- When Priority = True but no hit validates query No.1 , the queries No 2,3 if existent, will be read for finding a valid hit.
- The command line arguments -i, -o are flexible in position "
- The non overlapping peaks are saved in All_hits and in Best_hits table.
- All and Best hits will contain all peaks, with NAs in Best_tab when hit is in D > config "distance".
- Query column shown only if more than 1 query given.
- Check for all keys not to have EMPTY values.
- Check distance of p.center -gene.center,start,end for valid_dist of hit.
- Fix cases of checking peak columns(make 3 'if's for diff sizes).Also read strand and replace to None if strand == ".".
- Extract attribute value one by one from all queries and give "not.found" if key doesn't exist.(get_hit_attribute)
- When correct_dir but best_hit or All_hits already written, just "continue", no NAs bcs it overwrites best hit of same peak,or keeps NA while there is also hit.
- Hits from all queries are visible in All_hits, per query, and in Best Hits the best per Query. BestBest hits table has the best of all queries.
- Features of gtf are extracted and replaced as default if no key given. If wrong feat_value given ->Error proposing gtf features.
- Fix NAs when pr=True and quer>1
- Add genomic_location, min_pos of the Dmin, overlap ratio, in the output tables.Remove internal_features key, but Find 'inside' or 'includefeature'(genom_location)
- Add 'filter.attribute' & attribute.value' as extra keys in config for validating a hit.
- Add possibility of keeping different cut-off distance for Upstream and Downstream direction of peak when Distance = [x,y]
- Call script for Summary graphs and create file after creation of tables.