to account for unmapped reads. Thanks to John Marshall for spotting the issue. (#1158; fixed #1142) * Fixed the CRLF handling in `sam_parse_worker` method. Thanks to Anders Kaplan. (#1149; fixed #1148) * Included unistd.h and errno.h directly in HTSlib files, as opposed to including them indirectly, via third party code. Thanks to Andrew Patterson (#1143) and John Marshall (#1145). Noteworthy changes in release 1.11 (22nd September 2020) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Features and Updates -------------------- * Support added for remote reference files. fai_path() can take a remote reference file and will return the corresponding index file. Remote indexes can be handled by refs_load_fai(). UR tags in @SQ lines can now be set to remote URIs. (#1017) * Added tabix --separate-regions option, which adds header comment lines separating different regions' output records when multiple target regions are supplied on the command line. (#1108) * Added tabix --cache option to set a BGZF block cache size. Most beneficial when the -R option is used and the same blocks need to be re-read multiple times. (#1053) * Improved error checking in tabix and added a --verbosity option so it is possible to change the amount of logging when it runs. (#1040) * A note about the maximum chromosome length usable with TBI indexes has been added to the tabix manual page. Thanks to John Marshall. (#1070) * New method vcf_open_mode() changes the opening mode of a variant file based on its file extension. Similar to sam_open_mode(). (#1096) * The VCF parser has been made faster and easier to maintain. (#1057) * bcf_record_check() has been made faster, giving a 15% speed increase when reading an uncompressed BCF file. (#1130) * The VCF parser now recognises the "" symbolic allele produced by GATK. (#1045) * Support has been added for simultaneous reading of unindexed VCF/BCF files when using the synced_bcf_reader interface. Input files must have the chromosomes in the same order as each other and be consistent with the order of sequences in the header. (#1089) * The VCF and BCF readers will now attempt to fix up invalid INFO/END tags where the stored END value is less than POS, resulting in an apparently negative record length. Such files have been generated by programs which used END incorrectly, and by broken lift-over processes that failed to update any END tags present. (#1021; fixed samtools/bcftools#1154) * The htsFile interface can now detect the crypt4gh encrypted format (see https://samtools.github.io/hts-specs/crypt4gh.pdf). If HTSlib is built with external plug-in support, and the hfile_crypt4gh plug-in is present, the file will be passed to it for decryption. The plug-in can be obtained from https://github.com/samtools/htslib-crypt4gh. (#1046) * hts_srand48() now seeds the same POSIX-standard sequences of pseudo-random numbers regardless of platform, including on OpenBSD where plain srand48() produces a different cryptographically-strong non-deterministic sequence. Thanks to John Marshall. (#1002) * Iterators now work with 64 bit positions. (#1018) * Improved the speed of range queries when using BAI indexes by making better use of the linear index data included in the file. The best improvement is on low-coverage data. (#1031) * Alignments which consume no reference bases are now considered to have length 1. This would make such alignments cover 1 reference position in the same manner as alignments that are unmapped or have no CIGAR strings. These alignments can now be returned by iterator-based queries. Thanks to John Marshall. (#1063; fixed samtools/samtools#1240, see also samtools/hts-specs#521). * A bam_set_seqi() function to modify a single base in the BAM structure has been added. This is a companion function to bam_seqi(). (#1022) * Writing SAM format is around 30% faster. (#1035) * Added sam_format_aux1() which converts a BAM aux tag to a SAM format string. (#1134) * bam_aux_update_str() no longer requires NUL-terminated strings. It is also now possible to create tags containing part of a longer string. (#1088) * It is now possible to use external plug-ins in language bindings that dynamically load HTSlib. Note that a side-effect of this change is that some plug-ins now link against libhts.so, which means that they have to be able to find the shared library when they are started up. Thanks to John Marshall. (#1072) * bgzf_close(), and therefore hts_close(), will now return non-zero when closing a BGZF handle on which errors have been detected. (Part of #1117) * Added a special case to the kt_fisher_exact() test for when the table probability is too small to be represented in a double. This fixes a bug where it would, for some inputs, fail to correctly determine which side of the distribution the table was on resulting in swapped p-values being returned for the left- and right-tailed tests. The two-tailed test value was not affected by this problem. (#1126) * Improved error diagnostics in the CRAM decoder (#1042), BGZF (#1049), the VCF and BCF readers (#1059), and the SAM parser (#1073). * ks_resize() now allocates 1.5 times the requested size when it needs to expand a kstring instead of rounding up to the next power of two. This has been done mainly to make the inlined function smaller, but it also reduces the overhead of storing data in kstrings at the expense of possibly needing a few more reallocations. (#1129) CRAM improvements ----------------- * Delay CRAM crc32 checks until the data actually needs to be used. With other changes this leads to a 20x speed up in indexing and other sub-query based actions. (#988) * CRAM now handles the transition from mapped to unmapped data in a better way, improving compression of the unmapped data. (#961) * CRAM can now use libdeflate. (#961) * Fixed bug in MD tag generation with "b" read feature codes, causing the numbers in the tag to be too large. Note that HTSlib never uses this feature code so it is unlikely that this bug would be seen on real data. The problem was found when testing against hand-crafted CRAM files. (#1086) * Fixed a regression where the CRAM multi-region iterator became much less efficient when using threads. It now works more like the single iterator and does not preemptively decode