Tags: jonas-fuchs/varVAMP
Tags
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
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
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
PreviousNext