Related Issues (20)
- ctg_hex_pos and ctg_hex_dist is buggy when the contig has indels HOT 4
- Unify tail_side and tail_base, and other names that indicates the same information
- Deal with hardclip in xseq_minus.py HOT 1
- Refactor calc_genome_offset with skip_check_size
- Parallize the initial looping through contig HOT 5
- test edgecases
- Format test case doc strings
- Sum up num_suffix_reads is buggy
- visualize-alignment.py enhancement
- Inconsistent extracted seq for contig and reference HOT 1
- Make window_size adjustable when searching for polyadenylation signal hexamer
- Probably only one end o f a blank contiguous could support a clv depending on the the strand of the annotated genes
- Parallelize aggregating polyA evidence after groupby (seqname, strand, clv) HOT 1
- Output a comprehensive list of PAS hexamers available in upstream regardless of their strength
- Add two columns for ctg_hex_dist and ref_hex_dist
- Remove window default value for extract_seq in contig PAS hexamer search
- Think through hardclip from softclip
- Work out difference between query_length and infer_query_length HOT 1
- Maybe better never reverse reference genome when calc_genome_offset
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