the next container unless it will be used. (#1061) * Set CRAM default quality in lossy quality modes. If lossy quality is enabled and 'B', 'q' or 'Q' features are used, CRAM starts off with QUAL being all 255 (as per BAM spec and "*" quality) and then modifies individual qualities as dictated by the specific features. However that then produces ASCII quality " " (space, q=-1) for the unmodified bases. Instead ASCII quality "?" (q=30) is used, as per HTSJDK. Quality 255 is still used for sequences with no modifications at all. (#1094) Build changes ------------- These are compiler, configuration and makefile based changes. * `make all` now also builds htslib_static.mk and htslib-uninstalled.pc. Thanks to John Marshall. (#1011) * Various cppcheck-1.90 warnings have been fixed. (#995, #1011) * HTSlib now prefers its own headers when being compiled, fixing build failures on machines that already had a system-installed HTSlib. Thanks to John Marshall. (#1078; fixed #347) * Define HTSLIB_EXPORT without using a helper macro to reduce the length of compiler diagnostics that mention exported functions. Thanks to John Marshall. (#1029) * Fix dirty default build by including latest pkg.m4 instead of using aclocal.m4. Thanks to Damien Zammit. (#1091) * Struct tags have been added to htslib/*.h public typedefs. This makes it possible to forward declare htsFile without including htslib/hts.h. Thanks to Lucas Czech and John Marshall. (#1115; fixed #1106) * Fixed compiler warnings emitted by the latest gcc and clang releases when compiling HTSlib, along with some -Wextra warnings in the public include files. Thanks to John Marshall. (#1066, #1063, #1083) Bug fixes --------- * Fixed hfile_libcurl breakage when using libcurl 7.69.1 or later. Thanks to John Marshall for tracking down the exact libcurl change that caused the incompatibility. (#1105; fixed samtools/samtools#1254 and samtools/samtools#1284) * Fixed overflows kroundup32() and kroundup_size_t() which caused them to return zero when rounding up values where the most significant bit was set. When this happens they now return the highest value that can be stored (#1044). All of the kroundup macro definitions have also been gathered together into a unified implementation (#1051). * Fixed missing return parameter value in idx_test_and_fetch(). Thanks to Lilian Janin. (#1014) * Fixed crashes due to inconsistent selection between BGZF and plain (hFILE) interfaces when reading files. [fuzz] (#1019) * Added and/or fixed byte swapping code for big-endian platforms. Thanks to Jun Aruga, John Marshall, Michael R Crusoe and Gianfranco Costamagna for their help. (#1023; fixed #119 and #355) * Fixed a problem with multi-threaded on-the-fly indexes which would occasionally write virtual offsets pointing at the end of a BGZF block. Attempting to read from such an offset caused EOF to be incorrectly reported. These offsets are now handled correctly, and the indexer has been updated to avoid generating them. (#1028; fixed samtools/samtools#1197) * In sam_hdr_create(), free newly allocated SN strings when encountering an error. [fuzz] (#1034) * Prevent double free in case of idx_test_and_fetch() failure. Thanks to @fanwayne for the bug report. (#1047; fixed #1033) * In the header, link a new PG line only to valid chains. Prevents an explosive growth of PG lines on headers where PG lines are already present but not linked together correctly. (#1062; fixed samtools/samtools#1235) * Also in the header, when calling sam_hdr_update_line(), update target arrays only when the name or length is changed. (#1007) * Fixed buffer overflows in CRAM MD5 calculation triggered by files with invalid compression headers, or files with embedded references that were one byte too short. [fuzz] (#1024, #1068) * Fix mpileup regression between 1.9 and 1.10 where overlap detection was incorrectly skipped on reads where RNEXT, PNEXT and TLEN were set to the "unavailable" values ("*", 0, 0 in SAM). (#1097) * kputs() now checks for null pointer in source string. [fuzz] (#1087) * Fix potential bcf_update_alleles() crash on 0 alleles. Thanks to John Marshall. (#994) * Added bcf_unpack() calls to some bcf_update functions to fix a bug where updates made after a call to bcf_dup() could be lost. (#1032; fixed #1030) * Error message typo "Number=R" instead of "Number=G" fixed in bcf_remove_allele_set(). Thanks to Ilya Vorontsov. (#1100) * Fixed crashes that could occur in BCF files that use IDX= header annotations to create a sparse set of CHROM, FILTER or FORMAT indexes, and include records that use one of the missing index values. [fuzz] (#1092) * Fixed potential integer overflows in the VCF parser and ensured that the total length of FORMAT fields cannot go over 2Gbytes. [fuzz] (#1044, #1104; latter is CVE-2020-36403 affecting all HTSlib versions up to 1.10.2) * Download index files atomically in idx_test_and_fetch(). This prevents corruption when running parallel jobs on S3 files. Thanks to John Marshall. (#1112; samtools/samtools#1242). * The pileup constructor callback is now given the copy of the bam1_t struct made by pileup instead of the original one passed to bam_plp_push(). This makes it the same as the one passed to the destructor and ensures that cached data, for example the location of an aux tag, will remain valid. (#1127) * Fixed possible error in code_sort() on negative CRAM Huffman code length. (#1008) * Fixed possible undefined shift in cram_byte_array_stop_decode_init(). (#1009) * Fixed a bug where range queries to the end of a given reference would return incorrect results on CRAM files. (#1016; fixed samtools/samtools#1173) * Fixed an integer overflow in cram_read_slice(). [fuzz] (#1026) * Fixed a memory leak on failure in cram_decode_slice(). [fuzz] (#1054) * Fixed a regression which caused cram_transcode_rg() to fail, resulting in a crash in "samtools cat" on CRAM files. (#1093; fixed samtools/samtools#1276) * Fixed an undersized string reallocation in the threaded SAM reader which caused it to crash when reading SAM files with very long lines. Numerous memory allocation checks have also been added. (#1117) Noteworthy changes in release 1.10.2 (19th December 2019) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is a release fix that