Version 1.17.1

Bug fixes:

• Fix help message for parascopy cn and parascopy cn-using,
• Use bigger integer variables (32 instead of 16 bits) due to issues with overflow.

Version 1.17.0

Subset samples based on variance-mean ratio before CN analysis (--vmr).

Version 1.16.3

Replace deprecated numpy function

Version 1.16.2

Allow users to limit variant calling to a subset of regions using --regions for parascopy call.

Version 1.6.1

Sometimes, read pooling to CRAM produces corrupt files (pysam issue?). Therefore, by default we now pool to the BAM files. Use --pool-cram to override.

Version 1.16.0

• Speed up variant calling by using other Freebayes parameters,
• Changes to read pooling:
  • --only-regions argument to only generate pooling targets,
  • Pool reads into multiple CRAM/BAM files by default, instead of a single BAM file.

Full Changelog: v1.15.1...v1.16.0

Version 1.15.1

Patch possible Freebayes error (updated multichoose function)

Version 1.15.0

• Improved read pooling, keeping track of read mate positions,
• --force-agcn argument for parascopy cn and parascopy cn-using.

Version 1.14.1

Detect variant alleles that are supported mainly by reads without a proper pair.

Version 1.14.0

Bug fix in read pooling