hts-sys hts-sys-v0.1.0

Bug Fixes

• dummy release

Version 1.11.1-fix2 of hts-sys

Dummy release for technical reasons.

Version 0.37.0

Added

• bcf::Record methods end, clear, and rlen (@mbhall88).

Changes

• bcf::IndexReader::fetch parameter end is now an Option<u64>. This is inline with
  htslib regions, which do not require an end position (@mbhall88)
• Removed unused dependencies (@sreenathkrishnan).
• Improved documentation (@mbhall88).
• Improved error message when failing to load index files (@johanneskoester).
• Improved API for accessing AUX fields in BAM records (@jch-13).
• Fixed compiler warnings (@fxwiegand).
• BAM header representation is now always kept in sync between textual and binary (@jch-13).

Version 0.36.0

Changes

• Improved genotype API in VCF/BCF records (@malthesr).
• Read pair orientation inference for BAM records (@johanneskoester).

Version 0.35.2

This release contains a fix for problems with semantic versioning in Cargo when specifying the hts-sys dependency.

Version 0.35.1

• Fixed wrongly define missing value constants in bcf::record (@johanneskoester).
• Bump hts-sys depedency to the latest version, containing build fixes for macOS (@johanneskoester).

Version 0.35.0

Changes

• BREAKING: info and format field access in BCF records now allocates a separate buffer each time. In addition, it is also possible to pass a buffer that has been created manually before (@johanneskoester)
• Fixes for building on macOS (@brainstorm)

Added

• ability to push genotypes into BCF record (@malthesr, @tedil).

Version 0.34.0

Added

• Ability to set minimum refetch distance in bam::RecordBuffer.

Version 0.33.0

Changes

• BREAKING: Rename feature 'serde' as 'serde_feature' (for technical reasons)
• BREAKING: Consolidate module-wide errors into a crate-wide error module
• Making bcf::IndexedReader always unpack records to reflect the behaviour of bcf::Reader.
• Adding bcf::errors::Error::FileNotFound and using it.
• Fixes for musl compilation (@brainstorm).
• Improved BCF constants handling (@juliangehring)
• Fixes for tabix reader (@felix-clark, @brainstorm).
• Fixes for BCF handling (@holtgrewe, @tedil).
• Documentation improvements (@vsoch, @brainstorm, @edmundlth).
• BREAKING: Improved, more ergonomic BAM fetch API (@TyberiusPrime, @brainstorm, @tedil).
• BREAKING: Let BamRecordExtensions return iterators instead of vectors (@TyberiusPrime).
• Handle all errors via a unified single thiserror based enum (@landesfeind).
• BREAKING: BAM read API now returns Option (@slazicoicr).

Added

• Support for reading indexed FASTA files (@landesfeind, @pmarks, @brainstorm).
• Support for shared threadpools when reading and writing BAM (@pmarks, @nlhepler).
• Serde support for Cigar strings (@FelixMoelder, @pmarks, @johanneskoester).
• Expose bgzf functionality (@landesfeind).
• Iterator over BAM records using Rc-pointers (@TyberiusPrime, @tedil).
• Ability to obtain pairs of read and genome intervals from BAM (aligned_block_pairs) (@TyberiusPrime, @brainstorm).

Version 0.32.0

Changes

• Method seq_len() of bam::Record is now public.
• Speedup when parsing BAM headers (thanks to @juliangehring).
• Compatibility fixes for older rust versions (thanks to @pmarks and @brainstorm).