v1.5.0

Changes compared to previous release:

Options for unzipping and conversion of profiles.

• Add option '-o' to PopDel view for unzipping existing profiles.
• Add option '-x' to PopDel profile and PopDel call to write/read uncompressed profiles.
• Add option '-s' to PopDel view, for changing the index-region size when unzipping a profile.
• Add options '-c' and '-p' to automate partitioning of a profile into chunks of size 'c' base pairs with padding/overlap of 'p' base pairs.

v1.4.0

Changes compared to previous release:

• Improve memory management for many samples in PopDel call
• Add option '-e'/'--per-sample-rgid' to resolve conflicting read group names in PopDel profile.
• Fix "too big offset in window"-crash during PopDel profile.
• Fix bug in automatic determination of output profile path in PopDel profile.

v1.3.0

Changes compared to previous release:

• Add support for creating PopDel profile from CRAM files
• PopDel now requires a recent version of HTSlib to be installed!
• Fall back to version 2.1 of SeqAn, because SeqAnHTS is based SeqAn 2.1

v1.2.2_Zenodo

This release is an exact copy of v1.2.2 and necessary for triggering the DOI creation of Zenodo.

v1.2.2

Changes compared to previous release:

• Remove obsolete distinction based on "informativeness" of a read pair prior to likelihood calculations.
• Fix bug in VCF position calculation if the position of a variant was 1.

v1.2.1

Changes compared to previous release:

• Fix bug that could cause crashes during processing of the output.

v1.2.0

Changes compared to previous release:

• Improve genotyping. The genotyping model for HET variants no longer relies on the binomial distribution.
• Remove parameter '-q' ('--del-ref-ratio'), because it is no longer used in the new genotyping model.
• Improve resolution of deletion starting point estimation to 1 bp.
• Change error message for mismatch between contig names found in the BAM-file and those specified by the reference version.

v1.1.3

Changes compared to previous release:

• Added option to specify the reference build for some human genomes (for details see Wiki).
• Added default sampling regions for the added genome builds.
• Fixed a bug in the merging of subsequent windows that caused some deletions to be split into multiple calls, generating some false positives. This fix also makes the estimation of the position more robust to outliers in the alignments.

v1.1.2

Changes compared to previous release:

• Add SVMETHOD to INFO field of VCF output.
• Add END to INFO field of VCF output.
• Reduced README.md to a quickstart guide. More detailed instructions can now be found in the PopDel-Wiki.

v1.1.1

Changes compared to previous release:

• Fix LAD and DAD values in the FORMAT fields. Previously, the LAD and DAD values for the first window of a deletion were displayed, leading to confusing numbers, seemingly contradicting the given genotypes. Now, the median of the numbers making up the LAD and DAD across all windows of the deletion are given instead.