1.4.1

Bugfix release for 1.4, read pairs were not maintained in spike-in.

1.4

• Many fixes and enhancements and maintenence updates thanks to @Rapsssito

1.3

• Update to Python 3
• Numerous bugfixes and minor enhancements (e.g. integrated VCF output)
• Please don't use simulated data if suitable real data is a possibility

1.2

Features
Support snv and indel spikein to long noisy reads (ONT, PacBio) using minimap2 aligner
Support arbitrarily long insertions, deletions, and inversions
Support translocations in all possible orientations
Obey user input SV breakends exactly if possible, add option (--require_exact) to enforce this
Option to adjust noise around SV breakpoints

Miscellaneous / Bugfixes
Remove useless fraction-of-contig syntax from DEL type
Improvements to indels in noisy reads

v1.1

Bugfixes / cleanups:

error instead of crash if no contigs for left end of translocation 5b3ede6
ignore non-primary reads in target BAM when replacing reads 3d17e97
fix indel bug with long insertions 32b3fae
remove instructions with old bwa option b82d384
prevent insertion close to contig edge 54a2499
split actions by semicolon for multi-sv c8256ea
shoten mutation id string daa1f85
remove picard 4g memory request 213bd11
handle case where no contigs are generated 6ee1f8e

Features:

add option to ignore input vs output sanity check 310dbbf
add option to allow N bases in contigs d28a154
ability to select specific insertions from --inslib 143b6b3
explain single-end error if --single not given 01cd8ee
allow per-variant SV VAF adjustment via varfile b096aca

Initial versioning

v1.0.0

add dependency checks to setup