diff --git a/NEWS b/NEWS index 4a6c90cf1..7b60c913e 100644 --- a/NEWS +++ b/NEWS @@ -4,12 +4,114 @@ Noteworthy changes in release a.b Features and Updates -------------------- -* New method `hts_idx_nseq` returns the number of contigs covered by reads - from an index structure. - * 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. + +* 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) + Noteworthy changes in release 1.12 (17th March 2021) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~