v.1.2.0

Major varVAMP update to version 1.2

These changes are credited to @wm75 (#39).

CHANGELOG

(1) Changes around BLAST functionality:

• Off-target amplicons are now reported as intended in the logs
• Off-target amplicons are now always considered last for the final scheme (no penalty is used, but the fact that they had BLAST matches gets recorded)
• The BLAST_PENALTY config option is no longer needed and has been removed
• Added a new off_target_amplicons column to the qPCR design, the qPCR primer and the (single/tiled) primer tsv outputs to indicate which final amplicons had BLAST hits

(2) General reporting changes:

• Amplicon numbering now proceeds from 5' to 3' even across pools for the tiled mode and from lowest penalty to highest for the other modes (previously additional BLAST penalties weren't considered during penalty-sorting).
• In the primer bed file output in tiled mode, primers are now ordered according to the amplicon number without taking the pool into account
• In the primer bed file output in qPCR mode, oligos from the same set are now ordered LEFT, PROBE, RIGHT, i.e. by position on the reference
• The per-base mismatch plot now uses final primer names as panel titles
• The amplicon bed file, in all modes, is now formatted as proper six-column bed

(3) Algorithmic fixes and enhancements:

• The internal representation of amplicon schemes has been unified/simplified across the different modes and steps of the analysis
• Search for final non-overlapping amplicons in single mode and for non-overlapping amplicons passing deltaG in qpcr mode has been optimized and is now significantly faster
• Some off-by-one errors in internal primer and amplicon interval calculations have been fixed - generally more primers are now found and considered

Full Changelog: v.1.1.3...v.1.2.0