diff --git a/doc/release.rst b/doc/release.rst index 329a0971..29d21ab9 100644 --- a/doc/release.rst +++ b/doc/release.rst @@ -6,28 +6,35 @@ Release 0.8.3 ============= * samtools command now accept the "catch_stdout" option. -* get_aligned_pairs now works for soft-clipped reads + +* get_aligned_pairs now works for soft-clipped reads. + * query_position is now None when a PileupRead is not aligned to a particular position. + * AlignedSegments are now comparable and hashable. Release 0.8.2.1 =============== -* Installation bugfix release +* Installation bugfix release. Release 0.8.2 ============= -* Pysam now wraps htslib 1.2.1 and samtools version 1.2 -* Added CRAM file support to pysam +* Pysam now wraps htslib 1.2.1 and samtools version 1.2. + +* Added CRAM file support to pysam. + * New alignment info interface. * opt() and setTag are deprecated, use get_tag() and set_tag() instead. * added has_tag() * tags is deprecated, use get_tags() and set_tags() instead. + * FastqFile is now FastxFile to reflect that the latter permits iteration over both fastq- and fasta-formatted files. + * A Cython wrapper for htslib VCF/BCF reader/writer. The wrapper provides a nearly complete Pythonic interface to VCF/BCF metadata with reading and writing capability. However, the interface is still @@ -37,7 +44,7 @@ Release 0.8.2 Release 0.8.1 ============= -* Pysam now wraps htslib and samtools versions 1.1 +* Pysam now wraps htslib and samtools versions 1.1. * Bugfixes, most notable: * issue #43: uncompressed BAM output @@ -89,9 +96,9 @@ Release 0.8.1 as strings, no more bytes. Other changes: - * AlignmentFile.fetch(reopen) option is now multiple_iterators. The - default changed to not reopen a file unless requested by the user. - * FastaFile.getReferenceLength is now FastaFile.get_reference_length + * AlignmentFile.fetch(reopen) option is now multiple_iterators. The + default changed to not reopen a file unless requested by the user. + * FastaFile.getReferenceLength is now FastaFile.get_reference_length Backwards incompatible changes @@ -109,11 +116,11 @@ Release 0.8.0 ============= * Disabled features - * IteratorColumn.setMask() disabled as htslib does not implement - this functionality? + * IteratorColumn.setMask() disabled as htslib does not implement + this functionality? * Not implemented yet: - * reading SAM files without header + * reading SAM files without header Tabix files between version 0.7.8 and 0.8.0 are not compatible and need to be re-indexed.