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

v1.1.3

Changed OMV size back to 30

changed OMV size to 10 by mistake - lead to much longer runtime!

v1.1.2

• Change default minimap2 string from 'splice' to 'map-ont'
• Add sequencing summary parameter, if sequencing summary is not in the same dir as basecalls
• Fixed Typos in README

v1.1.1

Reference Difference File (.refdiff) handles complete IUPAC code now

• introducing possible substitutions for set-characters like Y, R, S, W, M, K and N
• similar to Ns in the reference, we cannot make a clear statement

Ref1: ACTTG
Ref2: ACTTG
-> match

Ref1: ACCTG
Ref2: ACTTG
-> substitution

Ref1: ACYTG
Ref2: ACTTG
-> possible substitution

Ref1: ACYTG
Ref2: ACATG
-> substitution

v1.1.0

Version 1.1.0

Removed

1. removed parameters:

• strict
• r2

2. removed coverage plots from nanosherlock

3. Reduce stored data in RED file

• removed base & motif columns

Added

1. Pytests

• added first tests, more to be written
• added tests to meta.yml, will be executed when using building conda package

2. Updated Help Message in README.md

Changed

1. Use IUPAC code for refdiff substitutions

   • Example: Y:C or Y:T is no subsitution mutation anymore, as Y = {C, T}

2. Reduced storage of plotting data in magnipore.py

v1.0.10

Remove Filter For 0 Coverage Positions

Before:

• positions with 0 coverage (in at least 1 of both samples) did not show up in the .magnipore output files, only in the .red files

Now:

• they show up containing 0s for mean and stdev and nans for tdscore and kl divergence

v1.0.9

Bug Fix In buildModels

Fixed the following:

• bug when multiple reference sequences were provided in buildModels
• when contig switch in nanopolish file signals were aggregated to the wrong contig

v1.0.8

Add Samtools To Dependencies

v1.0.7

• Update README & Help Message
• Bug Fix in Nanosherlock Call of Second Sample

v1.0.6

Add Cookiecutter Conda Recipe & Error Exit Codes

Error Codes:

• 11: Concatenating both reference files failed
• 12: Building mafft alignment failed
• 13: Running nanosherlock for the first sample failed
• 14: Running nanosherlock for the second sample failed
• 121: Guppy basecalling failed in first sample
• 122: minimap2 mapping failed in first sample
• 123: Samtools indexing failed in first sample
• 124: Nanopolish indexing failed in first sample
• 125: Nanopolish eventalign failed in first sample
• 126: Could not find provided fastq files for first sample
• 127: Could not find provided sequencing summary file for first sample
• 221: Guppy basecalling failed in second sample
• 222: minimap2 mapping failed in second sample
• 223: Samtools indexing failed in second sample
• 224: Nanopolish indexing failed in second sample
• 225: Nanopolish eventalign failed in second sample
• 226: Could not find provided fastq files for second sample
• 227: Could not find provided sequencing summary file for second sample