Releases: ChrisHIV/shiver
Releases · ChrisHIV/shiver
v1.7.3
Moved files around for clarity and so that the HXB2 file can be found in bioconda-installed shiver
v1.7.2
Removed tools/trimmomatic to avoid clash with more robust trimmomatic binary installed in the conda version of shiver
v1.7.0
Python code can now be run as Python 3 as well as Python 2.
Turned on some merging of overlapping blast hits for contigs for occasional slight improvement.
Removed fastaq as a dependency if primer trimming is not required.
Support unpaired reads
Added support for unpaired reads
v1.5.9
Minor bug fix for fastq files with descriptors on the ID lines
switch to user-specified python2 exe
Call all python scripts with user-specified python2 executable.
Thanks to @olli0601 !
v1.5.7
New release for packaging purposes; only a trivial tweak from text to csv format input for a script argument.
v1.5.6
tools/LinkIdentityToCoverage.py: now counts overlap between paired reads once instead of twice, and its output can be summarised with new script tools/LinkIdentityToCoverage_CombineBams.py. Also minor bug fixes.
v1.5.5
Minor bug fix: now when cleaning the reads, if none of the forward or none of the reverse reads blast at all, instead of crashing we proceed to mapping (which will likely map none of the read pairs). Changed tools/GetCoverageFromBamFile.py to output reference positions as 1-based instead of 0-based, for compatibility with other output.
