MHAP 2.1.3

This is a minor update:

• added ability to store full sequence ID in binary format (previously this was only supported with fasta inputs)
• improve allocation strategy for repeat filtering so large sets of filtered k-mers don't cause long startup times

MHAP 2.1.1

Fixes for incorrectly processed tf-idf flags.

MHAP 2.1

Changelog:

• Added repeat aggression flag (--repeat-weight) that controls how aggressively the transition is from no suppression to maximum suppression.
• Added an option to also supress rare k-mers (--supress-noise), defined as k-mers not listed in the k-mer filter file (-f).
• Various bugs

MHAP 2.0

Changelog:

• Up to 10X speedup (5x average).
• Second-stage filter is now a bottom-sketch rather than random sampling, improving memory usage and speed.
• Distance (1-identity) is reported from Jaccard score using the mash distance
• Complete switch to fastutil collections API for speed/memory improvements.
• Maven build system to consolidate into single jar and remove lib directory dependency.
• Code cleanup.
• Bug fixes.

MHAP 1.6

Changelog:

• Improved weighting (discretized td-idf) in first-stage filter.
• Code cleanup, leading to 15% speedup
• Support for bzip2/gzip input files
• Bug fixes

MHAP v1.5b1

Major updates:

• Eliminate repetitive k-mer filtering in index lookup, why filter k-mers when you can down-weight them.
• Increased performance of ordered k-mer second stage filter.

Changelog:

• Implemented weighted (discretized td-idf) MinHashing in first-stage filter.
• Random subsampling in second-stage filter.
• k-mer size is now unlimited.
• Reduced memory footprint and disk footprint of binary sketch representation, allowing a larger set of sequences to fit in memory.

Known Issues:

• If no repeat k-mer filter is specified, MHAP will use an experimental implementation of a count-min sketch to identify repeat k-mers and down-weight them. This option has not been full tested and may not always work. Users should always specify a filter file using the -f option.

Please see documentation at http://mhap.readthedocs.org/en/

MHAP v1.0

Minor update. Changelog:

• Fix issues #3 and #4
• Update overlap validation in EstimateROC
• Minor speed improvements

Please see documentation at http://mhap.readthedocs.org/en/

MHAP v0.1

First release of MHAP. Please see documentation at http://mhap.readthedocs.org/en/