corrects minor inconsistencies discovered in previous deliverables. Noteworthy changes in release 1.10.1 (17th December 2019) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ The support for 64-bit coordinates in VCF brought problems for files not conforming to VCF/BCF specification. While previous versions would make out-of-range values silently overflow creating nonsense values but parseable file, the version 1.10 would silently create an invalid BCF. Noteworthy changes in release 1.10 (6th December 2019) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Brief summary ------------- There are many changes in this release, so the executive summary is: * Addition of support for references longer than 2Gb (NB: SAM and VCF formats only, not their binary counterparts). This may need changes in code using HTSlib. See README.large_positions.md for more information. * Added a SAM header API. * Major speed up to SAM reading and writing. This also now supports multi-threading. * We can now auto-index on-the-fly while writing a file. This also includes to bgzipped SAM.gz. * Overhaul of the S3 interface, which now supports version 4 signatures. This also makes writing to S3 work. These also required some ABI changes. See below for full details. Features / updates ------------------ * A new SAM/BAM/CRAM header API has been added to HTSlib, allowing header data to be updated without having to parse or rewrite large parts of the header text. See htslib/sam.h for function definitions and documentation. (#812) The header typedef and several pre-existing functions have been renamed to have a sam_hdr_ prefix: sam_hdr_t, sam_hdr_init(), sam_hdr_destroy(), and sam_hdr_dup(). (The existing bam_hdr_-prefixed names are still provided for compatibility with existing code.) (#887, thanks to John Marshall) * Changes to hfile_s3, which provides support for the AWS S3 API. (#839) - hfile_s3 now uses version 4 signatures by default. Attempting to write to an S3 bucket will also now work correctly. It is possible to force version 2 signatures by creating environment variable HTS_S3_V2 (the exact value does not matter, it just has to exist). Note that writing depends on features that need version 4 signatures, so forcing version 2 will disable writes. - hfile_s3 will automatically retry requests where the region endpoint was not specified correctly, either by following the 301 redirect (when using path-style requests) or reading the 400 response (when using virtual-hosted style requests and version 4 signatures). The first region to try can be set by using the AWS_DEFAULT_REGION environment variable, by setting "region" in ".aws/credentials" or by setting "bucket_location" in ".s3cfg". - hfile_s3 now percent-escapes the path component of s3:// URLs. For backwards-compatibility it will ignore any paths that have already been escaped (detected by looking for '%' followed by two hexadecimal digits.) - New environment variables HTS_S3_V2, HTS_S3_HOST, HTS_S3_S3CFG and HTS_S3_PART_SIZE to force version-2 signatures, control the S3 server hostname, the configuration file and upload chunk sizes respectively. * Numerous SAM format improvements. - Bgzipped SAM files can now be indexed and queried. The library now recognises sam.gz as a format name to ease this usage. (#718, #916) - The SAM reader and writer now supports multi-threading via the thread-pool. (#916) Note that the multi-threaded SAM reader does not currently support seek operations. Trying to do this (for example with an iterator range request) will result in the SAM readers dropping back to single-threaded mode. - Major speed up of SAM decoding and encoding, by around 2x. (#722) - SAM format can now handle 64-bit coordinates and references. This has implications for the ABI too (see below). Note BAM and CRAM currently cannot handle references longer than 2Gb, however given the speed and threading improvements SAM.gz is a viable workaround. (#709) * We can now automatically build indices on-the-fly while writing SAM, BAM, CRAM, VCF and BCF files. (Note for SAM and VCF this only works when bgzipped.) (#718) * HTSlib now supports the @SQ-AN header field, which lists alternative names for reference sequences. This means given "@SQ SN:1 AN:chr1", tools like samtools can accept requests for "1" or "chr1" equivalently. (#931) * Zero-length files are no longer considered to be valid SAM files (with no header and no alignments). This has been changed so that pipelines such as `somecmd | samtools ...` with `somecmd` aborting before outputting anything will now propagate the error to the second command. (#721, thanks to John Marshall; #261 reported by Adrian Tan) * Added support for use of non-standard index names by pasting the data filename and index filename with ##idx##. For example "/path1/my_data.bam##idx##/path2/my_index.csi" will open bam file "/path1/my_data.bam" and index file "/path2/my_index.csi". (#884) This affects hts_idx_load() and hts_open() functions. * Improved the region parsing code to handle colons in reference names. Strings can be disambiguated by the use of braces, so for example when reference sequences called "chr1" and "chr1:100-200" are both present, the regions "{chr1}:100-200" and "{chr1:100-200}" unambiguously indicate which reference is being used. (#708) A new function hts_parse_region() has been added along with specialisations for sam_parse_region() and fai_parse_region(). * CRAM encoding now has additional checks for MD/NM validity. If they are incorrect, it stores the (incorrect copy) verbatim so round-trips "work". (#792) * Sped up decoding of CRAM by around 10% when the MD tag is being generated. (#874) * CRAM REF_PATH now supports %Ns (where N is a single digit) expansion in http URLs, similar to how it already supported this for directories. (#791) * BGZF now permits indexing and seeking using virtual offsets in completely uncompressed streams. (#904, thanks to Adam Novak) * bgzip now asks for extra confirmation before decompressing files that don't have a known compression extension (e.g. .gz). This avoids `bgzip -d foo.bam.bai` producing a foo.bam file that is very much not a BAM-formatted file. (#927, thanks to John Marshall) * The htsfile utility can now copy files (including to/from