v1.2.0

Added

• read5 to internaly handle the input formats:
  • fast5,
  • slow5, blow5 and
  • potentially pod5 in the future
• magnipore now via pip available
• more tests
  • testing file formats fast5, slow5 & blow5
  • testing event aggregation

Changed

1. replaced nanopolish eventalign with f5c eventalign
2. pod5 is now available via conda, no need for pip install pod5 anymore

Parameters

Changed

a lot of parameter names were shortened and short parameter names were added

• --path_to_fast5_first_sample -> --raw_data_first_sample
• --path_to_reference_first_sample -> --reference_first_sample
• --first_sample_label -> --label_first_sample
• --path_to_fast5_sec_sample -> --raw_data_sec_sample
• --path_to_reference_sec_sample -> --reference_sec_sample
• --sec_sample_label -> --label_sec_sample
• --path_to_first_basecalls -> -b1, --basecalls_first_sample
• --path_to_sec_basecalls -> -b2, --basecalls_sec_sample
• --path_to_first_sequencing_summary -> -s1, --sequencing_summary_first_sample
• --path_to_sec_sequencing_summary -> -s2, --sequencing_summary_sec_sample

Removed

• -f5, --fast5_out

Added

• -rna
• -r10
• -km, --kmer_model