pysam-0.9.1
This is a bugfix release addressing some installation problems
in pysam 0.9.0, in particular:
- patch included htslib to work with older libcurl versions, fixes #262.
- do not require cython for python 3 install, fixes #260
- FastaFile does not accept filepath_index any more, see #270
- add AlignedSegment.get_cigar_stats method.
- py3 bugfix in VariantFile.subset_samples, fixes #272
- add missing sysconfig import, fixes #278
- do not redirect stdout, but instead write to a separately
created file. This should resolve issues when pysam is used
in notebooks or other environments that redirect stdout. - wrap htslib-1.3.1, samtools-1.3.1 and bcftools-1.3.1
- use bgzf throughout instead of gzip
- allow specifying a fasta reference for CRAM file when opening
for both read and write, fixes #280