Fixes to BLAST functionality and refactoring (#39)

CHANGELOG

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

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

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

Update __init__.py

Update __init__.py

Bug fixes (#36)

* fixed bug that would cause crash in qpcr mode if -a = 0

* added end overlap logging and negative value error

* changed version number

* typo

Qpcr blast fix (#34)

* changed primer type qpcr

* further harmonized primer naming in the script

removed variable assignment for blast process

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Publication ready version (#23)

* renamed scores to penalties, renamed --n_threads to --threads and some changes to the graph

* renamed overshadowing names

* renaming

* some further minor code reformatting

* updated docs

* updated output.md

* updated workflow.png

* updated readme

* changed how dinuc repeats and polyx are counted to make it more intuitive

* tsv output now contains a more intuitive primer name and primers are given in fasta per pool

* fasta output for sanger/qpcr mode

Correct entropy (#22)

* fixed entropy normalization

* updated version

Further tweaks (#21)

* fixed alignment bug, tweaked config, fixed plot warnings

* changed kmer list to tuple to speed up kmer digestion

* checks now blast installation for qpcr mode

* adjusted best primer selection

* fixed unwanted sorting behaviour

* updated docs

* reworked output and dimer search

* docstring update

* adjusted cutoff for t=1