- Added new INFO fileds to the final vcf
- Changes to indel calling to reduce false calls
- Added burdens output to nanoseq plotter
- Fixed bugs in the VAF script
- Fixed bug in part with empty intervals at end of genome
- Modified BAM processing as to keep unmapped reads
- Fixed VCF filter bug in VAF script
- Fixed type error of VAF script
- Made changes to accomodate targeted NanoSeq
- Added quotes add various places to support ant chromosomes
- Fixed error with 1 bp intervals
- Fixed efficiency calculation problem with coordinates outside of chr ends
- Reverted to old efficiency calculation
- Added safe creation of tmp dir
- Re-read input file to reduce mem usage in efficiency calculation
- Cleaned up/ simplified variantcaller.R
- Added extra check for turncated dsa output
- Tested with targeted data
- Fixed issue with coverage done files
- Fixed bamcov so that it handles chromosomes without coverage
- Fixed required/optional arguments from docustring
- Fixed incorrect default argument (-d)
- Added argument for file name of results
- Removed plugin option from htslib that was causing issues with CRAM
- Set seqs_per_slice to 1000 in htslib for improved CRAM streaming
- Fixed off by one errors in part
- Fixed interval test in part
- Added consistency checks for contigs in BAM files
- Added CRAM support
- Fixed issue with sort in indel pipeline
- Fixed 1-off error in dsa code.
- Incorporated Indel scripts.
- Incorporated new code for quick coverage estimation.
- Rewrote Python wrapper.
- Updated licenses.
- Fixed bug with last interval for outlier case
- Added more error captures for htslib calls
- Updated R library installation script
- Added option to skip post processing step
- Simplified excluded chromosome option
- Reduced default coverage window
- Initial public release
- Updated to htslib 1.11
- Added licencing information
- Added error checks when reading