Beta-0.7.1

Fixes build problems on macOS-based systems.

Beta-0.7.0

Release 0.7.0

Most (if not all) of the codebase in Tomahawk has been rewritten. This release is not backward-compatible with any previous release.

beta-0.6.0

Release 0.6.0

Major Features And Improvements

• Concat operation now supports special modes to concatenate large number of files in parallel when the downstream operation is passed to sort (reported by @ekg). This mode is ~30-fold faster / thread and is parallelizable.
• Introducing the experimental aggregation subroutine. Modelled based on the Datashader pipeline, Tomahawk can now natively construct aggregated datasets of billions of points into datasets of pixels that can be plotted using raster operations efficiently.
• Slicing operator for two files has been re-instated. Use -O for output type (two or ld) when invoking the view subroutine

Bug Fixes and Other Changes

• Bug fixes
  • Problem when importing variants within 1-base of each other (reported by @ekg)
  • Memory requirement problems when parallel sort merging very large files (reported by @ekg)
  • Removed default missingness filter (from 0.2 to 1.0) to support importing bcf with few samples
  • Fixed problem with linked intervals during slicing. Now correctly selects targetted associations based on both mates (reported by @ekg)

beta-0.5.3

Release 0.5.3

beta-0.5.2

Release 0.5.2

Minor Features And Improvements

• Now correctly filters two files

Release 0.5.1

Minor Features And Improvements

• Meta index for faster queries of two files now builds correctly
• Interval slicing for sorted two files now outputs filtering hits for the from positions only
• Haplotype counts in binary two files are now stored as double instead of float

beta-0.3.3

Release 0.3.3

Major Features And Improvements

• None

Bug Fixes and Other Changes

• Bug fixes
  • Viewing sorted two files fixed for edge cases

beta-0.3.2

Release 0.3.2

Breaking Changes

• Sorted files needs to be resorted. Using old sorted files does not break functionality

Major Features And Improvements

• Sorting two files not correctly produces two indices used for fast queries
• Viewing sorted two files is significantly faster

Bug Fixes and Other Changes

• Bug fixes
  • Sort merge (tomahawk sort -M) now produces the correct index

beta-0.3.1

Release 0.3.1

Bug Fixes and Other Changes

• Bug fixes
  • Sort merge (tomahawk sort -M) now produces the correct output
  • view ABI command now correctly triggers -h/-H flag

beta-0.3.0

Release 0.3.0

Breaking Changes

• All changes are breaking. There is no backwards compatibility from this release!

Major Features And Improvements

• All major classes are now implemented as STL-like container and are as decoupled as possible
• External sort file handles now buffer a small amount of data to reduce random access lookups
• two/twk entries are no longer forced to be accessed by unaligned memory addresses
• Both two and twk are now self-indexing. All external indices are now invalid

Bug Fixes and Other Changes

• Bug fixes
  • Too many to list here
• Examples updates:
  • Added R script to demonstrate simple plotting using base
  • Added several figures demonstrating some keys concepts of Tomahawk

beta-0.2

Update TOI format. There is no backwards compatability with TOI. Delete legacy indices and reindex.
Use the attached archive as auto-generated archives does not contain submodules