URLs using HTSlib's remote access facilities) with the --copy option, in addition to its existing uses of identifying file formats and displaying sequence or variant data. (#756, thanks to John Marshall) * Added tabix --min-shift option. (#752, thanks to Garrett Stevens) * Tabix now has an -D option to disable storing a local copy of a remote index. (#870) * Improved support for MSYS Windows compiler environment. (#966) * External htslib plugins are now supported on Windows. (#966) API additions and improvements ------------------------------ * New API functions bam_set_mempolicy() and bam_get_mempolicy() have been added. These allow more control over the ownership of bam1_t alignment record data; see documentation in htslib/sam.h for more information. (#922) * Added more HTS_RESULT_USED checks, this time for VCF I/O. (#805) * khash can now hash kstrings. This makes it easier to hash non-NUL-terminated strings. (#713) * New haddextension() filename extension API function. (#788, thanks to John Marshall) * New hts_resize() macro, designed to replace uses of hts_expand() and hts_expand0(). (#805) * Added way of cleaning up unused jobs in the thread pool via the new hts_tpool_dispatch3() function. (#830) * New API functions hts_reglist_create() and sam_itr_regarray() are added to create hts_reglist_t region lists from `chr:-` type region specifiers. (#836) * Ksort has been improved to facilitate library use. See KSORT_INIT2 (adds scope / namespace capabilities) and KSORT_INIT_STATIC interfaces. (#851, thanks to John Marshall) * New kstring functions (#879): KS_INITIALIZE - Initializer for structure assignment ks_initialize() - Initializer for pointed-to kstrings ks_expand() - Increase kstring capacity by a given amount ks_clear() - Set kstring length to zero ks_free() - Free the underlying buffer ks_c_str() - Returns the kstring buffer as a const char *, or an empty string if the length is zero. * New API functions hts_idx_load3(), sam_index_load3(), tbx_index_load3() and bcf_index_load3() have been added. These allow control of whether remote indexes should be cached locally, and allow the error message printed when the index does not exist to be suppressed. (#870) * Improved hts_detect_format() so it no longer assumes all text is SAM unless positively identified otherwise. It also makes a stab at detecting bzip2 format and identifying BED, FASTA and FASTQ files. (#721, thanks to John Marshall; #200, #719 both reported by Torsten Seemann) * File format errors now set errno to EFTYPE (BSD, MacOS) when available instead of ENOEXEC. (#721) * New API function bam_set_qname (#942) * In addition to the existing hts_version() function, which reflects the HTSlib version being used at runtime, now also provides HTS_VERSION, a preprocessor macro reflecting the HTSlib version that a program is being compiled against. (#951, thanks to John Marshall; #794) ABI changes ----------- This release contains a number of things which change the Application Binary Interface (ABI). This means code compiled against an earlier library will require recompiling. The shared library soversion has been bumped. * On systems that support it, the default symbol visibility has been changed to hidden and the only exported symbols are ones that form part of the officially supported ABI. This is to make clear exactly which symbols are considered parts of the library interface. It also helps packagers who want to check compatibility between HTSlib versions. (#946; see for example issues #311, #616, and #695) * HTSlib now supports 64 bit reference positions. This means several structures, function parameters, and return values have been made bigger to allow larger values to be stored. While most code that uses HTSlib interfaces should still build after this change, some alterations may be needed - notably to printf() formats where the values of structure members are being printed. (#709) Due to file format limitations, large positions are only supported when reading and writing SAM and VCF files. See README.large_positions.md for more information. * An extra field has been added to the kbitset_t struct so bitsets can be made smaller (and later enlarged) without involving memory allocation. (#710, thanks to John Marshall) * A new field has been added to the bam_pileup1_t structure to keep track of which CIGAR operator is being processed. This is used by a new bam_plp_insertion() function which can be used to return the sequence of any inserted bases at a given pileup location. If the alignment includes CIGAR P operators, the returned sequence will include pads. (#699) * The hts_itr_t and hts_itr_multi_t structures have been merged and can be used interchangeably. Extra fields have been added to hts_itr_t to support this. hts_itr_multi_t is now a typedef for hts_itr_t; sam_itr_multi_next() is now an alias for sam_itr_next() and hts_itr_multi_destroy() is an alias for hts_itr_destroy(). (#836) * An improved regidx interface has been added. To allow this, struct reg_t has been removed, regitr_t has been modified and various new API functions have been added to htslib/regidx.h. While parts of the old regidx API have been retained for backwards compatibility, it is recommended that all code using regidx should be changed to use the new interface. (#761) * Elements in the hts_reglist_t structure have been reordered slightly so that they pack together better. (#761) * bgzf_utell() and bgzf_useek() now use type off_t instead of long for the offset. This allows them to work correctly on files longer than 2G bytes on Windows and 32-bit Linux. (#868) * A number of functions that used to return void now return int so that they can report problems like memory allocation failures. Callers should take care to check the return values from these functions. (#834) The affected functions are: ksort.h: ks_introsort(), ks_mergesort() sam.h: bam_mplp_init_overlaps() synced_bcf_reader.h: bcf_sr_regions_flush() vcf.h: bcf_format_gt(), bcf_fmt_array(), bcf_enc_int1(), bcf_enc_size(), bcf_enc_vchar(), bcf_enc_vfloat(), bcf_enc_vint(), bcf_hdr_set_version(), bcf_hrec_format() vcfutils.h: bcf_remove_alleles() * bcf_set_variant_type() now outputs VCF_OVERLAP for spanning deletions (ALT=*). (#726) * A new field (hrecs) has