https://github.com/cdcgov/seqruler - set version number to 4.4.4

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

- Java
Published by MikePone over 1 year ago

https://github.com/cdcgov/seqruler - 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.

- Java
Published by dannovikov over 1 year ago

https://github.com/cdcgov/seqruler - SeqRuler

Reverted ambiguity fraction implementation to last working version.

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - SeqRuler

Fixed ambiguity fraction parameter

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - SeqRuler

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

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - 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

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - SeqRuler

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

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - SeqRuler

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

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - SeqRuler

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

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - 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

- Java
Published by dannovikov over 2 years ago

https://github.com/cdcgov/seqruler - SeqRuler

Added input-as-pairs input mode. Changed handling of ambiguity fraction parameter to align with /veg/ C++ implementation.

- Java
Published by dannovikov almost 3 years ago

https://github.com/cdcgov/seqruler - SeqRuler

Added support for reading fasta from stdin, and writing distances to stdout, as an alternative to file based input-output.

- Java
Published by dannovikov almost 3 years ago

https://github.com/cdcgov/seqruler - SeqRuler

Ambiguity fraction threshold now considerers the effective length of the sequence (excluding terminal gaps), instead of the total length.

- Java
Published by dannovikov almost 3 years ago

https://github.com/cdcgov/seqruler - SeqRuler

Updated parallelization logic

- Java
Published by dannovikov almost 3 years ago

https://github.com/cdcgov/seqruler - SeqRuler

Big fixes and improvements.

- Java
Published by dannovikov about 3 years ago

https://github.com/cdcgov/seqruler - SeqRuler

Added the ability to calculate SNP distances using SeqRuler.

- Java
Published by dannovikov about 3 years ago

https://github.com/cdcgov/seqruler - SeqRuler

This release adds parallelization, enhanced file browser, and better tool tips.

- Java
Published by dannovikov about 3 years ago

https://github.com/cdcgov/seqruler - SeqRuler

This feature update adds the "maximum ambiguity fraction" field to the GUI.

- Java
Published by dannovikov over 3 years ago

https://github.com/cdcgov/seqruler - 1.0

TN93 with Ambiguity Handling modes

- Java
Published by dannovikov over 3 years ago