Release v1.2.5

Bugfix

• DP and AF values in indels were wrong as only reads with the indel was counted in DP

Release v1.2.4

Changes

• Maximum coverage when going through a pileup is not capped to 8000 anymore (this is pysam's default)
• Several refactors with the aim of improving performance although this did not happen...
• Added support for python 3.10 + upgraded several dependencies

Release v1.1.5

Fixes

• Update Nextflow workflow to use latest vafator version v.1.1.4

Release v1.1.4

Bugfixes:

• Issue #18
• Issue #19

Release v1.1.3

Changes:

• Nextflow workflow now has a more flexible input to allow using multiple samples

Release v1.1.2

Fixes

• VCFs with MNVs were crashing, this is fixed now. No annotation is added for MNVs

Non functional features

• Nextfllow workflow automated tests do not rely now on conda and hence work

Release v1.1.1

Fixes

• Fix error when --bam parameter is not provided

Non functional features

• Added automated integration tests that install vafator and run some different command line configurations

Release v1.1.0

Changes:

• Add script vafator2decifer
• Add parameter --bam sample_name bam_file to replace difficult to use --prefix

Release v1.0.0

Changes:

• Support for the annotation of indels
• Added better unit testing using data from GIAB
• Changed the thresholds --mapping-quality and --base-call-quality to filter all reads below the thresholds as opposed to previous behaviour filtering all reads equal or below the threshold. This was cause of a lot of confusion and pysam uses this thresholds
• Use pysam filtering of reads to avoid reading qualities manually, this increases performance around 60%

Release v0.4.3

• Change the name of the conda environment. Python package versions remains v0.4.0