been added to the bam_hdr_t structure for use by the new header API. The old sdict field is now not used and marked as deprecated. The l_text field has been changed from uint32_t to size_t, to allow for very large headers in SAM files. The text and l_text fields have been left for backwards compatibility, but should not be accessed directly in code that uses the new header API. To access the header text, the new functions sam_hdr_length() and sam_hdr_str() should be used instead. (#812) * The old cigar_tab field is now marked as deprecated; use the new bam_cigar_table[] instead. (#891, thanks to John Marshall) * The bam1_core_t structure's l_qname and l_extranul fields have been rearranged and enlarged; l_qname still includes the extra NULs. (Almost all code should use bam_get_qname(), bam_get_cigar(), etc, and has no need to use these fields directly.) HTSlib now supports the SAM specification's full 254 QNAME length again. (#900, thanks to John Marshall; #520) * bcf_index_load() no longer tries the '.tbi' suffix when looking for BCF index files (.tbi indexes are for text files, not binary BCF). (#870) * htsFile has a new 'state' member to support SAM multi-threading. (#916) * A new field has been added to the bam1_t structure, and others have been rearranged to remove structure holes. (#709; #922) Bug fixes --------- * Several BGZF format fixes: - Support for multi-member gzip files. (#744, thanks to Adam Novak; #742) - Fixed error handling code for native gzip formatted files. (64c4927) - CRCs checked when threading too (previously only when non-threaded). (#745) - Made bgzf_useek function work with threads. (#818) - Fixed rare threading deadlocks. (#831) - Reading of very short files (<28 bytes) that do not contain an EOF block. (#910) * Fixed some thread pool deadlocks caused by race conditions. (#746, #906) * Many additional memory allocation checks in VCF, BCF, SAM and CRAM code. This also changes the return type of some functions. See ABI changes above. (#920 amongst others) * Replace some sam parsing abort() calls with proper errors. (#721, thanks to John Marshall; #576) * Fixed to permit SAM read names of length 252 to 254 (the maximum specified by the SAM specification). (#900, thanks to John Marshall) * Fixed mpileup overlap detection heuristic to work with BAMs having long CIGARs (more than 65536 operations). (#802) * Security fix: CIGAR strings starting with the "N" operation can no longer cause underflow on the bam CIGAR structure. Similarly CIGAR strings that are entirely "D" ops could leak the contents of uninitialised variables. (#699) * Fixed bug where alignments starting 0M could cause an invalid memory access in sam_prob_realn(). (#699) * Fixed out of bounds memory access in mpileup when given a reference with binary characters (top-bit set). (#808, thanks to John Marshall) * Fixed crash in mpileup overlap_push() function. (#882; #852 reported by Pierre Lindenbaum) * Fixed various potential CRAM memory leaks when recovering from error cases. * Fixed CRAM index queries for unmapped reads (#911; samtools/samtools#958 reported by @acorvelo) * Fixed the combination of CRAM embedded references and multiple slices per container. This was incorrectly setting the header MD5sum. (No impact on default CRAM behaviour.) (b2552fd) * Removed unwanted explicit data flushing in CRAM writing, which on some OSes caused major slowdowns. (#883) * Fixed inefficiencies in CRAM encoding when many small references occur within the middle of large chromosomes. Previously it switched into multi-ref mode, but not back out of it which caused the read POS field to be stored poorly. (#896) * Fixed CRAM handling of references when the order of sequences in a supplied fasta file differs to the order of the @SQ headers. (#935) * Fixed BAM and CRAM multi-threaded decoding when used in conjunction with the multi-region iterator. (#830; #577, #822, #926 all reported by Brent Pedersen) * Removed some unaligned memory accesses in CRAM encoder and undefined behaviour in BCF reading (#867, thanks to David Seifert) * Repeated calling of bcf_empty() no longer crashes. (#741) * Fixed bug where some 8 or 16-bit negative integers were stored using values reserved by the BCF specification. These numbers are now promoted to the next size up, so -121 to -128 are stored using at least 16 bits, and -32761 to -32768 are stored using 32 bits. Note that while BCF files affected by this bug are technically incorrect, it is still possible to read them. When converting to VCF format, HTSlib (and therefore bcftools) will interpret the values as intended and write out the correct negative numbers. (#766, thanks to John Marshall; samtools/bcftools#874) * Allow repeated invocations of bcf_update_info() and bcf_update_format_*() functions. (#856, thanks to John Marshall; #813 reported by Steffen Möller) * Memory leak removed in knetfile's kftp_parse_url() function. (#759, thanks to David Alexander) * Fixed various crashes found by libfuzzer (invalid data leading to errors), mostly but not exclusively in CRAM, VCF and BCF decoding. (#805) * Improved robustness of BAI and CSI index creation and loading. (#870; #967) * Prevent (invalid) creation of TBI indices for BCF files. (#837; samtools/bcftools#707) * Better parsing of handling of remote URLs with ?param=val components and their interaction with remote index URLs. (#790; #784 reported by Mark Ebbert) * hts_idx_load() now checks locally for all possible index names before attempting to download a remote index. It also checks that the remote file it downloads is actually an index before trying to save and use it. (#870; samtools/samtools#1045 reported by Albert Vilella) * hts_open_format() now honours the compression field, no longer also requiring an explicit "z" in the mode string. Also fixed a 1 byte buffer overrun. (#880) * Removed duplicate hts_tpool_process_flush prototype. (#816, reported by James S Blachly) * Deleted defunct cram_tell declaration. (66c41e2; #915 reported by Martin Morgan) * Fixed overly aggressive filename suffix checking in bgzip. (#927, thanks to John Marshall; #129, reported by @hguturu) * Tabix and bgzip --help output now goes to standard output. (#754, thanks to John Marshall) * Fixed bgzip index creation when