set version number to 4.4.4

Set the version number (major.minor.release) in code to match version number in github.

SeqRuler

This update adds a fix for command line users who use the "pairs" input format through the "stdin" input method. Users who use this format usually use SeqRuler as part of larger, automated pipelines.

This input format reads pairs from stdin in batches, and previously, it wasn't processing the last batch, nor inputs smaller than the batch size. This led to missing distances in the output. The fix included in this update ensures the last batch is processed as well.

SeqRuler

Reverted ambiguity fraction implementation to last working version.

SeqRuler

Fixed ambiguity fraction parameter

SeqRuler

Simplified fraction parameter logic implementation which should increase performance slightly. Also added version information to the title.

SeqRuler

• Text fields for the fasta and output files can now be changed without needing to restart SeqRuler.
• Ambiguity fraction parameter now matches reference implementation at /veg/tn93

SeqRuler

TN93: Changed ambiguity fraction parameter, fixed issues with skip mode not applying, and updated ambiguity fraction parameter logic.

SeqRuler

Added an option in SNP mode for ignoring ambiguities when calculating distance.

SeqRuler

More sensible defaults in SNP mode. Edge thresholds are now expected as integers for SNP distance. Defaults to ignore all gaps.

SeqRuler

Fixed issues with loading bar progress exceeding 100% for large input files.

Added output enumeration mode with -e flag (command line online). It helps reduce output file size for large input data. When enabled, the output files will represent the source and target sequence names as numbers, enumerating them from 0...N-1, as in:

// distance output file:
Source, Target, Distance
0, 1, 0.123
0, 2, 0.456
1, 2, 0.567

It will then also produce a second output file giving the translation between a number and it's sequence id:

// translation (map) file
0,sequence_a,  
1,sequence_b,
2,sequence_c