pysam-v0.16.0
This release wraps htslib/bcftools version 1.10.2 and samtools version
1.10. The following bugs reported against pysam are fixed due to this:
- [#447] Writing out QNAME longer than 251 characters corrupts BAM
- [#640, #734, #843] Setting VariantRecord pos or stop raises error
- [#738, #919] FastxFile truncates concatenated plain gzip compressed files
Additional bugfixes:
- [#840] Pileup doesn't work on python3 when
index_filename
is used - [#886] FastqProxy raises ValueError when instantiated from python
- [#904] VariantFile.fetch() throws ValueError on files with no records
- [#909] Fix incorrect quoting in VariantFile contig records
- [#915, #916] Implement pileup() for unindexed files and/or SAM files
Backwards incompatible changes:
- The
samtools import
command was removed in samtools 1.10, so pysam
no longer exports asamimport
function. Usepysam.view()
instead.
Many thanks to @jmarshall who has done most of the heavy lifting.