using multiple threads. (#817) * Made bgzip -b option honour -I (index filename). (#817) * Bgzip -d no longer attempts to unlink(NULL) when decompressing stdin. (#718) Miscellaneous other changes --------------------------- * Integration with Google OSS fuzzing for automatic detection of more bugs. (Thanks to Google for their assistance and the bugs it has found.) (#796, thanks to Markus Kusano) * aclocal.m4 now has the pkg-config macros. (6ec3b94d; #733 reported by Thomas Hickman) * Improved C++ compatibility of some header files. (#772; #771 reported by @cwrussell) * Improved strict C99 compatibility. (#860, thanks to John Marshall) * Travis and AppVeyor improvements to aid testing. (#747; #773 thanks to Lennard Berger; #781; #809; #804; #860; #909) * Various minor compiler warnings fixed. (#708; #765; #846, #860, thanks to John Marshall; #865; #966; #973) * Various new and improved error messages. * Documentation updates (mostly in the header files). * Even more testing with "make check". * Corrected many copyright dates. (#979) * The default non-configure Makefile now uses libcurl instead of knet, so it can support https. (#895) Noteworthy changes in release 1.9 (18th July 2018) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * 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. (#711, thanks to John Marshall) * 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' (#682, thanks to @sd4B75bJ, @jrayner) * 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. (#701) * New API interfaces to add or update integer, float and array aux tags. (#694) * Add `level=` option to `hts_set_opt()` to allow the compression level to be set. Setting `level=0` enables uncompressed output. (#715) * Improved bgzip error reporting. * Better error reporting when CRAM reference files can't be opened. (#706) * Fixes to make tests work properly on Windows/MinGW - mainly to handle line ending differences. (#716) * Efficiency improvements: - Small speed-up for CRAM indexing. - Reduce the number of unnecessary wake-ups in the thread pool. (#703) - Avoid some memory copies when writing data, notably for uncompressed BGZF output. (#703) * Bug fixes: - Fix multi-region iterator bugs on CRAM files. (#684) - Fixed multi-region iterator bug that caused some reads to be skipped incorrectly when reading BAM files. (#687) - Fixed synced_bcf_reader() bug when reading contigs multiple times. (#691, reported by @freeseek) - Fixed bug where bcf_hdr_set_samples() did not update the sample dictionary when removing samples. (#692, reported by @freeseek) - 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. (#700) - 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. (CVE-2018-13845, #731, reported by @fCorleone) - Fixed bug where cram range queries could incorrectly report an error when using multiple threads. (#734, reported by Brent Pedersen) - Fixed very rare rANS normalisation bug that could cause an assertion failure when writing CRAM files. (#739, reported by @carsonhh) Noteworthy changes in release 1.8 (3rd April 2018) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * The URL to get sequences from the EBI reference server has been changed to https://. This is because the EBI no longer serve sequences via plain HTTP - requests to the http:// endpoint just get redirected. HTSlib needs to be linked against libcurl to download https:// URLs, so CRAM users who want to get references from the EBI will need to run configure and ensure libcurl support is enabled using the --enable-libcurl option. * Added libdeflate as a build option for alternative faster compression and decompression. Results vary by CPU but compression should be twice as fast and decompression faster. * It is now possible to set the compression level in bgzip. (#675; thanks to Nathan Weeks). * bgzip now gets its own manual page. * CRAM encoding now stored MD and NM tags verbatim where the reference contains 'N' characters, to work around ambiguities in the SAM specification (samtools #717/762). Also added "store_md" and "store_nm" cram-options for forcing these tags to be stored at all locations. This is best when combined with a subsequent decode_md=0 option while reading CRAM. * Multiple CRAM bug fixes, including a fix to free and the subsequent reuse of references with `-T ref.fa`. (#654; reported by Chris Saunders) * CRAM multi-threading bugs fixed: don't try to call flush on reading; processing of multiple range queries; problems with multi-slice containers. * Fixed crashes caused when decoding some cramtools produced CRAM files. * Fixed a couple of minor rANS issues with handling invalid data. * Fixed bug where probaln_glocal() tried to allocate far more memory than needed when the query sequence was much longer than the reference. This caused crashes in samtools and bcftools mpileup when used on data with very long reads. (#572, problem reported by Felix Bemm via minimap2). * sam_prop_realn() now returns -1 (the same value as for unmapped reads) on reads that do not include at least one 'M', 'X' or '=' CIGAR operator, and no longer adds BQ or ZQ tags. BAQ adjustments are only made to bases covered by these operators so there is no point in trying to align reads that do not have them. (#572) Noteworthy changes in release 1.7 (26th January 2018) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * BAM: HTSlib now supports BAMs which include CIGARs with more than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8). * BCF/VCF: - Removed the need for long double in pileup calculations. - Sped up the synced reader in some situations. - Bug fixing: removed memory leak in bcf_copy. * CRAM: - Added support for HTS_IDX_START in cram iterators. - Easier to build when lzma header files are absent. - Bug fixing: a region query with REQUIRED_FIELDS option to disable sequence retrieval now gives correct results. - Bug fixing: stop queries to regions starting after the last read on a chromosome from incorrectly reporting errors (#651, #653; reported by Imran Haque and @egafni via pysam). * Multi-region iterator: The new structure takes a list of regions and iterates over all, deduplicating reads in the process, and producing a full list of file offset intervals. This is usually much faster than repeatedly