v0.3.2

• Changed behaviour of potential SNV identification: unexpected bases now replaced with N rather than bailing.

v0.3.1

• Added a filter based on fishers exact test to remove potential SNVs that have a strand (forward or reverse) bias
• Updated rust-htslib to 0.22.0
• Switched to hashbrown crate for HashSets and HashMaps

v0.3.0

• potential SNV identification step is significantly (>10x) faster.
• added min alt count and min alt fraction parameters (2 and 0.125 by default)
• updated rust-bio to 0.25.0 resulting in a performance boost due to log probability optimizations
• fixed a bug that could cause haplotyping iteration to loop indefinitely in certain scenarios
• fixed a bug that was causing "potential SNV cutoff" to be assigned the value of "haplotype assignment qual"
• changed default minimum coverage to 6 reads

v0.2.1

Implemented proper error handling throughout the Longshot program using the error-chain crate.

v0.2.0

Introduced since 0.1:

• faster execution with new convergence criteria
• changed max coverage behaviour. By default the max coverage is 8000 but added -A option to automatically decide a max coverage at mean_cov+5*sqrt(mean_cov)
• changed default ts/tv ratio for genotype priors to 0.5

v0.1

This is the initial release for longshot.