htslib release 1.13:
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)