using the old single-region iterator on a series of regions. * Curl improvements: - Add Bearer token support via HTS_AUTH_LOCATION env (#600). - Use CURL_CA_BUNDLE environment variable to override the CA (#622; thanks to Garret Kelly & David Alexander). - Speed up (removal of excessive waiting) for both http(s) and ftp. - Avoid repeatedly reconnecting by removal of unnecessary seeks. - Bug fixing: double free when libcurl_open fails. * BGZF block caching, if enabled, now performs far better (#629; reported by Ram Yalamanchili). * Added an hFILE layer for in-memory I/O buffers (#590; thanks to Thomas Hickman). * Tidied up the drand48 support (intended for systems that do not provide this function). Noteworthy changes in release 1.6 (28th September 2017) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Fixed bug where iterators on CRAM files did not propagate error return values to the caller correctly. Thanks go to Chris Saunders. * Overhauled Windows builds. Building with msys2/mingw64 now works correctly and passes all tests. * More improvements to logging output (thanks again to Anders Kaplan). * Return codes from sam_read1() when reading cram have been made consistent with those returned when reading sam/bam. Thanks to Chris Saunders (#575). * BGZF CRC32 checksums are now always verified. * It's now possible to set nthreads = 1 for cram files. * hfile_libcurl has been modified to make it thread-safe. It's also better at handling web servers that do not honour byte range requests when attempting to seek - it now sets errno to ESPIPE and keeps the existing connection open so callers can revert to streaming mode it they want to. * hfile_s3 now recalculates access tokens if they have become stale. This fixes a reported problem where authentication failed after a file had been in use for more than 15 minutes. * Fixed bug where remote index fetches would fail to notice errors when writing files. * bam_read1() now checks that the query sequence length derived from the CIGAR alignment matches the sequence length in the BAM record. Noteworthy changes in release 1.5 (21st June 2017) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ * Added a new logging API: hts_log(), along with hts_log_error(), hts_log_warn() etc. convenience macros. Thanks go to Anders Kaplan for the implementation. (#499, #543, #551) * Added a new file I/O option "block_size" (HTS_OPT_BLOCK_SIZE) to alter the hFILE buffer size. * Fixed various bugs, including compilation issues samtools/bcftools#610, samtools/bcftools#611 and robustness to corrupted data #537, #538, #541, #546, #548, #549, #554. Noteworthy changes in release 1.4.1 (8th May 2017) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is primarily a security bug fix update. * Fixed SECURITY (CVE-2017-1000206) issue with buffer overruns with malicious data. (#514) * S3 support for non Amazon AWS endpoints. (#506) * Support for variant breakpoints in bcftools. (#516) * Improved handling of BCF NaNs. (#485) * Compilation / portability improvements. (#255, #423, #498, #488) * Miscellaneous bug fixes (#482, #521, #522, #523, #524). * Sanitise headers (#509) Release 1.4 (13 March 2017) * Incompatible changes: several functions and data types have been changed in this release, and the shared library soversion has been bumped to 2. - bam_pileup1_t has an additional field (which holds user data) - bam1_core_t has been modified to allow for >64K CIGAR operations and (along with bam1_t) so that CIGAR entries are aligned in memory - hopen() has vararg arguments for setting URL scheme-dependent options - the various tbx_conf_* presets are now const - auxiliary fields in bam1_t are now always stored in little-endian byte order (previously this depended on if you read a bam, sam or cram file) - index metadata (accessible via hts_idx_get_meta()) is now always stored in little-endian byte order (previously this depended on if the index was in tbi or csi format) - bam_aux2i() now returns an int64_t value - fai_load() will no longer save local copies of remote fasta indexes - hts_idx_get_meta() now takes a uint32_t * for l_meta (was int32_t *) * HTSlib now links against libbz2 and liblzma by default. To remove these dependencies, run configure with options --disable-bz2 and --disable-lzma, but note that this may make some CRAM files produced elsewhere unreadable. * Added a thread pool interface and replaced the bgzf multi-threading code to use this pool. BAM and CRAM decoding is now multi-threaded too, using the pool to automatically balance the number of threads between decode, encode and any data processing jobs. * New errmod_cal(), probaln_glocal(), sam_cap_mapq(), and sam_prob_realn() functions, previously internal to SAMtools, have been added to HTSlib. * Files can now be accessed via Google Cloud Storage using gs: URLs, when HTSlib is configured to use libcurl for network file access rather than the included basic knetfile networking. * S3 file access now also supports the "host_base" setting in the $HOME/.s3cfg configuration file. * Data URLs ("data:,text") now follow the standard RFC 2397 format and may be base64-encoded (when written as "data:;base64,text") or may include percent-encoded characters. HTSlib's previous over-simplified "data:text" format is no longer supported -- you will need to add an initial comma. * When plugins are enabled, S3 support is now provided by a separate hfile_s3 plugin rather than by hfile_libcurl itself as previously. When --enable-libcurl is used, by default both GCS and S3 support and plugins will also be built; they can be individually disabled via --disable-gcs and --disable-s3. * The iRODS file access plugin has been moved to a separate repository. Configure no longer has a --with-irods option; instead build the plugin found at . * APIs to portably read and write (possibly unaligned) data in little-endian byte order have been added. * New functions bam_auxB_len(), bam_auxB2i() and bam_auxB2f() have been added to make accessing array-type auxiliary data easier. bam_aux2i() can now return the full range of values that can be stored in an integer tag (including unsigned 32 bit tags). bam_aux2f() will return the value of integer tags (as a double) as well as floating-point ones. All of the bam_aux2 and bam_auxB2 functions will set errno if the requested conversion is not valid. * New functions fai_load3() and fai_build3() allow fasta indexes to be stored in a different location to the indexed fasta file. * New functions bgzf_index_dump_hfile() and bgzf_index_load_hfile() allow bgzf index files (.gzi) to be written to / read from an existing hFILE handle. * hts_idx_push() will report when trying to add a range to an index that is beyond the limits that the given index can handle. This means trying to index chromosomes longer than 2^29 bases with a .bai or .tbi index will report an error instead of apparently working but creating an invalid index entry. * VCF formatting is now approximately 4x faster. (Whether this is noticeable depends on what was creating the VCF.) * CRAM lossy_names mode now works with TLEN of 0 or TLEN within +/- 1 of the computed value. Note in these situations TLEN will be generated / fixed during CRAM decode. * CRAM now supports bzip2 and lzma codecs. Within htslib these are disabled by default, but can be enabled by specifying "use_bzip2" or "use_lzma" in an hts_opt_add() call or via the mode string of the hts_open_format() function. Noteworthy changes in release 1.3.2 (13 September 2016) * Corrected bin calculation when converting directly from CRAM to BAM. Previously a small fraction of converted reads would fail Picard's validation with "bin field of BAM record does not equal value computed" (SAMtools issue #574). * Plugins can now signal to HTSlib which of RTLD_LOCAL and RTLD_GLOBAL they wish to be opened with -- previously they were always RTLD_LOCAL. Noteworthy changes in release 1.3.1 (22 April 2016) * Improved error checking and reporting, especially of I/O errors when writing output files (#17, #315, PR #271, PR #317). * Build fixes for 32-bit systems; be sure to run configure to enable large file support and access to 2GiB+ files. * Numerous VCF parsing fixes (#321, #322, #323, #324, #325; PR #370). Particular thanks to Kostya Kortchinsky of the Google Security Team for testing and numerous input parsing bug reports. * HTSlib now prints an informational message when initially creating a CRAM reference cache in the default location under your $HOME directory. (No message is printed if you are using $REF_CACHE to specify a location.) * Avoided rare race condition when caching downloaded CRAM reference sequence files, by using distinctive names for temporary files (in addition to O_EXCL, which has always been used). Occasional corruption would previously occur when multiple tools were simultaneously caching the same reference sequences on an NFS filesystem that did not support O_EXCL (PR #320). * Prevented race condition in file access plugin loading (PR #341). * Fixed mpileup memory leak, so no more "[bam_plp_destroy] memory leak [...] Continue anyway" warning messages (#299). * Various minor CRAM fixes. * Fixed documentation problems #348 and #358. Noteworthy changes in release 1.3 (15 December 2015) * Files can now be accessed via HTTPS and Amazon S3 in addition to HTTP and FTP, when HTSlib is configured to use libcurl for network file access rather than the included basic knetfile networking. * HTSlib can be built to use remote access hFILE backends (such as iRODS and libcurl) via a plugin mechanism. This allows other backends to be easily added and facilitates building tools that use HTSlib, as they don't need to be linked with the backends' various required libraries. * When writing CRAM output, sam_open() etc now default to writing CRAM v3.0 rather than v2.1. * fai_build() and samtools faidx now accept initial whitespace in ">" headers (e.g., "> chr1 description" is taken to refer to "chr1"). * tabix --only-header works again (was broken in 1.2.x; #249). * HTSlib's configure script and Makefile now fully support the standard convention of allowing CC/CPPFLAGS/CFLAGS/LDFLAGS/LIBS to be overridden as needed. Previously the Makefile listened to $(LDLIBS) instead; if you were overriding that, you should now override LIBS rather than LDLIBS. * Fixed bugs #168, #172, #176, #197, #206, #225, #245, #265, #295, and #296. Noteworthy changes in release 1.2.1 (3 February 2015) * Reinstated hts_file_type() and FT_* macros, which were available until 1.1 but briefly removed in 1.2. This function is deprecated and will be removed in a future release -- you should use hts_detect_format() etc instead Noteworthy changes in release 1.2 (2 February 2015) * HTSlib now has a configure script which checks your build environment and allows for selection of optional extras. See INSTALL for details * By default, reference sequences are fetched from the EBI CRAM Reference Registry and cached in your $HOME cache directory. This behaviour can be controlled by setting REF_PATH and REF_CACHE environment variables (see the samtools(1) man page for details) * Numerous CRAM improvements: - Support for CRAM v3.0, an upcoming revision to CRAM supporting better compression and per-container checksums - EOF checking for v2.1 and v3.0 (similar to checking BAM EOF blocks) - Non-standard values for PNEXT and TLEN fields are now preserved - hts_set_fai_filename() now provides a reference file when encoding - Generated read names are now numbered from 1, rather than being labelled 'slice:record-in-slice' - Multi-threading and speed improvements * New htsfile command for identifying file formats, and corresponding file format detection APIs * New tabix --regions FILE, --targets FILE options for filtering via BED files * Optional iRODS file access, disabled by default. Configure with --with-irods to enable accessing iRODS data objects directly via 'irods:DATAOBJ' * All occurrences of 2^29 in the source have been eliminated, so indexing and querying against reference sequences larger than 512Mbp works (when using CSI indices) * Support for plain GZIP compression in various places * VCF header editing speed improvements * Added seq_nt16_int[] (equivalent to the samtools API's bam_nt16_nt4_table) * Reinstated faidx_fetch_nseq(), which was accidentally removed from 1.1. Now faidx_fetch_nseq() and faidx_nseq() are equivalent; eventually faidx_fetch_nseq() will be deprecated and removed [#156] * Fixed bugs #141, #152, #155, #158, #159, and various memory leaks